Illumina (ILMN) 10-Q 29 Oct 14 2014 Q3 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	9 Months Ended
In Millions, unless otherwise specified	Sep. 28, 2014	Oct. 08, 2014
Document and Entity Information [Abstract]	'	'
Entity Registrant Name	'Illumina Inc	'
Entity Central Index Key	'0001110803	'
Document Type	'10-Q	'
Document Period End Date	28-Sep-14	'
Amendment Flag	'false	'
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q3	'
Current Fiscal Year End Date	'--12-28	'
Entity Filer Category	'Large Accelerated Filer	'
Entity Common Stock, Shares Outstanding	'	142

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (Unaudited) (USD $)	Sep. 28, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$829,895	$711,637
Short-term investments	441,532	453,966
Accounts receivable, net	276,675	238,946
Inventory	199,298	154,099
Deferred tax assets, current portion	101,930	36,076
Prepaid expenses and other current assets	57,624	22,811
Total current assets	1,906,954	1,617,535
Property and equipment, net	247,643	202,666
Goodwill	724,887	723,061
Intangible assets, net	299,345	331,173
Deferred tax assets, long-term portion	39,729	88,480
Other assets	59,648	56,091
Total assets	3,278,206	3,019,006
Current liabilities:	'	'
Accounts payable	96,069	73,655
Accrued liabilities	304,133	219,120
Accrued legal contingencies	155,080	'
Long-term debt, current portion	301,119	29,288
Total current liabilities	856,401	322,063
Long-term debt	979,836	839,305
Long-term legal contingencies	'	132,933
Other long-term liabilities	167,656	191,221
Conversion option subject to cash settlement	'	282
Stockholders' equity:	'	'
Preferred stock	0	0
Common stock	1,794	1,753
Additional paid-in capital	2,101,183	2,562,705
Accumulated other comprehensive income	361	1,234
Retained earnings	407,926	207,855
Treasury stock, at cost	-1,236,951	-1,240,345
Total stockholders’ equity	1,274,313	1,533,202
Total liabilities and stockholders’ equity	$3,278,206	$3,019,006

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Income (Unaudited) (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
Revenue:	'	'	'	'
Product revenue	$416,163	$318,603	$1,169,182	$928,270
Service and other revenue	64,467	38,197	179,797	105,582
Total revenue	480,630	356,800	1,348,979	1,033,852
Cost of revenue:	'	'	'	'
Cost of product revenue	113,103	119,954	338,851	308,082
Cost of service and other revenue	23,909	17,643	68,598	48,732
Amortization of acquired intangible assets	9,677	9,263	28,757	24,397
Total cost of revenue	146,689	146,860	436,206	381,211
Gross profit	333,941	209,940	912,773	652,641
Operating expense:	'	'	'	'
Research and development	85,082	70,957	245,108	200,015
Selling, general and administrative	119,888	95,617	344,110	269,391
Legal contingencies	7,705	'	7,705	115,369
Acquisition related expense (gain), net	903	-3,942	-335	-5,846
Headquarter relocation	870	518	4,357	-232
Unsolicited tender offer related expense	'	1,326	'	13,621
Total operating expense	214,448	164,476	600,945	592,318
Income from operations	119,493	45,464	311,828	60,323
Other income (expense):	'	'	'	'
Interest income	534	1,267	2,954	3,922
Interest expense	-10,987	-9,954	-30,652	-29,746
Cost-method investment related gain	4,427	'	4,427	6,113
Other (expense) income, net	-1,024	370	-31,860	-1,667
Total other expense, net	-7,050	-8,317	-55,131	-21,378
Income before income taxes	112,443	37,147	256,697	38,945
Provision for (benefit from) income taxes	18,954	5,790	56,626	-5,702
Net income	$93,489	$31,357	$200,071	$44,647
Net income per basic share	$0.66	$0.25	$1.50	$0.36
Net income per diluted share	$0.63	$0.22	$1.34	$0.32
Shares used in calculating basic net income per share	141,142	125,465	133,290	124,532
Shares used in calculating diluted net income per share	147,512	140,601	149,084	138,630

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Income (Unaudited) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
Statement of Comprehensive Income [Abstract]	'	'	'	'
Net income	$93,489	$31,357	$200,071	$44,647
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	-972	205	-873	-755
Total comprehensive income	$92,517	$31,562	$199,198	$43,892

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Cash Flows (Unaudited) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013
Cash flows from operating activities:	'	'
Net income	$200,071	$44,647
Adjustments to reconcile net income to net cash provided by operating activities:	'	'
Depreciation expense	44,783	37,081
Amortization of intangible assets	37,839	33,677
Share-based compensation expense	114,089	76,080
Accretion of debt discount	27,989	27,095
Loss on extinguishment of debt	31,360	'
Contingent compensation expense	2,553	4,109
Incremental tax benefit related to share-based compensation	-102,639	-27,225
Deferred income taxes	30,428	-58,643
Change in fair value of contingent consideration	-2,958	-11,031
Impairments	'	25,214
Change in estimated cease-use loss	4,357	-232
Cost-method investment related gain	-4,427	-6,113
Other	3,816	2,531
Changes in operating assets and liabilities:	'	'
Accounts receivable	-37,733	-12,504
Inventory	-44,693	-398
Prepaid expenses and other current assets	-20,152	-1,390
Other assets	-5,262	-3,427
Accounts payable	14,748	-10,876
Accrued liabilities	40,598	11,932
Accrued legal contingencies	22,147	127,012
Other long-term liabilities	3,808	2,043
Net cash provided by operating activities	360,722	259,582
Cash flows from investing activities:	'	'
Purchases of available-for-sale securities	-428,700	-178,512
Sales of available-for-sale securities	324,554	512,517
Maturities of available-for-sale securities	118,229	233,413
Net cash paid for acquisitions	-3,285	-437,478
Net (purchases of) sales proceeds from strategic investments	-6,755	5,971
Purchases of property and equipment	-71,164	-51,905
Cash paid for intangible assets	-6,720	-2,845
Net cash (used in) provided by investing activities	-73,841	81,161
Cash flows from financing activities:	'	'
Payments on financing obligations	-29,880	-10,721
Payments on acquisition related contingent consideration liability	'	-3,985
Proceeds from issuance of convertible notes	1,132,378	'
Repurchases of convertible notes	-1,244,721	'
Incremental tax benefit related to share-based compensation	102,639	27,225
Common stock repurchases	-202,431	-50,020
Taxes paid related to net share settlement of equity awards	-9,668	'
Payments on retirement of warrants	'	-125,000
Proceeds from issuance of common stock	84,733	80,226
Net cash used in financing activities	-166,950	-82,275
Effect of exchange rate changes on cash and cash equivalents	-1,673	-613
Net increase in cash and cash equivalents	118,258	257,855
Cash and cash equivalents at beginning of period	711,637	433,981
Cash and cash equivalents at end of period	$829,895	$691,836

Summary_of_Significant_Account

Summary of Significant Accounting Policies	9 Months Ended
	Sep. 28, 2014
Accounting Policies [Abstract]	'
Summary of Significant Accounting Policies	'
	Summary of Significant Accounting Policies
	Basis of Presentation
	The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) for interim financial information and the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. The unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. All intercompany transactions and balances have been eliminated in consolidation. In management’s opinion, the accompanying financial statements reflect all adjustments, consisting of normal recurring adjustments, considered necessary for a fair presentation of the results for the interim periods presented.
	Interim financial results are not necessarily indicative of results anticipated for the full year. These unaudited condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and footnotes included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 29, 2013, from which the balance sheet information herein was derived.
	The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, and expense, and related disclosure of contingent assets and liabilities. Actual results could differ from those estimates.
	Segment Information
	Effective December 30, 2013, the Company reorganized and separated the roles of the Chief Executive Officer and the President, with core market and operational functions centralized and reporting to the President, for the primary purpose of achieving scalability in business operations to support the growth in the Company’s strategic markets. Corporate functions and the President report to the CEO. As a result, the Company operates under one operating segment and reports under one reportable segment.
	Fiscal Year
	The Company’s fiscal year consists of 52 or 53 weeks ending the Sunday closest to December 31, with quarters of 13 or 14 weeks ending the Sunday closest to March 31, June 30, September 30, and December 31. The three and nine months ended September 28, 2014 and September 29, 2013 were both 13 and 39 weeks, respectively.
	Recent Accounting Pronouncements
	In May 2014, the Financial Accounting Standards Board issued Accounting Standards Update (ASU) 2014-09, Revenue from Contracts with Customers. The new standard is based on the principle that revenue should be recognized to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. ASU 2014-09 will be effective for the Company beginning in the first quarter of fiscal 2017 and allows for a full retrospective or a modified retrospective adoption approach. The Company is currently evaluating the impact of ASU 2014-09 on its consolidated financial statements.
	Goodwill, Intangible Assets and Other Long-Lived Assets
	Goodwill, which has an indefinite useful life, represents the excess of cost over fair value of net assets acquired. The change in the carrying value of goodwill during the nine months ended September 28, 2014 was due to a current year acquisition and adjustments to the purchase price subsequent to the preliminary allocation of purchase price related to prior year acquisitions. Goodwill is reviewed for impairment at least annually during the second quarter, or more frequently if an event occurs indicating the potential for impairment. During its goodwill impairment review, the Company may assess qualitative factors to determine whether it is more likely than not that the fair value of its reporting unit is less than its carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance of the Company. If, after assessing the totality of these qualitative factors, the Company determines that it is not more likely than not that the fair value of its reporting unit is less than its carrying amount, then no additional assessment is deemed necessary. Otherwise, the Company proceeds to perform a two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with its carrying value, including goodwill. If the carrying amount of the reporting unit exceeds its fair value, the Company performs the second step of the goodwill impairment test to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. The Company may also elect to bypass the qualitative assessment in a period and elect to proceed to perform the first step of the goodwill impairment test. The Company performed its annual assessment for goodwill impairment in the second quarter of 2014, noting no impairment.
	The Company’s identifiable intangible assets are typically comprised of acquired core technologies, licensed technologies, license agreements, customer relationships, and trade names. The cost of identifiable intangible assets with finite lives is generally amortized on a straight-line basis over the assets’ respective estimated useful lives.
	The Company regularly performs reviews to determine if any event has occurred that may indicate its intangible assets with finite useful lives and other long-lived assets are potentially impaired. If indicators of impairment exist, the Company performs an impairment test to assess the recoverability of the affected assets by determining whether the carrying amount of such assets exceeds the undiscounted expected future cash flows. If the affected assets are not recoverable, the Company estimates the fair value of the assets and records an impairment loss if the carrying value of the assets exceeds the fair value. Factors that may indicate potential impairment include a significant decline in the Company’s stock price and market capitalization compared to its net book value, significant changes in the ability of a particular asset to generate positive cash flows, the Company’s strategic business objectives, and the pattern of utilization of a particular asset. The Company performed quarterly reviews of its intangible assets with finite useful lives and other long-lived assets and noted no significant impairments for the three and nine months ended September 28, 2014.
	During 2013, the Company decided to discontinue its Eco and NuPCR product lines to better align its product portfolio with its core strategy. As a result, the Company recorded a total impairment charge of $25.2 million in cost of product revenue during the three months ended September 29, 2013, $22.9 million of which related to identifiable intangible assets.
	Derivatives
	The Company is exposed to foreign exchange rate risks in the normal course of business. To manage a portion of the accounting exposure resulting from changes in foreign currency exchange rates, the Company enters into foreign exchange contracts to hedge monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. These foreign exchange contracts are carried at fair value and are not designated as hedging instruments. Changes in the value of the derivative are recognized in other expense, net, along with an offsetting remeasurement gain or loss on the underlying foreign currency denominated assets or liabilities.
	As of September 28, 2014, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of September 28, 2014 and December 29, 2013, the total notional amounts of outstanding forward contracts in place for foreign currency purchases were $51.2 million and $54.7 million, respectively.
	Reserve for Product Warranties
	The Company generally provides a one-year warranty on instruments. Additionally, the Company provides a warranty on consumables through the expiration date, which generally ranges from six to twelve months after the manufacture date. At the time revenue is recognized, the Company establishes an accrual for estimated warranty expenses based on historical experience as well as anticipated product performance. The Company periodically reviews its warranty reserve for adequacy and adjusts the warranty accrual, if necessary, based on actual experience and estimated costs to be incurred. Warranty expense is recorded as a component of cost of product revenue.
	Revenue Recognition
	The Company’s revenue is generated primarily from the sale of products and services. Product revenue primarily consists of sales of instruments and consumables used in genetic analysis. Service and other revenue primarily consists of revenue generated from genotyping and sequencing services and instrument service contracts.
	The Company recognizes revenue when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the seller’s price to the buyer is fixed or determinable, and collectibility is reasonably assured. In instances where final acceptance of the product or system is required, revenue is deferred until all the acceptance criteria have been met. All revenue is recorded net of discounts.
	Revenue from product sales is recognized generally upon transfer of title to the customer, provided that no significant obligations remain and collection of the receivable is reasonably assured. Revenue from instrument service contracts is recognized as the services are rendered, typically evenly over the contract term. Revenue from genotyping and sequencing services is recognized when earned, which is generally at the time the genotyping or sequencing analysis data is made available to the customer or agreed upon milestones are reached.
	In order to assess whether the price is fixed or determinable, the Company evaluates whether refund rights exist. If there are refund rights or payment terms based on future performance, the Company defers revenue recognition until the price becomes fixed or determinable. The Company assesses collectibility based on a number of factors, including past transaction history with, and the creditworthiness of, the customer. If the Company determines that collection of a payment is not reasonably assured, revenue recognition is deferred until receipt of payment.
	The Company regularly enters into contracts where revenue is derived from multiple deliverables including products or services. These products or services are generally delivered within a short time frame, approximately three to six months, after the contract execution date. Revenue recognition for contracts with multiple deliverables is based on the individual units of accounting determined to exist in the contract. A delivered item is considered a separate unit of accounting when the delivered item has value to the customer on a stand-alone basis. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis. Consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence (VSOE) of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence exists, the Company uses its best estimate of the selling price for the deliverable.
	In order to establish VSOE of selling price, the Company must regularly sell the product or service on a standalone basis with a substantial majority priced within a relatively narrow range. VSOE of selling price is usually the midpoint of that range. If there are not a sufficient number of standalone sales and VSOE of selling price cannot be determined, then the Company considers whether third party evidence can be used to establish selling price. Due to the lack of similar products and services sold by other companies within the industry, the Company has rarely established selling price using third-party evidence. If neither VSOE nor third party evidence of selling price exists, the Company determines its best estimate of selling price using average selling prices over a rolling 12-month period coupled with an assessment of current market conditions. If the product or service has no history of sales or if the sales volume is not sufficient, the Company relies upon prices set by the Company’s pricing committee adjusted for applicable discounts. The Company recognizes revenue for delivered elements only when it determines there are no uncertainties regarding customer acceptance.
	In certain markets, the Company sells products and provides services to customers through distributors that specialize in life science products. In most sales through distributors, the product is delivered directly to customers. In cases where the product is delivered to a distributor, revenue recognition is deferred until acceptance is received from the distributor, and/or the end-user, if required by the applicable sales contract. The terms of sales transactions through distributors are consistent with the terms of direct sales to customers. These transactions are accounted for in accordance with the Company’s revenue recognition policy described herein.
	Net Income per Share
	Basic net income per share is computed based on the weighted average number of common shares outstanding during the period. Diluted net income per share is computed based on the sum of the weighted average number of common shares and dilutive potential common shares outstanding during the period.
	Dilutive potential common shares consist of shares issuable under convertible senior notes, equity awards, and warrants. Convertible senior notes have a dilutive impact when the average market price of the Company’s common stock exceeds the applicable conversion price of the respective notes. Potentially dilutive common shares from equity awards and warrants are determined using the average share price for each period under the treasury stock method. In addition, the following amounts are assumed to be used to repurchase shares: proceeds from exercise of equity awards and warrants; the average amount of unrecognized compensation expense for equity awards; and estimated tax benefits that will be recorded in additional paid-in capital when expenses related to equity awards become deductible. In loss periods, basic net loss per share and diluted net loss per share are identical because the otherwise dilutive potential common shares become anti-dilutive and are therefore excluded.
	The following table presents the calculation of weighted average shares used to calculate basic and diluted net income per share (in thousands):
		Three Months Ended		Nine Months Ended
		September 28,	September 29,	September 28,	September 29,
		2014	2013	2014	2013
	Weighted average shares outstanding	141,142	125,465	133,290	124,532
	Effect of dilutive potential common shares from:
	Convertible senior notes	1,972	1,028	3,967	1,052
	Equity awards	4,124	4,596	4,367	4,290
	Warrants	274	9,512	7,460	8,756
	Weighted average shares used in calculation of diluted net income per share	147,512	140,601	149,084	138,630
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	54	317	112	1,305

Balance_Sheet_Account_Details

Balance Sheet Account Details	9 Months Ended
	Sep. 28, 2014
Balance Sheet Account Details [Abstract]	'
Balance Sheet Account Details	'
	Balance Sheet Account Details
	Short-Term Investments
	The following is a summary of short-term investments (in thousands):
		September 28, 2014												December 29, 2013
		Amortized			Gross			Gross			Estimated			Amortized		Gross		Gross			Estimated
		Cost			Unrealized			Unrealized			Fair Value			Cost		Unrealized		Unrealized			Fair Value
					Gains			Losses								Gains		Losses
	Available-for-sale securities:
	Debt securities in government sponsored entities	$	46,021		$	17		$	(47	)	$	45,991		$	82,226	$	18	$	(101	)	$	82,143
	Corporate debt securities	332,735			136			(1,621		)	331,250			342,034		312		(376		)	341,970
	U.S. Treasury securities	64,272			47			(28		)	64,291			29,795		58		—			29,853
	Total available-for-sale securities	$	443,028		$	200		$	(1,696	)	$	441,532		$	454,055	$	388	$	(477	)	$	453,966
	As of September 28, 2014, the Company had 118 available-for-sale securities in a gross unrealized loss position, all of which had been in such position for less than twelve months. There were no impairments considered other-than-temporary as it is more likely than not the Company will hold the securities until maturity or the recovery of the cost basis. The following table shows the fair values and the gross unrealized losses of such available-for-sale securities that were in an unrealized loss position for less than twelve months as of September 28, 2014 and December 29, 2013, aggregated by investment category (in thousands):
		September 28, 2014						December 29, 2013
		Estimated			Gross			Estimated			Gross
		Fair Value			Unrealized			Fair Value			Unrealized
					Losses						Losses
	Debt securities in government sponsored entities	$	26,058		$	(47	)	$	73,362		$	(101	)
	Corporate debt securities	190,175			(1,621		)	168,118			(373		)
	U.S. Treasury securities	18,958			(28		)	—			—
	Total	$	235,191		$	(1,696	)	$	241,480		$	(474	)
	Realized gains and losses are determined based on the specific identification method and are reported in interest income.
	Contractual maturities of available-for-sale debt securities as of September 28, 2014 were as follows (in thousands):
		Estimated
		Fair Value
	Due within one year	$	162,248
	After one but within five years	279,284
	Total	$	441,532
	Cost-Method Investments
	As of September 28, 2014 and December 29, 2013, the aggregate carrying amounts of the Company’s cost-method investments in non-publicly traded companies were $32.2 million and $22.1 million, respectively, which were included in other assets. During the three months ended September 28, 2014, the Company recognized a gain of $4.4 million associated with additional proceeds received for a cost-method investment sold in a prior period. During the three months ended March 31, 2013, the Company sold a cost-method investment and recognized a $6.1 million gain. The Company’s cost-method investments are assessed for impairment quarterly. No impairment loss was recorded during the three and nine months ended September 28, 2014 or September 29, 2013. The Company does not reassess the fair value of cost-method investments if there are no identified events or changes in circumstances that may have a significant adverse effect on the fair value of the investments.
	Inventory
	Inventory consists of the following (in thousands):
		September 28,			December 29,
		2014			2013
	Raw materials	$	68,624		$	57,398
	Work in process	96,068			70,016
	Finished goods	34,606			26,685
	Total inventory	$	199,298		$	154,099
	Goodwill
	Changes in the Company’s goodwill balance during the nine months ended September 28, 2014 are as follows (in thousands):
		Goodwill
	Balance as of December 29, 2013	$	723,061
	Current period acquisition	3,321
	Purchase price allocation adjustments related to prior year acquisitions	(1,495		)
	Balance as of September 28, 2014	$	724,887
	Accrued Liabilities
	Accrued liabilities consist of the following (in thousands):
		September 28,			December 29,
		2014			2013
	Accrued compensation expenses	$	95,041		$	82,705
	Deferred revenue, current portion	72,391			50,834
	Acquisition related contingent liability, current portion	46,522			6,719
	Accrued taxes payable	36,035			30,435
	Customer deposits	14,822			13,569
	Reserve for product warranties	14,433			10,407
	Facility exit obligation, current portion	4,337			5,570
	Other	20,552			18,881
	Total accrued liabilities	$	304,133		$	219,120
	Warranties
	Changes in the Company’s reserve for product warranties during the three and nine months ended September 28, 2014 and September 29, 2013 are as follows (in thousands):
		Three Months Ended						Nine Months Ended
		September 28,			September 29,			September 28,			September 29,
		2014			2013			2014			2013
Balance at beginning of period	$	13,000		$	10,826		$	10,407		$	10,136
Additions charged to cost of revenue	6,803			3,631			16,616			13,929
Repairs and replacements	(5,370		)	(3,140		)	(12,590		)	(12,748		)
Balance at end of period	$	14,433		$	11,317		$	14,433		$	11,317
Leases
Changes in the Company’s facility exit obligation related to its former headquarters lease during the three and nine months ended September 28, 2014 and September 29, 2013 are as follows (in thousands):
	Three Months Ended						Nine Months Ended
	September 28,			September 29,			September 28,			September 29,
	2014			2013			2014			2013
Balance at beginning of period	$	38,480		$	39,351		$	38,218		$	45,352
Adjustment to facility exit obligation	57			—			2,065			(1,948		)
Accretion of interest expense	666			518			1,948			1,716
Cash payments	(1,153		)	(2,723		)	(4,181		)	(7,974		)
Balance at end of period	$	38,050		$	37,146		$	38,050		$	37,146
During the three months ended September 28, 2014, the Company entered into an operating lease related to an additional building on its current headquarters campus. Minimum lease payments during the initial term are estimated to be $47.6 million in total.

Acquisitions

Acquisitions	9 Months Ended
	Sep. 28, 2014
Business Combinations [Abstract]	'
Acquisitions	'
	Acquisitions
	2013 Acquisitions
	On February 21, 2013, the Company acquired all of the outstanding capital stock of Verinata Health, Inc., a provider of non-invasive tests for the early identification of fetal chromosomal abnormalities. The aggregate purchase price was $396.3 million, including total cash payment of $339.3 million, $56.2 million in fair value of the contingent milestone payments of up to $100.0 million, $0.2 million in fair value of converted stock options attributed to pre-combination services, and $0.5 million in loss realized on settlement of preexisting relationships.
	Assumptions used to estimate the acquisition date fair value of the contingent consideration included discount rates ranging from 6% to 20%, volatility of 50%, risk-free rate of 0.26%, revenue projections, and the probability of achieving regulatory milestones. This fair value measurement of the contingent consideration is based on significant inputs not observed in the market and thus represents a Level 3 measurement. Level 3 instruments are valued based on unobservable inputs that are supported by little or no market activity and reflect the Company’s own assumptions in measuring fair value.
	During 2013, the Company also completed acquisitions of Advanced Liquid Logic Inc., a provider of liquid handling solutions, NextBio, a provider of clinical and genomic informatics tools, and another development-stage company. As a result of these transactions, the Company recorded $126.3 million in goodwill. The purchase price allocation for the NextBio acquisition is preliminary and subject to change as more detailed analyses are completed and additional information with respect to the fair values of the assets and liabilities acquired becomes available.
	2012 Acquisition
	On September 19, 2012, the Company announced the acquisition of BlueGnome Ltd., a provider of cytogenetics and in vitro fertilization screening products. Total consideration for the acquisition was $95.5 million, which included $88.0 million in initial cash payments and $7.5 million in fair value of contingent cash consideration of up to $20.0 million based on the achievement of certain revenue based milestones.
	Summary of Contingent Compensation Expenses
	Contingent compensation expenses recorded as a result of acquisitions consist of the following (in thousands):
		Three Months Ended				Nine Months Ended
		September 28,		September 29,		September 28,		September 29,
		2014		2013		2014		2013
	Contingent compensation, included in research and development expense	$	496	$	106	$	1,075	$	432
	Contingent compensation, included in selling, general and administrative expense	—		2,337		2,757		7,692
	Total contingent compensation expense	$	496	$	2,443	$	3,832	$	8,124

Fair_Value_Measurements

Fair Value Measurements	9 Months Ended
	Sep. 28, 2014
Fair Value Disclosures [Abstract]	'
Fair Value Measurements	'
	Fair Value Measurements
	The following table presents the Company’s hierarchy for assets and liabilities measured at fair value on a recurring basis as of September 28, 2014 and December 29, 2013 (in thousands):
		September 28, 2014									December 29, 2013
		Level 1			Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	Assets:
	Money market funds (cash equivalents)	$	574,878		$	—	$	—	$	574,878	$	478,755	$	—	$	—	$	478,755
	Debt securities in government-sponsored entities	—			45,991		—		45,991		—		82,143		—		82,143
	Corporate debt securities	—			331,250		—		331,250		—		341,970		—		341,970
	U.S. Treasury securities	64,291			—		—		64,291		29,853		—		—		29,853
	Deferred compensation plan assets	—			23,402		—		23,402		—		17,805		—		17,805
	Total assets measured at fair value	$	639,169		$	400,643	$	—	$	1,039,812	$	508,608	$	441,918	$	—	$	950,526
	Liabilities:
	Acquisition related contingent consideration liabilities	$	—		$	—	$	46,522	$	46,522	$	—	$	—	$	49,480	$	49,480
	Deferred compensation liability	—			19,920		—		19,920		—		14,957		—		14,957
	Total liabilities measured at fair value	$	—		$	19,920	$	46,522	$	66,442	$	—	$	14,957	$	49,480	$	64,437
	The Company holds available-for-sale securities that consist of highly liquid, investment grade debt securities. The Company considers information provided by the Company’s investment accounting and reporting service provider in the measurement of fair value of its debt securities. The investment service provider provides valuation information from an industry-recognized valuation service. Such valuations may be based on trade prices in active markets for identical assets or liabilities (Level 1 inputs) or valuation models using inputs that are observable either directly or indirectly (Level 2 inputs), such as quoted prices for similar assets or liabilities, yield curve, volatility factors, credit spreads, default rates, loss severity, current market and contractual prices for the underlying instruments or debt, broker and dealer quotes, as well as other relevant economic measures. The Company’s deferred compensation plan assets consist primarily of mutual funds. The Company performs control procedures to corroborate the fair value of its holdings, including comparing valuations obtained from its investment service provider to valuations reported by the Company’s asset custodians, validation of pricing sources and models, and review of key model inputs if necessary.
	The Company reassesses the fair value of contingent consideration to be settled in cash related to acquisitions on a quarterly basis using the income approach. This is a Level 3 measurement. Significant assumptions used in the measurement include probabilities of achieving the remaining milestones and the discount rates, which depend on the milestone risk profiles. The changes in the fair value of the contingent considerations during the three and nine months ended September 28, 2014 were due to changes in the estimated payments and a shorter discounting period.
	Changes in estimated fair value of contingent consideration liabilities during the nine months ended September 28, 2014 are as follows (in thousands):
		Contingent
		Consideration
		Liability
		(Level 3
		Measurement)
	Balance as of December 29, 2013	$	49,480
	Change in estimated fair value, recorded in acquisition related expense (gain), net	(2,958		)
	Balance as of September 28, 2014	$	46,522

Convertible_Senior_Notes

Convertible Senior Notes	9 Months Ended
	Sep. 28, 2014
Debt Disclosure [Abstract]	'
Convertible Senior Notes	'
	Convertible Senior Notes
	0% Convertible Senior Notes due 2019 and 0.5% Convertible Senior Notes due 2021
	On June 11, 2014, the Company issued $632.5 million aggregate principal amount of 0% convertible senior notes due 2019 (2019 Notes) and $517.5 million aggregate principal amount of 0.5% convertible senior notes due 2021 (2021 Notes) in an offering conducted in accordance with Rule 144A under the Securities Act of 1933, as amended. The Notes were issued at 100% of par value. The net proceeds from the issuance, after deducting the offering expenses payable by the Company, was $1,132.4 million. The Company used the net proceeds plus cash on hand to repurchase a portion of the outstanding 2016 Notes in privately negotiated transactions concurrently with the issuance of the 2019 and 2021 Notes.
	Both the 2019 and 2021 Notes will be convertible into cash, shares of common stock, or a combination of cash and shares of common stock, at the Company's election, based on an initial conversion rate, subject to adjustment, of 3.9318 shares per $1,000 principal amount of the notes (which represents an initial conversion price of approximately $254.34 per share), only in the following circumstances and to the following extent: (1) during the five business-day period after any 10 consecutive trading day period (the “measurement period”) in which the trading price per 2019 and 2021 Note for each day of such measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such day; (2) during any calendar quarter (and only during that quarter) after the calendar quarter ending September 30, 2014, if the last reported sale price of the Company’s common stock for 20 or more trading days in the period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeds 130% of the applicable conversion price in effect on the last trading day of the immediately preceding calendar quarter; (3) upon the occurrence of specified events described in the indenture for the 2019 and 2021 Notes; and (4) at any time on or after March 15, 2019 for the 2019 Notes, or March 15, 2021 for the 2021 Notes, through the second scheduled trading day immediately preceding the maturity date.
	As noted in the indentures for the 2019 and 2021 Notes, it is the Company's intent and policy to settle conversions through combination settlement, which essentially involves repayment of an amount of cash equal to the “principal portion” and delivery of the “share amount” in excess of the conversion value over the principal portion in shares of common stock. In general, for each $1,000 in principal the “principal portion” of cash upon settlement is defined as the lesser of $1,000 and the conversion value during the 20-day observation period. The conversion value is the sum of the daily conversion value which is the product of the effective conversion rate divided by 20 days and the daily volume weighted average price (VWAP) of the Company's common stock. The “share amount” is the cumulative “daily share amount” during the observation period, which is calculated by dividing the daily VWAP into the difference between the daily conversion value (i.e., conversion rate x daily VWAP) and $1,000.
	The 2019 Notes carry no coupon interest. The Company pays 0.5% interest per annum on the principal amount of the 2021 Notes, payable semiannually in arrears in cash on June 15 and December 15 of each year, beginning on December 15, 2014. The 2019 and 2021 Notes mature on June 15, 2019 and June 15, 2021, respectively. If a designated event, as defined in the indentures for the 2019 and 2021 Notes, such as acquisition, merger, or liquidation, occurs prior to the maturity date, subject to certain limitations, holders of the notes may require the Company to repurchase all or a portion of their notes for cash at a repurchase price equal to 100% of the principal amount of the notes to be repurchased, plus any accrued and unpaid interest to, but excluding, the repurchase date.
	The Company accounts separately for the liability and equity components of the 2019 and 2021 Notes in accordance with authoritative guidance for convertible debt instruments that may be settled in cash upon conversion. The guidance requires the carrying amount of the liability component to be estimated by measuring the fair value of a similar liability that does not have an associated conversion feature. Because the Company has no outstanding non-convertible public debt, the Company determined that market-traded senior, unsecured corporate bonds represent a similar liability to the convertible senior notes without the conversion option. Based on market data available for publicly traded, senior, unsecured corporate bonds issued by companies in the same industry as the Company, and with similar maturities to the 2019 and 2021 Notes, the Company estimated the implied interest rates of its 2019 and 2021 Notes to be 2.9% and 3.5%, respectively, assuming no conversion option. Assumptions used in the estimate represent what market participants would use in pricing the liability component, including market interest rates, credit standing, and yield curves, all of which are defined as Level 2 observable inputs. The estimated implied interest rates were applied to the 2019 and 2021 Notes, which resulted in a fair value of the liability component in aggregate of $971.5 million upon issuance, calculated as the present value of implied future payments based on the $1,150.0 million aggregate principal amount. The $161.2 million difference between the cash proceeds of $1,132.7 million and the estimated fair value of the liability component was recorded in additional paid-in capital as the 2019 and 2021 Notes are not considered redeemable.
	As a policy election under applicable guidance related to the calculation of diluted net income per share, the Company elected the combination settlement method as its stated settlement policy and applied the treasury stock method in the calculation of the potential dilutive impact of the 2019 and 2021 Notes. Neither the 2019 nor the 2021 Notes were convertible as of September 28, 2014 and had no dilutive impact during the three and nine months ended September 28, 2014. If the 2019 and 2021 Notes were converted as of September 28, 2014, the if-converted value would not exceed the principal amount.
	0.25% Convertible Senior Notes due 2016
	In 2011, the Company issued $920.0 million aggregate principal amount of 0.25% convertible senior notes due 2016 (2016 Notes). The Company pays 0.25% interest per annum on the principal amount of the 2016 Notes semiannually in arrears in cash on March 15 and September 15 of each year. The 2016 Notes mature on March 15, 2016. The effective rate of the liability component was estimated to be 4.5%.
	The 2016 Notes are convertible into cash, shares of common stock, or a combination of cash and shares of common stock, at the Company’s election, based on an initial conversion rate, subject to adjustment, of 11.9687 shares per $1,000 principal amount of the 2016 Notes (which represents an initial conversion price of approximately $83.55 per share), only in the following circumstances and to the following extent: (1) during the five business-day period after any 10 consecutive trading day period (the “measurement period”) in which the trading price per 2016 Note for each day of such measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such day; (2) during any calendar quarter (and only during that quarter) after the calendar quarter ending March 31, 2011, if the last reported sale price of the Company’s common stock for 20 or more trading days in the period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeds 130% of the applicable conversion price in effect on the last trading day of the immediately preceding calendar quarter; (3) upon the occurrence of specified events described in the indenture for the 2016 Notes; and (4) at any time on or after December 15, 2015 through the second scheduled trading day immediately preceding the maturity date. Based upon meeting the stock trading price conversion requirement during the three months ended March 30, 2014, the 2016 Notes became convertible on April 1, 2014 and continue to be convertible through December 31, 2014.
	In conjunction with the issuance of the 2019 and 2021 Notes, the Company used the net proceeds from the issuance plus cash on hand to repurchase $600.0 million in principal amount of the outstanding 2016 Notes in privately negotiated transactions. The aggregate cash used for the repurchase was $1,244.7 million. The repurchase is accounted for as an extinguishment of debt. Extinguishment accounting requires the purchase price to be allocated to the liability and equity components of the repurchased notes based on the fair value of the liability component, and the difference between the fair value and the carrying value of the liability component to be recognized as loss on extinguishment of debt. An interest rate of 1.2% upon settlement, which was estimated using Level 2 inputs, was applied to measure the fair value of the liability component of the extinguished debt. This calculation resulted in $588.8 million allocated to the debt component and $655.9 million allocated to the equity component. The $31.4 million difference between the $588.8 million fair value of debt component and the carrying value of the repurchased 2016 Notes was recorded as a loss on extinguishment of debt within other expense, net, during the three and six months ended June 29, 2014. The $655.9 million of the repurchase price allocated to the equity component was recorded as a reduction of additional paid-in capital.
	As a policy election under applicable guidance related to the calculation of diluted net income per share, the Company elected the combination settlement method as its stated settlement policy and applied the treasury stock method in the calculation of the dilutive impact of the 2016 Notes. The calculation of dilutive potential common shares outstanding for the three and nine months ended September 28, 2014 reflects the dilutive impact from the 2016 Notes. If the 2016 Notes were converted as of September 28, 2014, the if-converted value would exceed the principal amount by $346.1 million.
	0.625% Convertible Senior Notes due 2014
	In 2007, the Company issued $400.0 million principal amount of 0.625% convertible senior notes due 2014 (2014 Notes) with a maturity date of February 15, 2014. At the time of the issuance, the effective interest rate of the liability component was estimated to be 8.3%.
	The 2014 Notes were convertible into cash and shares of the Company’s common stock in various prior periods and became convertible again from April 1, 2012 through, and including, February 12, 2014, by which date all notes were converted. In all cases of conversions of the 2014 Notes, the principal amount converted was repaid with cash and the excess of the conversion value over the principal amount was paid in shares of common stock. The equity dilution resulting from the issuance of common stock related to the conversion of the 2014 Notes was offset by repurchase of the same amount of shares under the convertible note hedge transactions, which were automatically exercised in accordance with their terms at the time of each conversion.
	Upon conversions, the Company recorded losses on extinguishment of debt calculated as the difference between the estimated fair value of the debt and the carrying value of the notes as of the settlement dates. To measure the fair value of the converted notes as of the settlement dates, the applicable interest rates were estimated using Level 2 observable inputs and applied to the converted notes using the same methodology utilized for the issuance date valuation.
	The following table summarizes information about the conversions of the 2014 Notes during the nine months ended September 28, 2014 (in thousands):
		2014 Notes
	Cash paid for principal of notes converted	$	29,570
	Conversion value over principal amount paid in shares of common stock	$	196,095
	Number of shares of common stock issued upon conversion	1,151
	Summary of Convertible Senior Notes
	The following table summarizes information about the equity and liability components of all convertible senior notes outstanding as of the period reported (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices.
		September 28,			December 29,
		2014			2013
	Principal amount of convertible notes outstanding	$	1,470,027		$	949,570
	Unamortized discount of liability component	(189,072		)	(80,977		)
	Net carrying amount of liability component	1,280,955			868,593
	Less: current portion	(301,119		)	(29,288		)
	Long-term debt	$	979,836		$	839,305
	Conversion option subject to cash settlement	—			$	282
	Carrying value of equity component, net of debt issuance cost	$	215,283		$	274,304
	Fair value of outstanding notes	$	1,850,360		$	1,428,743
	Weighted-average remaining amortization period of discount on the liability component	5.4 years			2.2 years

Sharebased_Compensation_Expens

Share-based Compensation Expense	9 Months Ended
	Sep. 28, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Share-based Compensation Expense	'
	Share-based Compensation Expense
	Share-based compensation expense for all stock awards consists of the following (in thousands):
		Three Months Ended						Nine Months Ended
		September 28,			September 29,			September 28,			September 29,
		2014			2013			2014			2013
	Cost of product revenue	$	2,572		$	1,524		$	6,816		$	4,410
	Cost of service and other revenue	311			233			880			544
	Research and development	14,589			9,561			39,043			26,521
	Selling, general and administrative	27,197			16,091			67,350			44,605
	Share-based compensation expense before taxes	44,669			27,409			114,089			76,080
	Related income tax benefits	(14,852		)	(8,059		)	(37,103		)	(23,123		)
	Share-based compensation expense, net of taxes	$	29,817		$	19,350		$	76,986		$	52,957
	The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share for stock purchased under the Employee Stock Purchase Plan (ESPP) during the nine months ended September 28, 2014 are as follows:
		Employee Stock Purchase Rights
	Risk-free interest rate	0.05 - 0.13%
	Expected volatility	39% - 41%
	Expected term	0.5 - 1.0 year
	Expected dividends	—
	Weighted-average fair value per share	$	44.64
	As of September 28, 2014, approximately $210.3 million of unrecognized compensation cost related to stock options, restricted stock, and ESPP shares granted to date is expected to be recognized over a weighted-average period of approximately 1.8 years.

Stockholders_Equity

Stockholders' Equity	9 Months Ended
	Sep. 28, 2014
Equity [Abstract]	'
Stockholders' Equity	'
	Stockholders’ Equity
	As of September 28, 2014, approximately 6.6 million shares remained available for future grants under the 2005 Stock Plan, the 2005 Solexa Equity Plan, and the 2008 Verinata Health Stock Plan.
	Stock Options
	The Company’s stock option activity under all stock option plans during the nine months ended September 28, 2014 is as follows:
		Options		Weighted-Average
		(in thousands)		Exercise Price
	Outstanding at December 29, 2013	5,724		$	32.64
	Exercised	(2,071	)	$	30.72
	Cancelled	(35	)	$	31.74
	Outstanding at September 28, 2014	3,618		$	33.74
	At September 28, 2014, outstanding options to purchase 3.2 million shares were exercisable with a weighted-average exercise price per share of $34.63.
	Restricted Stock
	A summary of the Company’s restricted stock activity and related information for the nine months ended September 28, 2014 is as follows:
		Restricted Stock Awards		Restricted Stock Units		Performance Stock Units		Weighted-Average
		(RSA)		(RSU)		(PSU)		Grant-Date Fair Value per Share
								RSA		RSU		PSU
	Outstanding at December 29, 2013	248		3,628		1,101		$	53.46	$	59.66	$	54.64
	Awarded	—		312		198		—		$	147.77	$	148.78
	Vested	(123	)	(643	)	—		$	47.9	$	53.14	—
	Cancelled	—		(158	)	(59	)	—		$	63.11	$	52.87
	Outstanding at September 28, 2014	125		3,139		1,240		$	55.44	$	69.6	$	69.72
	Employee Stock Purchase Plan
	The price at which common stock is purchased under the ESPP is equal to 85% of the fair market value of the common stock on the first or last day of the offering period, whichever is lower. During the nine months ended September 28, 2014, approximately 0.3 million shares were issued under the ESPP. As of September 28, 2014, there were approximately 14.7 million shares available for issuance under the ESPP.
	Warrants
	In connection with the offering of the 2014 Notes, the Company sold warrants to purchase 18.3 million shares of common stock to counterparties to the convertible note hedge transactions. The warrants had an exercise price of $31.435 per share, and the proceeds from the sale of such warrants were used by the Company to partially offset the cost of the transactions. In July 2013, the Company settled with a hedging counterparty outstanding warrants to purchase approximately 3.0 million shares of the Company’s common stock for $125.0 million in cash. The remaining warrants were exercised in full during the nine months ended September 28, 2014, with warrants to purchase 4.1 million shares of the Company’s common stock exercised during the three months ended September 28, 2014.
	Share Repurchases
	In April 2012 the Company’s Board of Directors authorized share repurchases for up to $250.0 million via a combination of Rule 10b5-1 and discretionary share repurchase programs. In addition, on January 30, 2014, the Company’s Board of Directors authorized up to $250.0 million to repurchase shares of the Company’s common stock on a discretionary basis. During the nine months ended September 28, 2014, the Company repurchased approximately 1.3 million shares for $202.4 million in the aggregate and no shares were repurchased during the three months ended September 28, 2014. Authorizations to repurchase up to an additional $165.1 million of the Company’s common stock remained as of September 28, 2014.

Income_Taxes

Income Taxes	9 Months Ended
	Sep. 28, 2014
Income Tax Disclosure [Abstract]	'
Income Taxes	'
	Income Taxes
	The Company’s effective tax rate may vary from the U.S. federal statutory tax rate due to the change in the mix of earnings in tax jurisdictions with different statutory rates, benefits related to tax credits, and the tax impact of non-deductible expenses and other permanent differences between income before income taxes and taxable income. The effective tax rates for the three and nine months ended September 28, 2014 were 16.9% and 22.1%, respectively. For the three and nine months ended September 28, 2014, the variances of effective tax rates from the U.S. federal statutory tax rate of 35% were primarily attributable to the reversal of the valuation allowance on foreign tax credits and the removal of uncertain tax positions associated with statute expirations, which were recorded as discrete items during the three months ended September 28, 2014. The differences from the statutory rate also resulted from a higher mix of foreign earnings, such as earnings in Singapore and the United Kingdom, which were taxed at lower rates than the U.S. federal statutory tax rate, and the tax treatment of the loss on extinguishment of debt.
	In May 2013, the Internal Revenue Service began an audit of the Company’s corporate income tax return filed for fiscal year 2011. The Internal Revenue Service continues to analyze the information provided by the Company and has not yet proposed any adjustments to the filed return.

Legal_Proceedings

Legal Proceedings	9 Months Ended
	Sep. 28, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Legal Proceedings	'
	Legal Proceedings
	The Company is involved in various lawsuits and claims arising in the ordinary course of business, including actions with respect to intellectual property, employment, and contractual matters. In connection with these matters, the Company assesses, on a regular basis, the probability and range of possible loss based on the developments in these matters. A liability is recorded in the financial statements if it is believed to be probable that a loss has been incurred and the amount of the loss can be reasonably estimated. Because litigation is inherently unpredictable and unfavorable results could occur, assessing contingencies is highly subjective and requires judgments about future events. The Company regularly reviews outstanding legal matters to determine the adequacy of the liabilities accrued and related disclosures. The amount of ultimate loss may differ from these estimates. Each matter presents its own unique circumstances, and prior litigation does not necessarily provide a reliable basis on which to predict the outcome, or range of outcomes, in any individual proceeding. Because of the uncertainties related to the occurrence, amount, and range of loss on any pending litigation or claim, the Company is currently unable to predict their ultimate outcome, and, with respect to any pending litigation or claim where no liability has been accrued, to make a meaningful estimate of the reasonably possible loss or range of loss that could result from an unfavorable outcome. In the event that opposing litigants in outstanding litigations or claims ultimately succeed at trial and any subsequent appeals on their claims, any potential loss or charges in excess of any established accruals, individually or in the aggregate, could have a material adverse effect on the Company’s business, financial condition, results of operations, and/or cash flows in the period in which the unfavorable outcome occurs or becomes probable, and potentially in future periods.
	On November 24, 2010, Syntrix Biosystems, Inc. filed suit against the Company in the United States District Court for the Western District of Washington at Tacoma (Case No. C10-5870-BHS) alleging that the Company willfully infringed U.S. Patent No. 6,951,682 by selling its BeadChip array products, and that the Company misappropriated Syntrix’s trade secrets. On January 30, 2013, the Court granted the Company’s motion for summary judgment on Syntrix’s trade secret claims, and dismissed those claims from the case. On March 14, 2013, a jury reached a verdict in favor of Syntrix, finding that Illumina’s BeadChip kits infringe the Syntrix patent. During trial, the Court dismissed Syntrix’s claim that the alleged infringement was willful. On July 1, 2013, the Court entered a Final Amended Judgment for $115.1 million, in accordance with the jury verdict, including supplemental damages and prejudgment interest. In addition, the Court awarded Syntrix an ongoing royalty of 8% for accused sales from March 15, 2013 until the patent expires on September 16, 2019. The Company believes that it did not infringe the Syntrix patent and that the patent is invalid. Therefore, the Company disagrees with the judgment and contends that the judgment is not supported by the law or facts. Accordingly, on December 3, 2013, the Company filed a Notice of Appeal to the Court of Appeals for the Federal Circuit challenging the Final Amended Judgment. On December 16, 2013, Syntrix cross appealed the Court’s dismissal of its trade secret claims and denial of its willfulness claim.
	As a result of the amended judgment, the Company recorded a legal contingency accrual of $148.8 million and $132.9 million as of September 28, 2014 and December 29, 2013, respectively, including damages and interest awarded to Syntrix. During the nine months ended September 28, 2014, the Company recorded a related charge of $15.8 million to cost of product revenue. During the nine months ended September 29, 2013, the Company recorded charges of $127.0 million, with $114.6 million charged to operating expenses and the remainder to cost of product revenue. During the three months ended September 28, 2014, the Company reclassified the legal contingency accrual to short-term liabilities as a decision by the Court of Appeals is reasonably expected to be made within one year. The judgment amount has been secured by a supersedeas bond, and as of September 28, 2014, $28.3 million was deposited with the Court for the accrued post-judgment ongoing royalty amounts. The Company will continue to deposit with the Court ongoing royalties on future sales at the royalty rate stated in the Final Amended Judgment during the appeal process. Funds deposited with the Court are reported as restricted cash in prepaid expenses and other current assets.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 28, 2014
Accounting Policies [Abstract]	'
Basis of Presentation	'
	Basis of Presentation
	The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) for interim financial information and the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. The unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. All intercompany transactions and balances have been eliminated in consolidation. In management’s opinion, the accompanying financial statements reflect all adjustments, consisting of normal recurring adjustments, considered necessary for a fair presentation of the results for the interim periods presented.
	Interim financial results are not necessarily indicative of results anticipated for the full year. These unaudited condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and footnotes included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 29, 2013, from which the balance sheet information herein was derived.
	The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, and expense, and related disclosure of contingent assets and liabilities. Actual results could differ from those estimates.
Segment Information	'
	Segment Information
	Effective December 30, 2013, the Company reorganized and separated the roles of the Chief Executive Officer and the President, with core market and operational functions centralized and reporting to the President, for the primary purpose of achieving scalability in business operations to support the growth in the Company’s strategic markets. Corporate functions and the President report to the CEO. As a result, the Company operates under one operating segment and reports under one reportable segment.
Fiscal Year	'
	Fiscal Year
	The Company’s fiscal year consists of 52 or 53 weeks ending the Sunday closest to December 31, with quarters of 13 or 14 weeks ending the Sunday closest to March 31, June 30, September 30, and December 31. The three and nine months ended September 28, 2014 and September 29, 2013 were both 13 and 39 weeks, respectively.
Recent Accounting Pronouncements	'
	Recent Accounting Pronouncements
	In May 2014, the Financial Accounting Standards Board issued Accounting Standards Update (ASU) 2014-09, Revenue from Contracts with Customers. The new standard is based on the principle that revenue should be recognized to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. ASU 2014-09 will be effective for the Company beginning in the first quarter of fiscal 2017 and allows for a full retrospective or a modified retrospective adoption approach. The Company is currently evaluating the impact of ASU 2014-09 on its consolidated financial statements.
Goodwill, Intangible Assets and Other Long-Lived Assets	'
	Goodwill, Intangible Assets and Other Long-Lived Assets
	Goodwill, which has an indefinite useful life, represents the excess of cost over fair value of net assets acquired. The change in the carrying value of goodwill during the nine months ended September 28, 2014 was due to a current year acquisition and adjustments to the purchase price subsequent to the preliminary allocation of purchase price related to prior year acquisitions. Goodwill is reviewed for impairment at least annually during the second quarter, or more frequently if an event occurs indicating the potential for impairment. During its goodwill impairment review, the Company may assess qualitative factors to determine whether it is more likely than not that the fair value of its reporting unit is less than its carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance of the Company. If, after assessing the totality of these qualitative factors, the Company determines that it is not more likely than not that the fair value of its reporting unit is less than its carrying amount, then no additional assessment is deemed necessary. Otherwise, the Company proceeds to perform a two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with its carrying value, including goodwill. If the carrying amount of the reporting unit exceeds its fair value, the Company performs the second step of the goodwill impairment test to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. The Company may also elect to bypass the qualitative assessment in a period and elect to proceed to perform the first step of the goodwill impairment test. The Company performed its annual assessment for goodwill impairment in the second quarter of 2014, noting no impairment.
	The Company’s identifiable intangible assets are typically comprised of acquired core technologies, licensed technologies, license agreements, customer relationships, and trade names. The cost of identifiable intangible assets with finite lives is generally amortized on a straight-line basis over the assets’ respective estimated useful lives.
	The Company regularly performs reviews to determine if any event has occurred that may indicate its intangible assets with finite useful lives and other long-lived assets are potentially impaired. If indicators of impairment exist, the Company performs an impairment test to assess the recoverability of the affected assets by determining whether the carrying amount of such assets exceeds the undiscounted expected future cash flows. If the affected assets are not recoverable, the Company estimates the fair value of the assets and records an impairment loss if the carrying value of the assets exceeds the fair value. Factors that may indicate potential impairment include a significant decline in the Company’s stock price and market capitalization compared to its net book value, significant changes in the ability of a particular asset to generate positive cash flows, the Company’s strategic business objectives, and the pattern of utilization of a particular asset. The Company performed quarterly reviews of its intangible assets with finite useful lives and other long-lived assets and noted no significant impairments for the three and nine months ended September 28, 2014.
	During 2013, the Company decided to discontinue its Eco and NuPCR product lines to better align its product portfolio with its core strategy. As a result, the Company recorded a total impairment charge of $25.2 million in cost of product revenue during the three months ended September 29, 2013, $22.9 million of which related to identifiable intangible assets.
Derivatives	'
	Derivatives
	The Company is exposed to foreign exchange rate risks in the normal course of business. To manage a portion of the accounting exposure resulting from changes in foreign currency exchange rates, the Company enters into foreign exchange contracts to hedge monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. These foreign exchange contracts are carried at fair value and are not designated as hedging instruments. Changes in the value of the derivative are recognized in other expense, net, along with an offsetting remeasurement gain or loss on the underlying foreign currency denominated assets or liabilities.
	As of September 28, 2014, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of September 28, 2014 and December 29, 2013, the total notional amounts of outstanding forward contracts in place for foreign currency purchases were $51.2 million and $54.7 million, respectively.
Reserve for Product Warranties	'
	Reserve for Product Warranties
	The Company generally provides a one-year warranty on instruments. Additionally, the Company provides a warranty on consumables through the expiration date, which generally ranges from six to twelve months after the manufacture date. At the time revenue is recognized, the Company establishes an accrual for estimated warranty expenses based on historical experience as well as anticipated product performance. The Company periodically reviews its warranty reserve for adequacy and adjusts the warranty accrual, if necessary, based on actual experience and estimated costs to be incurred. Warranty expense is recorded as a component of cost of product revenue.
Revenue Recognition	'
	Revenue Recognition
	The Company’s revenue is generated primarily from the sale of products and services. Product revenue primarily consists of sales of instruments and consumables used in genetic analysis. Service and other revenue primarily consists of revenue generated from genotyping and sequencing services and instrument service contracts.
	The Company recognizes revenue when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the seller’s price to the buyer is fixed or determinable, and collectibility is reasonably assured. In instances where final acceptance of the product or system is required, revenue is deferred until all the acceptance criteria have been met. All revenue is recorded net of discounts.
	Revenue from product sales is recognized generally upon transfer of title to the customer, provided that no significant obligations remain and collection of the receivable is reasonably assured. Revenue from instrument service contracts is recognized as the services are rendered, typically evenly over the contract term. Revenue from genotyping and sequencing services is recognized when earned, which is generally at the time the genotyping or sequencing analysis data is made available to the customer or agreed upon milestones are reached.
	In order to assess whether the price is fixed or determinable, the Company evaluates whether refund rights exist. If there are refund rights or payment terms based on future performance, the Company defers revenue recognition until the price becomes fixed or determinable. The Company assesses collectibility based on a number of factors, including past transaction history with, and the creditworthiness of, the customer. If the Company determines that collection of a payment is not reasonably assured, revenue recognition is deferred until receipt of payment.
	The Company regularly enters into contracts where revenue is derived from multiple deliverables including products or services. These products or services are generally delivered within a short time frame, approximately three to six months, after the contract execution date. Revenue recognition for contracts with multiple deliverables is based on the individual units of accounting determined to exist in the contract. A delivered item is considered a separate unit of accounting when the delivered item has value to the customer on a stand-alone basis. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis. Consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence (VSOE) of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence exists, the Company uses its best estimate of the selling price for the deliverable.
	In order to establish VSOE of selling price, the Company must regularly sell the product or service on a standalone basis with a substantial majority priced within a relatively narrow range. VSOE of selling price is usually the midpoint of that range. If there are not a sufficient number of standalone sales and VSOE of selling price cannot be determined, then the Company considers whether third party evidence can be used to establish selling price. Due to the lack of similar products and services sold by other companies within the industry, the Company has rarely established selling price using third-party evidence. If neither VSOE nor third party evidence of selling price exists, the Company determines its best estimate of selling price using average selling prices over a rolling 12-month period coupled with an assessment of current market conditions. If the product or service has no history of sales or if the sales volume is not sufficient, the Company relies upon prices set by the Company’s pricing committee adjusted for applicable discounts. The Company recognizes revenue for delivered elements only when it determines there are no uncertainties regarding customer acceptance.
	In certain markets, the Company sells products and provides services to customers through distributors that specialize in life science products. In most sales through distributors, the product is delivered directly to customers. In cases where the product is delivered to a distributor, revenue recognition is deferred until acceptance is received from the distributor, and/or the end-user, if required by the applicable sales contract. The terms of sales transactions through distributors are consistent with the terms of direct sales to customers. These transactions are accounted for in accordance with the Company’s revenue recognition policy described herein.
Net Income per Share	'
	Net Income per Share
	Basic net income per share is computed based on the weighted average number of common shares outstanding during the period. Diluted net income per share is computed based on the sum of the weighted average number of common shares and dilutive potential common shares outstanding during the period.
	Dilutive potential common shares consist of shares issuable under convertible senior notes, equity awards, and warrants. Convertible senior notes have a dilutive impact when the average market price of the Company’s common stock exceeds the applicable conversion price of the respective notes. Potentially dilutive common shares from equity awards and warrants are determined using the average share price for each period under the treasury stock method. In addition, the following amounts are assumed to be used to repurchase shares: proceeds from exercise of equity awards and warrants; the average amount of unrecognized compensation expense for equity awards; and estimated tax benefits that will be recorded in additional paid-in capital when expenses related to equity awards become deductible. In loss periods, basic net loss per share and diluted net loss per share are identical because the otherwise dilutive potential common shares become anti-dilutive and are therefore excluded.
	The following table presents the calculation of weighted average shares used to calculate basic and diluted net income per share (in thousands):
		Three Months Ended		Nine Months Ended
		September 28,	September 29,	September 28,	September 29,
		2014	2013	2014	2013
	Weighted average shares outstanding	141,142	125,465	133,290	124,532
	Effect of dilutive potential common shares from:
	Convertible senior notes	1,972	1,028	3,967	1,052
	Equity awards	4,124	4,596	4,367	4,290
	Warrants	274	9,512	7,460	8,756
	Weighted average shares used in calculation of diluted net income per share	147,512	140,601	149,084	138,630
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	54	317	112	1,305

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	9 Months Ended
	Sep. 28, 2014
Accounting Policies [Abstract]	'
Weighted average shares used to calculate basic and diluted net income per share	'
	The following table presents the calculation of weighted average shares used to calculate basic and diluted net income per share (in thousands):
		Three Months Ended		Nine Months Ended
		September 28,	September 29,	September 28,	September 29,
		2014	2013	2014	2013
	Weighted average shares outstanding	141,142	125,465	133,290	124,532
	Effect of dilutive potential common shares from:
	Convertible senior notes	1,972	1,028	3,967	1,052
	Equity awards	4,124	4,596	4,367	4,290
	Warrants	274	9,512	7,460	8,756
	Weighted average shares used in calculation of diluted net income per share	147,512	140,601	149,084	138,630
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	54	317	112	1,305

Balance_Sheet_Account_Details_

Balance Sheet Account Details (Tables)	9 Months Ended
	Sep. 28, 2014
Balance Sheet Account Details [Abstract]	'
Short-term investments	'
	The following is a summary of short-term investments (in thousands):
		September 28, 2014												December 29, 2013
		Amortized			Gross			Gross			Estimated			Amortized		Gross		Gross			Estimated
		Cost			Unrealized			Unrealized			Fair Value			Cost		Unrealized		Unrealized			Fair Value
					Gains			Losses								Gains		Losses
	Available-for-sale securities:
	Debt securities in government sponsored entities	$	46,021		$	17		$	(47	)	$	45,991		$	82,226	$	18	$	(101	)	$	82,143
	Corporate debt securities	332,735			136			(1,621		)	331,250			342,034		312		(376		)	341,970
	U.S. Treasury securities	64,272			47			(28		)	64,291			29,795		58		—			29,853
	Total available-for-sale securities	$	443,028		$	200		$	(1,696	)	$	441,532		$	454,055	$	388	$	(477	)	$	453,966
Available-for-sale securities in unrealized loss positions	'
	The following table shows the fair values and the gross unrealized losses of such available-for-sale securities that were in an unrealized loss position for less than twelve months as of September 28, 2014 and December 29, 2013, aggregated by investment category (in thousands):
		September 28, 2014						December 29, 2013
		Estimated			Gross			Estimated			Gross
		Fair Value			Unrealized			Fair Value			Unrealized
					Losses						Losses
	Debt securities in government sponsored entities	$	26,058		$	(47	)	$	73,362		$	(101	)
	Corporate debt securities	190,175			(1,621		)	168,118			(373		)
	U.S. Treasury securities	18,958			(28		)	—			—
	Total	$	235,191		$	(1,696	)	$	241,480		$	(474	)
Contractual maturities of available-for-sale securities	'
	Contractual maturities of available-for-sale debt securities as of September 28, 2014 were as follows (in thousands):
		Estimated
		Fair Value
	Due within one year	$	162,248
	After one but within five years	279,284
	Total	$	441,532
Inventory	'
	Inventory consists of the following (in thousands):
		September 28,			December 29,
		2014			2013
	Raw materials	$	68,624		$	57,398
	Work in process	96,068			70,016
	Finished goods	34,606			26,685
	Total inventory	$	199,298		$	154,099
Goodwill	'
	Changes in the Company’s goodwill balance during the nine months ended September 28, 2014 are as follows (in thousands):
		Goodwill
	Balance as of December 29, 2013	$	723,061
	Current period acquisition	3,321
	Purchase price allocation adjustments related to prior year acquisitions	(1,495		)
	Balance as of September 28, 2014	$	724,887
Accrued liabilities	'
	Accrued liabilities consist of the following (in thousands):
		September 28,			December 29,
		2014			2013
	Accrued compensation expenses	$	95,041		$	82,705
	Deferred revenue, current portion	72,391			50,834
	Acquisition related contingent liability, current portion	46,522			6,719
	Accrued taxes payable	36,035			30,435
	Customer deposits	14,822			13,569
	Reserve for product warranties	14,433			10,407
	Facility exit obligation, current portion	4,337			5,570
	Other	20,552			18,881
	Total accrued liabilities	$	304,133		$	219,120
Warranties	'
	Changes in the Company’s reserve for product warranties during the three and nine months ended September 28, 2014 and September 29, 2013 are as follows (in thousands):
		Three Months Ended						Nine Months Ended
		September 28,			September 29,			September 28,			September 29,
		2014			2013			2014			2013
	Balance at beginning of period	$	13,000		$	10,826		$	10,407		$	10,136
	Additions charged to cost of revenue	6,803			3,631			16,616			13,929
	Repairs and replacements	(5,370		)	(3,140		)	(12,590		)	(12,748		)
	Balance at end of period	$	14,433		$	11,317		$	14,433		$	11,317
Leases	'
	Changes in the Company’s facility exit obligation related to its former headquarters lease during the three and nine months ended September 28, 2014 and September 29, 2013 are as follows (in thousands):
		Three Months Ended						Nine Months Ended
		September 28,			September 29,			September 28,			September 29,
		2014			2013			2014			2013
	Balance at beginning of period	$	38,480		$	39,351		$	38,218		$	45,352
	Adjustment to facility exit obligation	57			—			2,065			(1,948		)
	Accretion of interest expense	666			518			1,948			1,716
	Cash payments	(1,153		)	(2,723		)	(4,181		)	(7,974		)
	Balance at end of period	$	38,050		$	37,146		$	38,050		$	37,146

Acquisitions_Tables

Acquisitions (Tables)	9 Months Ended
	Sep. 28, 2014
Business Combinations [Abstract]	'
Contingent compensation expenses	'
	Contingent compensation expenses recorded as a result of acquisitions consist of the following (in thousands):
		Three Months Ended				Nine Months Ended
		September 28,		September 29,		September 28,		September 29,
		2014		2013		2014		2013
	Contingent compensation, included in research and development expense	$	496	$	106	$	1,075	$	432
	Contingent compensation, included in selling, general and administrative expense	—		2,337		2,757		7,692
	Total contingent compensation expense	$	496	$	2,443	$	3,832	$	8,124

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 28, 2014
Fair Value Disclosures [Abstract]	'
Fair value measurements	'
	The following table presents the Company’s hierarchy for assets and liabilities measured at fair value on a recurring basis as of September 28, 2014 and December 29, 2013 (in thousands):
		September 28, 2014									December 29, 2013
		Level 1			Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	Assets:
	Money market funds (cash equivalents)	$	574,878		$	—	$	—	$	574,878	$	478,755	$	—	$	—	$	478,755
	Debt securities in government-sponsored entities	—			45,991		—		45,991		—		82,143		—		82,143
	Corporate debt securities	—			331,250		—		331,250		—		341,970		—		341,970
	U.S. Treasury securities	64,291			—		—		64,291		29,853		—		—		29,853
	Deferred compensation plan assets	—			23,402		—		23,402		—		17,805		—		17,805
	Total assets measured at fair value	$	639,169		$	400,643	$	—	$	1,039,812	$	508,608	$	441,918	$	—	$	950,526
	Liabilities:
	Acquisition related contingent consideration liabilities	$	—		$	—	$	46,522	$	46,522	$	—	$	—	$	49,480	$	49,480
	Deferred compensation liability	—			19,920		—		19,920		—		14,957		—		14,957
	Total liabilities measured at fair value	$	—		$	19,920	$	46,522	$	66,442	$	—	$	14,957	$	49,480	$	64,437
Changes in estimated fair value of contingent consideration liabilities	'
	Changes in estimated fair value of contingent consideration liabilities during the nine months ended September 28, 2014 are as follows (in thousands):
		Contingent
		Consideration
		Liability
		(Level 3
		Measurement)
	Balance as of December 29, 2013	$	49,480
	Change in estimated fair value, recorded in acquisition related expense (gain), net	(2,958		)
	Balance as of September 28, 2014	$	46,522

Convertible_Senior_Notes_Table

Convertible Senior Notes (Tables)	9 Months Ended
	Sep. 28, 2014
Debt Disclosure [Abstract]	'
Summarized information about the conversions during the period	'
	The following table summarizes information about the conversions of the 2014 Notes during the nine months ended September 28, 2014 (in thousands):
		2014 Notes
	Cash paid for principal of notes converted	$	29,570
	Conversion value over principal amount paid in shares of common stock	$	196,095
	Number of shares of common stock issued upon conversion	1,151
Summarized information about equity and liability components of convertible senior notes	'
	The following table summarizes information about the equity and liability components of all convertible senior notes outstanding as of the period reported (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices.
		September 28,			December 29,
		2014			2013
	Principal amount of convertible notes outstanding	$	1,470,027		$	949,570
	Unamortized discount of liability component	(189,072		)	(80,977		)
	Net carrying amount of liability component	1,280,955			868,593
	Less: current portion	(301,119		)	(29,288		)
	Long-term debt	$	979,836		$	839,305
	Conversion option subject to cash settlement	—			$	282
	Carrying value of equity component, net of debt issuance cost	$	215,283		$	274,304
	Fair value of outstanding notes	$	1,850,360		$	1,428,743
	Weighted-average remaining amortization period of discount on the liability component	5.4 years			2.2 years

Sharebased_Compensation_Expens1

Share-based Compensation Expense (Tables)	9 Months Ended
	Sep. 28, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Share-based compensation expense for all stock awards	'
	Share-based compensation expense for all stock awards consists of the following (in thousands):
		Three Months Ended						Nine Months Ended
		September 28,			September 29,			September 28,			September 29,
		2014			2013			2014			2013
	Cost of product revenue	$	2,572		$	1,524		$	6,816		$	4,410
	Cost of service and other revenue	311			233			880			544
	Research and development	14,589			9,561			39,043			26,521
	Selling, general and administrative	27,197			16,091			67,350			44,605
	Share-based compensation expense before taxes	44,669			27,409			114,089			76,080
	Related income tax benefits	(14,852		)	(8,059		)	(37,103		)	(23,123		)
	Share-based compensation expense, net of taxes	$	29,817		$	19,350		$	76,986		$	52,957
Assumptions used to estimate the fair value per share of employee stock purchase rights granted	'
	The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share for stock purchased under the Employee Stock Purchase Plan (ESPP) during the nine months ended September 28, 2014 are as follows:
		Employee Stock Purchase Rights
	Risk-free interest rate	0.05 - 0.13%
	Expected volatility	39% - 41%
	Expected term	0.5 - 1.0 year
	Expected dividends	—
	Weighted-average fair value per share	$	44.64

Stockholders_Equity_Tables

Stockholders' Equity (Tables)	9 Months Ended
	Sep. 28, 2014
Equity [Abstract]	'
Stock option activity under all stock option plans	'
	The Company’s stock option activity under all stock option plans during the nine months ended September 28, 2014 is as follows:
		Options		Weighted-Average
		(in thousands)		Exercise Price
	Outstanding at December 29, 2013	5,724		$	32.64
	Exercised	(2,071	)	$	30.72
	Cancelled	(35	)	$	31.74
	Outstanding at September 28, 2014	3,618		$	33.74
Restricted stock activity	'
	A summary of the Company’s restricted stock activity and related information for the nine months ended September 28, 2014 is as follows:
		Restricted Stock Awards		Restricted Stock Units		Performance Stock Units		Weighted-Average
		(RSA)		(RSU)		(PSU)		Grant-Date Fair Value per Share
								RSA		RSU		PSU
	Outstanding at December 29, 2013	248		3,628		1,101		$	53.46	$	59.66	$	54.64
	Awarded	—		312		198		—		$	147.77	$	148.78
	Vested	(123	)	(643	)	—		$	47.9	$	53.14	—
	Cancelled	—		(158	)	(59	)	—		$	63.11	$	52.87
	Outstanding at September 28, 2014	125		3,139		1,240		$	55.44	$	69.6	$	69.72

Summary_of_Significant_Account3

Summary of Significant Accounting Policies (Details)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
Weighted average shares used to calculate basic and diluted net income per share	'	'	'	'
Weighted average shares outstanding	141,142	125,465	133,290	124,532
Effect of dilutive potential common shares from:	'	'	'	'
Convertible senior notes	1,972	1,028	3,967	1,052
Equity awards	4,124	4,596	4,367	4,290
Warrants	274	9,512	7,460	8,756
Weighted average shares used in calculation of diluted net income per share	147,512	140,601	149,084	138,630
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	54	317	112	1,305

Summary_of_Significant_Account4

Summary of Significant Accounting Policies (Details Textual) (USD $)	3 Months Ended		9 Months Ended
	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013	Dec. 29, 2013
			segments
Number of operating segments	'	'	1	'	'
Number of reportable segments	'	'	1	'	'
Quarterly operating cycle	'P13W	'P13W	'P39W	'P39W	'
Impairments	'	'	'	$25,214,000	'
Total notional amount of outstanding forward contract in place for foreign currency purchase	51,200,000	'	51,200,000	'	54,700,000
Instrument warranty period	'	'	'1 year	'	'
Period of time average selling prices are observed to establish best estimate of selling price	'	'	'12 months	'	'
Minimum [Member]	'	'	'	'	'
Warranty on consumable sales through the expiration date	'	'	'6 months	'	'
Product or service delivery period	'	'	'3 months	'	'
Maximum [Member]	'	'	'	'	'
Warranty on consumable sales through the expiration date	'	'	'12 months	'	'
Product or service delivery period	'	'	'6 months	'	'
Cost of Sales [Member]	'	'	'	'	'
Impairments	'	25,200,000	'	'	'
Intangible asset impairments	'	22,900,000	'	'	'

Balance_Sheet_Account_Details_1

Balance Sheet Account Details (Details) (USD $)	Sep. 28, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	$443,028	$454,055
Available for sale securities, Gross Unrealized Gains	200	388
Available for sale securities, Gross Unrealized Losses	-1,696	-477
Available for sale securities, Estimated Fair Value	441,532	453,966
Debt securities in government sponsored entities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	46,021	82,226
Available for sale securities, Gross Unrealized Gains	17	18
Available for sale securities, Gross Unrealized Losses	-47	-101
Available for sale securities, Estimated Fair Value	45,991	82,143
Corporate debt securities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	332,735	342,034
Available for sale securities, Gross Unrealized Gains	136	312
Available for sale securities, Gross Unrealized Losses	-1,621	-376
Available for sale securities, Estimated Fair Value	331,250	341,970
U.S. Treasury securities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	64,272	29,795
Available for sale securities, Gross Unrealized Gains	47	58
Available for sale securities, Gross Unrealized Losses	-28	'
Available for sale securities, Estimated Fair Value	$64,291	$29,853

Balance_Sheet_Account_Details_2

Balance Sheet Account Details (Details 1) (USD $)	Sep. 28, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	$235,191	$241,480
Available-for-sale Securities, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	-1,696	-474
Debt securities in government sponsored entities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	26,058	73,362
Available-for-sale Securities, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	-47	-101
Corporate debt securities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	190,175	168,118
Available-for-sale Securities, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	-1,621	-373
U.S. Treasury securities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	18,958	'
Available-for-sale Securities, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	($28)	'

Balance_Sheet_Account_Details_3

Balance Sheet Account Details (Details 2) (USD $)	Sep. 28, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Available-for-sale Securities, Debt Maturities, Fair Value, Fiscal Year Maturity [Abstract]	'	'
Due within one year	$162,248	'
After one but within five years	279,284	'
Available for sale securities, Estimated Fair Value	$441,532	$453,966

Balance_Sheet_Account_Details_4

Balance Sheet Account Details (Details 3) (USD $)	Sep. 28, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Inventory [Abstract]	'	'
Raw materials	$68,624	$57,398
Work in process	96,068	70,016
Finished goods	34,606	26,685
Total inventory	$199,298	$154,099

Balance_Sheet_Account_Details_5

Balance Sheet Account Details (Details 4) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014
Goodwill [Roll Forward]	'
Balance as of December 29, 2013	$723,061
Current period acquisition	3,321
Purchase price allocation adjustments related to prior year acquisitions	-1,495
Balance as of September 28, 2014	$724,887

Balance_Sheet_Account_Details_6

Balance Sheet Account Details (Details 5) (USD $)	Sep. 28, 2014	Jun. 29, 2014	Dec. 29, 2013	Sep. 29, 2013	Jun. 30, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Accrued Liabilities, Current [Abstract]	'	'	'	'	'	'
Accrued compensation expenses	$95,041	'	$82,705	'	'	'
Deferred revenue, current portion	72,391	'	50,834	'	'	'
Acquisition related contingent liability, current portion	46,522	'	6,719	'	'	'
Accrued taxes payable	36,035	'	30,435	'	'	'
Customer deposits	14,822	'	13,569	'	'	'
Reserve for product warranties	14,433	13,000	10,407	11,317	10,826	10,136
Facility exit obligation, current portion	4,337	'	5,570	'	'	'
Other	20,552	'	18,881	'	'	'
Total accrued liabilities	$304,133	'	$219,120	'	'	'

Balance_Sheet_Account_Details_7

Balance Sheet Account Details (Details 6) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
Reserve for product warranties [Roll Forward]	'	'	'	'
Balance at beginning of period	$13,000	$10,826	$10,407	$10,136
Additions charged to cost of revenue	6,803	3,631	16,616	13,929
Repairs and replacements	-5,370	-3,140	-12,590	-12,748
Balance at end of period	$14,433	$11,317	$14,433	$11,317

Balance_Sheet_Account_Details_8

Balance Sheet Account Details (Details 7) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
Headquarter Facility Exit Obligation [Roll Forward]	'	'	'	'
Balance at beginning of period	$38,480	$39,351	$38,218	$45,352
Adjustment to facility exit obligation	57	'	2,065	-1,948
Accretion of interest expense	666	518	1,948	1,716
Cash payments	-1,153	-2,723	-4,181	-7,974
Balance at end of period	$38,050	$37,146	$38,050	$37,146

Balance_Sheet_Account_Details_9

Balance Sheet Account Details (Details Textual) (USD $)	3 Months Ended		9 Months Ended
	Sep. 28, 2014	Mar. 31, 2013	Sep. 28, 2014	Sep. 29, 2013	Dec. 29, 2013
	securities		securities
Balance Sheet Account Details [Abstract]	'	'	'	'	'
Number of available-for-sale securities in a gross unrealized loss position	118	'	118	'	'
Company's cost-method investments in non-publicly traded company	$32,200,000	'	$32,200,000	'	$22,100,000
Cost-method investment related gain	4,427,000	6,100,000	4,427,000	6,113,000	'
Future minimum payment due for lease addition in period	$47,600,000	'	$47,600,000	'	'

Acquisitions_Details

Acquisitions (Details) (Contingent compensation expense [Member], USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
Business Combination, Separately Recognized Transactions [Line Items]	'	'	'	'
Contingent compensation expense	$496	$2,443	$3,832	$8,124
Research and Development Expense [Member]	'	'	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'	'	'
Contingent compensation expense	496	106	1,075	432
Selling, general and administrative [Member]	'	'	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'	'	'
Contingent compensation expense	'	$2,337	$2,757	$7,692

Acquisitions_Details_Textual

Acquisitions (Details Textual) (USD $)	Sep. 28, 2014	Dec. 29, 2013	Feb. 21, 2013	Dec. 29, 2013	Sep. 19, 2012	Feb. 21, 2013	Feb. 21, 2013	Feb. 21, 2013
			Verinata [Member]	Series of Individually Immaterial Business Acquisitions [Member]	BlueGnome [Member]	Minimum [Member]	Maximum [Member]	Preexisting relationship [Member]
						Verinata [Member]	Verinata [Member]	Verinata [Member]
Business Combination, Consideration Transferred [Abstract]	'	'	'	'	'	'	'	'
Aggregate purchase price	'	'	$396,300,000	'	$95,500,000	'	'	'
Cash consideration	'	'	339,300,000	'	88,000,000	'	'	'
Fair value of contingent consideration to be settled in cash	'	'	56,200,000	'	7,500,000	'	'	'
Contingent consideration payments, maximum	'	'	100,000,000	'	20,000,000	'	'	'
Fair value of assumed equity attributed to pre-combination services	'	'	200,000	'	'	'	'	'
Loss realized on settlement of preexisting relationship	'	'	'	'	'	'	'	500,000
Fair value inputs, discount rate	'	'	'	'	'	6.00%	20.00%	'
Fair Value Assumptions, Expected Volatility Rate	'	'	50.00%	'	'	'	'	'
Fair Value Assumptions, Risk Free Interest Rate	'	'	0.26%	'	'	'	'	'
Goodwill	$724,887,000	$723,061,000	'	$126,300,000	'	'	'	'

Fair_Value_Measurements_Detail

Fair Value Measurements (Details) (USD $)

9 Months Ended

9 Months Ended

In Thousands, unless otherwise specified

Sep. 28, 2014

Sep. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Sep. 28, 2014

Dec. 29, 2013

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 3 [Member]

Fair Value, Inputs, Level 3 [Member]

Fair Value, Inputs, Level 3 [Member]

Debt securities in government sponsored entities [Member]

Debt securities in government sponsored entities [Member]

Debt securities in government sponsored entities [Member]

Debt securities in government sponsored entities [Member]

Corporate debt securities [Member]

Corporate debt securities [Member]

Corporate debt securities [Member]

Corporate debt securities [Member]

U.S. Treasury securities [Member]

U.S. Treasury securities [Member]

U.S. Treasury securities [Member]

U.S. Treasury securities [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Assets:

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Money market funds (cash equivalents)

'

'

$574,878

$478,755

$574,878

$478,755

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Investments, fair value disclosure

'

'

'

'

'

'

'

'

'

'

'

45,991

82,143

45,991

82,143

331,250

341,970

331,250

341,970

64,291

29,853

64,291

29,853

Deferred compensation plan assets

'

'

23,402

17,805

'

'

23,402

17,805

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total assets measured at fair value

'

'

1,039,812

950,526

639,169

508,608

400,643

441,918

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Liabilities:

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Acquisition related contingent consideration liabilities

'

'

46,522

49,480

'

'

'

'

46,522

46,522

49,480

'

'

'

'

'

'

'

'

'

'

'

'

Deferred compensation liability

'

'

19,920

14,957

'

'

19,920

14,957

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total liabilities measured at fair value

'

'

66,442

64,437

'

'

19,920

14,957

'

46,522

49,480

'

'

'

'

'

'

'

'

'

'

'

'

Change in estimated fair value of the contingent consideration liability

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Balance as of December 29, 2013

'

'

46,522

49,480

'

'

'

'

49,480

46,522

49,480

'

'

'

'

'

'

'

'

'

'

'

'

Change in estimated fair value, recorded in acquisition related expense (gain), net

-2,958

-11,031

'

'

'

'

'

'

-2,958

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Balance as of September 28, 2014

'

'

$46,522

$49,480

'

'

'

'

$46,522

$46,522

$49,480

'

'

'

'

'

'

'

'

'

'

'

'

Convertible_Senior_Notes_Detai

Convertible Senior Notes (Details) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014
Extinguishment of Debt [Line Items]	'
Cash paid for principal of notes converted	$1,244,721
0.625% Convertible Senior Notes due 2014 [Member]	'
Extinguishment of Debt [Line Items]	'
Cash paid for principal of notes converted	29,570
Conversion value over principal amount paid in shares of common stock	$196,095
Number of shares of common stock issued upon conversion	1,151

Convertible_Senior_Notes_Detai1

Convertible Senior Notes (Details 1) (USD $)	9 Months Ended	12 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Dec. 29, 2013
Summarized information about equity and liability components of convertible senior notes	'	'
Principal amount of convertible notes outstanding	$1,470,027	$949,570
Unamortized discount of liability component	-189,072	-80,977
Net carrying amount of liability component	1,280,955	868,593
Less: current portion	-301,119	-29,288
Long-term debt	979,836	839,305
Conversion option subject to cash settlement	'	282
Carrying value of equity component, net of debt issuance cost	215,283	274,304
Fair value of outstanding notes	$1,850,360	$1,428,743
Weighted average remaining amortization period of discount on the liability component	'5 years 5 months	'2 years 2 months

Convertible_Senior_Notes_Detai2

Convertible Senior Notes (Details Textual) (USD $)	9 Months Ended		0 Months Ended				9 Months Ended	12 Months Ended	9 Months Ended	12 Months Ended
	Sep. 28, 2014	Dec. 29, 2013	Jun. 11, 2014	Jun. 11, 2014	Jun. 11, 2014	Jun. 11, 2014	Sep. 28, 2014	Jan. 01, 2012	Sep. 28, 2014	Dec. 30, 2007
			0% Convertible Senior Notes due 2019 [Member]	0.5% Convertible Senior Notes due 2021 [Member]	Convertible Senior Notes due 2019 and 2021 [Member]	0.25% Convertible Senior Notes due 2016 [Member]	0.25% Convertible Senior Notes due 2016 [Member]	0.25% Convertible Senior Notes due 2016 [Member]	0.625% Convertible Senior Notes due 2014 [Member]	0.625% Convertible Senior Notes due 2014 [Member]
Debt Instrument [Line Items]	'	'	'	'	'	'	'	'	'	'
Issuance of convertible senior notes	'	'	$632,500,000	$517,500,000	$1,150,000,000	'	'	$920,000,000	'	$400,000,000
Interest rate on convertible senior notes	'	'	0.00%	0.50%	'	'	'	0.25%	'	0.63%
Debt issuance price as a percentage of principal	'	'	'	'	100.00%	'	'	'	'	'
Net proceeds from issuance of convertible notes	1,132,378,000	'	'	'	1,132,400,000	'	'	'	'	'
Conversion rate per $1,000 principal amount of notes (in shares per thousand dollars)	'	'	'	'	3.9318	'	'	11.9687	'	'
Principal amount used in calculating incremental share settlement amount	'	'	'	'	1,000	'	'	1,000	'	'
Conversion price (in dollars per share)	'	'	'	'	$254.34	'	'	$83.55	'	'
Circumstances of converting notes at referred conversion ratio	'	'	'	'	'(1) during the five business-day period after any 10 consecutive trading day period (the “measurement period”) in which the trading price per 2019 and 2021 Note for each day of such measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such day; (2) during any calendar quarter (and only during that quarter) after the calendar quarter ending September 30, 2014, if the last reported sale price of the Company’s common stock for 20 or more trading days in the period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeds 130% of the applicable conversion price in effect on the last trading day of the immediately preceding calendar quarter; (3) upon the occurrence of specified events described in the indenture for the 2019 and 2021 Notes; and (4) at any time on or after March 15, 2019 for the 2019 Notes, or March 15, 2021 for the 2021 Notes, through the second scheduled trading day immediately preceding the maturity date	'	'	'(1) during the five business-day period after any 10 consecutive trading day period (the “measurement period”) in which the trading price per 2016 Note for each day of such measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such day; (2) during any calendar quarter (and only during that quarter) after the calendar quarter ending March 31, 2011, if the last reported sale price of the Company’s common stock for 20 or more trading days in the period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeds 130% of the applicable conversion price in effect on the last trading day of the immediately preceding calendar quarter; (3) upon the occurrence of specified events described in the indenture for the 2016 Notes; and (4) at any time on or after December 15, 2015 through the second scheduled trading day immediately preceding the maturity date.	'	'
Number of consecutive trading days in the measurement period (in days)	'	'	'	'	'10 days	'	'	'10 days	'	'
Conversion triggering common stock trading price as a percentage of price last reported in Measurement period converted at conversion rate	'	'	'	'	'less than 98%	'	'	'less than 98%	'	'
Minimum number of consecutive trading days on which trading price is examined for triggering of conversion (in days)	'	'	'	'	'20 days	'	'	'20 days	'	'
Number of consecutive trading days on which trading price is examined for triggering of conversion	'	'	'	'	'30 days	'	'	'30 days	'	'
Conversion triggering common stock price as a percentage of applicable conversion price in effect on the last trading day of the immediately preceding calendar quarter	'	'	'	'	'exceeds 130%	'	'	'exceeds 130%	'	'
Date after which notes will become convertible at any time	'	'	15-Mar-19	15-Mar-21	'	'	'	15-Dec-15	'	'
Debt maturity date	'	'	15-Jun-19	15-Jun-21	'	'	'	15-Mar-16	'	15-Feb-14
Repurchase price as a percentage of principal amount upon designated events	'	'	'	'	100.00%	'	'	'	'	'
Effective interest rates of liability component	'	'	2.90%	3.50%	'	'	'	4.50%	'	8.30%
Fair value of liability component	1,280,955,000	868,593,000	'	'	971,500,000	'	'	'	'	'
Carrying value of equity component, net of debt issuance cost	215,283,000	274,304,000	'	'	161,200,000	'	'	'	'	'
Cash proceeds	'	'	'	'	1,132,700,000	'	'	'	'	'
Convertible senior note conversion start period	'	'	'	'	'	'	1-Apr-14	'	1-Apr-12	'
Convertible senior note conversion end period	'	'	'	'	'	'	31-Dec-14	'	12-Feb-14	'
Repurchased principal amount	'	'	'	'	'	600,000,000	'	'	'	'
Repurchase amount	1,244,721,000	'	'	'	'	'	1,244,700,000	'	29,570,000	'
Fair value inputs, discount rate	'	'	'	'	'	1.20%	'	'	'	'
Repayment of convertible debt - debt component	'	'	'	'	'	588,800,000	'	'	'	'
Repayment of convertible debt - equity component	'	'	'	'	'	655,900,000	'	'	'	'
Loss on extinguishment of debt	-31,360,000	'	'	'	'	31,400,000	'	'	'	'
If-converted value in excess of principal	'	'	'	'	'	'	$346,100,000	'	'	'

Sharebased_Compensation_Expens2

Share-based Compensation Expense (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 28, 2014	Sep. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
Share-based Compensation	'	'	'	'
Share-based compensation expense before taxes	$44,669	$27,409	$114,089	$76,080
Related income tax benefits	-14,852	-8,059	-37,103	-23,123
Share-based compensation expense, net of taxes	29,817	19,350	76,986	52,957
Cost of product revenue	'	'	'	'
Share-based Compensation	'	'	'	'
Share-based compensation expense before taxes	2,572	1,524	6,816	4,410
Cost of service and other revenue	'	'	'	'
Share-based Compensation	'	'	'	'
Share-based compensation expense before taxes	311	233	880	544
Research and development	'	'	'	'
Share-based Compensation	'	'	'	'
Share-based compensation expense before taxes	14,589	9,561	39,043	26,521
Selling, general and administrative	'	'	'	'
Share-based Compensation	'	'	'	'
Share-based compensation expense before taxes	$27,197	$16,091	$67,350	$44,605

Sharebased_Compensation_Expens3

Share-based Compensation Expense (Details 1) (Employee Stock Purchase Rights [Member], USD $)	9 Months Ended
	Sep. 28, 2014
Assumptions used to estimate the fair value per share of employee stock purchase rights granted	'
Risk-free interest rate, minimum	0.05%
Risk-free interest rate, maximum	0.13%
Expected volatility, minimum	39.00%
Expected volatility, maximum	41.00%
Expected dividends	0.00%
Weighted average fair value per share (in dollars per share)	$44.64
Minimum [Member]	'
Assumptions used to estimate the fair value per share of employee stock purchase rights granted	'
Expected term (in years)	'6 months
Maximum [Member]	'
Assumptions used to estimate the fair value per share of employee stock purchase rights granted	'
Expected term (in years)	'1 year

Sharebased_Compensation_Expens4

Share-based Compensation Expense (Details Textual) (USD $)	9 Months Ended
In Millions, unless otherwise specified	Sep. 28, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Unrecognized compensation cost related to stock options, restricted stock, and ESPP shares issued to date	$210.30
Weighted-average period of unrecognized compensation cost related to stock options, restricted stock, and ESPP shares granted to date (in years)	'1 year 9 months

Stockholders_Equity_Details

Stockholders' Equity (Details) (USD $)	9 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Sep. 28, 2014
Stock option activity	'
Outstanding at period start (in shares)	5,724
Options, Exercised (in shares)	-2,071
Options, Cancelled (in shares)	-35
Outstanding at period end (in shares)	3,618
Weighted-Average Exercise Price, Outstanding at period start (in dollars per share)	$32.64
Weighted Average Exercise Price, Exercised (in dollars per share)	$30.72
Weighted Average Exercise Price, Cancelled (in dollars per share)	$31.74
Weighted-Average Exercise Price, Outstanding at period end (in dollars per share)	$33.74

Stockholders_Equity_Details_1

Stockholders' Equity (Details 1) (USD $)	9 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Sep. 28, 2014
Restricted Stock Awards (RSAs) [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Outstanding at period start (in shares)	248
Vested (in shares)	-123
Outstanding at period end (in shares)	125
Weighted Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share)	$53.46
Weighted Average Grant Date Fair Value per Share, Vested (in dollars per share)	$47.90
Weighted Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share)	$55.44
Restricted Stock Units (RSUs) [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Outstanding at period start (in shares)	3,628
Awarded (in shares)	312
Vested (in shares)	-643
Cancelled (in shares)	-158
Outstanding at period end (in shares)	3,139
Weighted Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share)	$59.66
Weighted Average Grant Date Fair Value per Share, Awarded (in dollars per share)	$147.77
Weighted Average Grant Date Fair Value per Share, Vested (in dollars per share)	$53.14
Weighted Average Grant Date Fair Value per Share, Cancelled (in dollars per share)	$63.11
Weighted Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share)	$69.60
Performance Shares [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Outstanding at period start (in shares)	1,101
Awarded (in shares)	198
Cancelled (in shares)	-59
Outstanding at period end (in shares)	1,240
Weighted Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share)	$54.64
Weighted Average Grant Date Fair Value per Share, Awarded (in dollars per share)	$148.78
Weighted Average Grant Date Fair Value per Share, Cancelled (in dollars per share)	$52.87
Weighted Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share)	$69.72

Stockholders_Equity_Details_Te

Stockholders' Equity (Details Textual) (USD $)	1 Months Ended	3 Months Ended	9 Months Ended						9 Months Ended
Share data in Millions, except Per Share data, unless otherwise specified	Jul. 28, 2013	Sep. 28, 2014	Sep. 28, 2014	Sep. 29, 2013	Jan. 30, 2014	Apr. 29, 2012	Dec. 30, 2007	Sep. 28, 2014	Sep. 28, 2014
					January 30 2014 Stock Repurchase Program [Member]	April 18, 2012 Stock Repurchase Plan [Member]	Warrant [Member]	2005 Illumina, Solexa, and Verinata Plans [Member]	Employee Stock Purchase Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'	'	'	'	'	'
Shares available for issuance	'	'	'	'	'	'	'	6.6	14.7
Stock options exercisable (in shares)	'	3.2	3.2	'	'	'	'	'	'
Stock options exercisable outstanding weighted average exercise price per share (in dollars per share)	'	$34.63	$34.63	'	'	'	'	'	'
Specified percentage of the fair market value of the common stock on the first or last day of the offering period whichever is lower at which stock is purchased	'	'	'	'	'	'	'	'	85.00%
Total shares issued under the ESPP	'	'	'	'	'	'	'	'	0.3
Number of shares that can be purchased under outstanding warrants	'	'	'	'	'	'	18.3	'	'
Warrant exercise price	'	'	'	'	'	'	$31.43	'	'
Number of shares called by warrants settled in period	3	4.1	'	'	'	'	'	'	'
Payments for warrant settlements	$125,000,000	'	'	$125,000,000	'	'	'	'	'
Stock repurchase program, authorized amount	'	'	'	'	250,000,000	250,000,000	'	'	'
Number of shares repurchased	'	0	1.3	'	'	'	'	'	'
Stock repurchase, amount	'	'	202,400,000	'	'	'	'	'	'
Stock repurchase program, remaining authorized repurchase amount	'	$165,100,000	$165,100,000	'	'	'	'	'	'

Income_Taxes_Details_Textual

Income Taxes (Details Textual)	3 Months Ended	9 Months Ended
	Sep. 28, 2014	Sep. 28, 2014
Income Tax Disclosure [Abstract]	'	'
Effective tax rate	16.90%	22.10%
U.S. statutory rate	35.00%	35.00%

Legal_Proceedings_Details_Text

Legal Proceedings (Details Textual) (USD $)	3 Months Ended	9 Months Ended		0 Months Ended	9 Months Ended			9 Months Ended
	Sep. 28, 2014	Sep. 28, 2014	Sep. 29, 2013	Jul. 02, 2013	Sep. 29, 2013	Sep. 28, 2014	Dec. 29, 2013	Sep. 28, 2014	Sep. 29, 2013
				Syntrix [Member]	Syntrix [Member]	Syntrix [Member]	Syntrix [Member]	Syntrix [Member]	Syntrix [Member]
								Cost of Sales [Member]	Operating Expense [Member]
Loss Contingencies [Line Items]	'	'	'	'	'	'	'	'	'
Legal contingencies, damages awarded	'	'	'	$115,100,000	'	'	'	'	'
Loss contingency, damages awarded, royalty rate	'	'	'	8.00%	'	'	'	'	'
Loss contingency accrual	'	'	'	'	'	148,800,000	132,900,000	'	'
Legal contingencies	7,705,000	7,705,000	115,369,000	'	127,000,000	'	'	15,800,000	114,600,000
Deposit with the court for post-judgment ongoing royalty	'	'	'	'	'	$28,300,000	'	'	'