Exhibit 10.1



|[***] | Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to
the omitted portions.
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AMENDMENT NO. 3

to

ASSIGNMENT AGREEMENT

This AMENDMENT TO ASSIGNMENT AGREEMENT (Amendment), effective as of March 30, 2009 (the Amendment
Date), is made and entered into by and between PHARMACYCLICS, INC., a Delaware corporation having a place of business at 995 East Arques Avenue, Sunnyvale, California 94085, (Pharmacyclics) and CELERA
CORPORATION having a place of business at 1401 Harbor Bay Parkway, Alameda, California 94502 (Celera). Pharmacyclics and Celera may each be referred to herein individually as a Party or, collectively, as
Parties.

WHEREAS, Applera Corporation, through its Celera Group, entered into an assignment agreement with
Pharmacyclics, effective as of April 7, 2006, whereby the Celera Group assigned to Pharmacyclics certain proprietary technology and know-how related to the Celera Programs, including but not limited to the HDAC Program (the Original
Assignment Agreement);

WHEREAS, Pharmacyclics and the Applera Corporation, through its Celera Group, subsequently
executed Amendment No. 1 to the Original Assignment Agreement, effective May 12, 2008, in order to amend certain payment terms of the Assignment Agreement relating to [***] (the First Amendment);

WHEREAS, Pharmacyclics and Celera Corporation, through its Celera Group, subsequently executed Amendment No. 2 to the Original Assignment
Agreement, effective March 2, 2009, in order to amend certain payment terms of the Assignment Agreement relating to [***] (the Second Amendment) (the Original Assignment Agreement, as amended by the First Amendment and the
Second Amendment, hereinafter the Assignment Agreement);

WHEREAS, Pharmacyclics desires that certain terms of
the Assignment Agreement should be amended; and

WHEREAS, Celera desires that such terms should be amended, subject to the terms and
conditions set forth below.

NOW, THEREFORE, in consideration of the mutual covenants and obligations set forth herein, and for
other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, Pharmacyclics and Celera hereby agree as follows:

1.
In General.

All terms defined in the Assignment Agreement shall have a meaning in this Amendment as in the Assignment Agreement, unless otherwise
expressly defined in this Amendment.



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2. Amendment of the Assignment Agreement.

2.1 Payment by Pharmacyclics.Pharmacyclics will pay to Celera $1,000,000, due upon execution of this Amendment. The foregoing payment will be
fully creditable against any amounts otherwise payable by Pharmacyclics to Celera under the Assignment Agreement.

2.2 Amendment
of Section 6.5. Section 6.5 of the Assignment Agreement is hereby amended to read in its entirety as follows:

6.5 Term of Royalties Payments.Pharmacyclics obligation to pay Royalties under Section 6.4 will continue, on an Assigned Product-by-Assigned Product basis, in each country of the world:



| | (a) | In the case of any Assigned Product described in Section 1.5, Section 1.28 (except in the case of Assigned Products described in Section 1.28(b)(iii)) and
Section 1.35 (except in the case of Assigned Products described in Section 1.35(b)(iii)) for as long as the manufacture, use, sale, offer for sale or import of such Assigned Product is covered by a Celera Patent in the country in which
such Assigned Product is used or sold.
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| | (i) | With respect to an Assigned Product that is an [***] (including, without limitation, [***], any backup [***] and [***]):
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(1)Royalties will be due only when the sale of such [***] is covered by a Valid Claim of a Celera Patent in the country in which such product is
sold; and

(2)If an [***] is covered by a Valid Claim of a Celera Patent in the country of sale, but if the product is nonetheless
subject to generic competition, then the royalty rate will be reduced from [***]% to [***]% with respect to sales in such country [***] and its territories.



| | (b) | In the case of any Assigned Product described in Section 1.28(b)(iii), for a period of [***] years beginning on the date of first commercial sale of such Assigned
Product.
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3. Reference to and Effect on the Assignment Agreement.

3.1 Pursuant to Section 13.1 of the Assignment Agreement, this Amendment shall be effective upon the Amendment Date, whereupon the Assignment
Agreement shall be, and hereby is, amended as set forth herein.

3.2 On and after the Amendment Date, each reference in the Assignment
Agreement to this Agreement, hereunder, hereof, herein or words of like import shall mean and be a reference to the Assignment Agreement as amended hereby. No reference to this Amendment need be made
in any instrument or document at any time referring to the Assignment Agreement, a reference to the Assignment Agreement in any of such to be deemed to be a reference to the Assignment Agreement as amended hereby.





|[***] | Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to
the omitted portions.
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3.3 All provisions of the Assignment Agreement not expressly modified by this Amendment shall remain in
full force and effect.

4. Counterparts.

This Amendment may be executed in one or more counterparts, each of which shall be deemed to be an original, but all of which together shall constitute a single instrument.

IN WITNESS THEREOF, the Parties have caused this Amendment to be duly executed by their respective duly authorized officers as of the Amendment
Date.



|                                      |  |                         |  |                               |  |     |  |                     
|------------------------------------- |  | ----------------------- |  | ----------------------------- |  | --- |  | --------------------
|PHARMACYCLICS, INC. (Pharmacyclics) |  |                         |  | CELERA CORPORATION (Celera)
|                                      |  |                         |  |                              
|By:                                   |  | /s/    Robert W. Duggan |  |                               |  | By: |  | /s/    Kathy Ordonez

|            |  |                  |  |  |  |             |  |              
|----------- |  | ---------------- |  |  |  | ----------- |  | -------------
|            |  |                  |  | 
|Print Name: |  | Robert W. Duggan |  |  |  | Print Name: |  | Kathy Ordonez

|       |  |                |  |  |  |        |  |    
|------ |  | -------------- |  |  |  | ------ |  | ---
|       |  |                |  | 
|Title: |  | Chairman & CEO |  |  |  | Title: |  | CEO





|[***] | Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to
the omitted portions.
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