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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549





FORM 10-K/A

(Amendment No. 2)



|x | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------

For the Fiscal Year Ended December 31, 2011.



| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transition period from             to

Commission File Number: 001-34810





Vermillion, Inc.

(Exact name of registrant as specified in its charter)



|                                                               |  |                                     
|-------------------------------------------------------------- |  | ------------------------------------
|Delaware                                                       |  | 33-0595156                          
|(State or other jurisdiction of
incorporation or organization) |  | (I.R.S. Employer Identification No.)
|                                                               | 
|12117 Bee Caves Road, Building Three, Suite 100,
Austin, Texas |  | 78738                               
|(Address of principal executive offices)                       |  | (Zip Code)                          

Registrants telephone number, including area code: (512) 519-0400





Securities registered pursuant to Section 12(b) of the Act:



|                                         |  |                                          
|---------------------------------------- |  | -----------------------------------------
|Title of each class to be so registered  |  | Name of each exchange on which registered
|Common Stock, par value $0.001 per share |  | The NASDAQ Stock Market, LLC             

Securities registered pursuant to Section 12(g) of the Act: None





Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities
Act.    Yes   ̈    No  x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes   ̈    No  x

Indicate
by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was
required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No   ̈

Indicate by check mark whether the registrant has submitted electronically and posted on its
corporate Web site, if any, every Interactive Date File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such
files).    Yes  x    No   ̈

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrants knowledge, in
definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K  x.

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting
company. See the definitions of large accelerated filer, accelerated filer and smaller reporting company in Rule 12b-2 of the Exchange Act. (Check one):



|                        |  |   |  |                           |  |  
|----------------------- |  | - |  | ------------------------- |  | -
|Large accelerated filer |  |  ̈ |  | Accelerated filer         |  |  ̈
|                        |  |   | 
|NonAccelerated filer   |  |  ̈ |  | Smaller reporting company |  | x

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the
Act).    Yes   ̈    No  x

Indicate by check mark whether the registrant has filed all documents and reports required to be filed by Section 12, 13 or 15(d) of the Securities Exchange Act of 1934 subsequent to the
distribution of securities under a plan confirmed by a court.    Yes  x    No   ̈

The aggregate market value of voting common stock held by non-affiliates of the Registrant is $45,564,126 and is based upon the last sales price as
quoted on The NASDAQ Global Market as of June 30, 2011.

As of May 30, 2012, the Registrant had 14,936,913 shares of common stock,
par value $0.001 per share, outstanding.

DOCUMENTS INCORPORATED BY REFERENCE:

None.









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VERMILLION, INC.

FORM 10-K/A

For the Fiscal Year Ended December 31, 2011

Table of Contents



|                                                        |  |          |   | 
|------------------------------------------------------- |  | -------- | - | 
|                                                        |  | Page No. |  
|                                                        | 
|EXPLANATORY NOTE                                        |  |          | 2 | 
|                                                        | 
|PART IV                                                 |  |          | 3 | 
|                                                        | 
|ITEM 15.     EXHIBITS AND FINANCIAL STATEMENT SCHEDULES |  |          | 3 | 
|                                                        | 
|SIGNATURES                                              |  |          |   | 
|                                                        | 
|INDEX TO EXHIBITS                                       |  |          |   | 



1



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EXPLANATORY NOTE

Vermillion, Inc. (the Company) is filing this Amendment No. 2 to the Companys Annual Report on Form 10-K/A (this
Amendment No. 2) to amend the Companys Annual Report on Form 10-K for the year ended December 31, 2011 filed with the Securities and Exchange Commission (the Commission) on March 27, 2012 (the
Annual Report), as amended by the Companys Amendment No. 1 to Annual Report on Form 10-K/A, filed with the Commission on April 27, 2012 (Amendment No. 1). The Company is filing this Amendment No. 2
in response to communications with the Commission in connection with a request for confidential treatment under Rule 24b-2 promulgated under the Securities Exchange Act of 1934, as amended (the Exchange Act), with respect to Exhibit
10.51 (the Exhibit) originally filed with the Annual Report. The sole purpose of this Amendment No. 2 is to file a revised version of the Exhibit in order to disclose certain information for which confidential treatment had been
previously requested and is no longer being sought by the Company and to make a corresponding update to the index to exhibits. The revised version of the Exhibit supersedes in its entirety the Exhibit as originally filed with the Annual Report.

Except for the revised Exhibit and the corresponding update to the index to exhibits, this Amendment No. 2 does not
amend any other information set forth in the Annual Report. This Amendment No. 2 speaks as of the filing date of the Annual Report, does not reflect any events that may have occurred subsequent to the filing date of the Annual Report, and does
not modify or update in any way any disclosures made in the Annual Report. Additionally, in connection with the filing of this Amendment No. 2 and pursuant to Rule 12b-15 of the Exchange Act, the certifications of the Companys
principal executive officer and principal financial officer are also attached as exhibits hereto. This Amendment No. 2 should be read in conjunction with the Annual Report, Amendment No. 1 and our filings with the Commission subsequent to
the Annual Report.



2



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PART IV



|ITEM 15. | EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
|-------- | ------------------------------------------



|(a) | LIST OF DOCUMENTS FILED AS PART OF THIS REPORT:
|--- | -----------------------------------------------



| | 1. | Financial Statements
| | -- | --------------------

| |  | The financial statements and notes thereto, and the report of the independent registered public accounting firm thereon, are set forth on pages F-1 through F-31 of the
Annual Report on Form 10-K, filed with the Securities and Exchange Commission on March 27, 2012.
| |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | 2. | Exhibits
| | -- | --------

| |  | The exhibits listed in the accompanying index to exhibits are filed or incorporated by reference as part of this Amendment No. 2 to the Annual Report on Form
10-K/A.
| |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------



3



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SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be
signed on its behalf by the undersigned, thereunto duly authorized.



|                   |  |  |  |  |  |                                                                                 
|------------------ |  |  |  |  |  | --------------------------------------------------------------------------------
|                   |  |  |  |  |  | Vermillion, Inc.                                                                
|                   |  |  | 
|Date: May 30, 2012 |  |  |  |  |  | /s/ Gail S. Page                                                                
|                   |  |  |  |  |  | Gail S. Page President and
Chief Executive Officer (Principal Executive Officer)
|                   |  |  | 
|Date: May 30, 2012 |  |  |  |  |  | /s/ Eric J. Schoen                                                              
|                   |  |  |  |  |  | Eric J. Schoen Chief
Accounting Officer (Principal Financial Officer)           

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following
persons on behalf of the registrant and in the capacities and on the dates indicated.



|                                  |  |                                                                     |  |             
|--------------------------------- |  | ------------------------------------------------------------------- |  | ------------
|Name                              |  | Title                                                               |  | Date        
|                                  |  |                                                                    
|/s/ Gail S. Page Gail S. Page     |  | President and Chief Executive Officer (Principal Executive Officer) |  | May 30, 2012
|                                  |  |                                                                    
|/s/ Eric J. Schoen Eric J. Schoen |  | Chief Accounting Officer (Principal Financial Officer)              |  | May 30, 2012



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##### Table of Contents

INDEX TO EXHIBITS



|               |  |                                                                                                                                                                                            |  |                           |  |               |  |  |             |  |  |                    |  | 
|-------------- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |  | ------------------------- |  | ------------- |  |  | ----------- |  |  | ------------------ |  | 
|Exhibit Number |  | Exhibit Description                                                                                                                                                                        |  | Incorporated by Reference |  | FiledHerewith
|               |  | Form                                                                                                                                                                                       |  | File No.                  |  | Exhibit       |  |  | Filing Date | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|2.1            |  | Findings of Fact, Conclusions of Law and Order Confirming Debtors (Vermillion Inc.s) Second Amended Plan of Reorganization Under Chapter 11 of the Bankruptcy Code dated
January 7, 2010 |  | 8-K                       |  | 000-31617     |  |  | 2.1         |  |  | January 12, 2010   |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|3.1            |  | Fourth Amended and Restated Certificate of Incorporation of Vermillion, Inc. dated January 22, 2010                                                                                        |  | 8-K                       |  | 000-31617     |  |  | 3.1         |  |  | January 25, 2010   |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|3.2            |  | Third Amended and Restated Bylaws of Vermillion, Inc.                                                                                                                                      |  | 10-K                      |  | 000-34810     |  |  | 3.2         |  |  | March 27, 2012     |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|4.1            |  | Form of Vermillion, Inc.s (formerly Ciphergen Biosystems, Inc.) Common Stock Certificate                                                                                                  |  | S-1/A                     |  | 333-32812     |  |  | 4.1         |  |  | August 24, 2000    |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|4.2            |  | Preferred Shares Rights Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Continental Stock Transfer & Trust Company dated March 20,
2002                       |  | 8-A                       |  | 000-31617     |  |  | 4.2         |  |  | March 21, 2002     |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|4.3            |  | Amendment to Rights Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Wells Fargo Bank, N.A. dated July 22, 2005                                                |  | 8-K                       |  | 000-31617     |  |  | 4.4         |  |  | July 28, 2005      |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|4.4            |  | Second Amendment to Rights Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Wells Fargo Bank, N.A. dated September 30, 2005                                    |  | 8-K                       |  | 000-31617     |  |  | 4.5         |  |  | October 4, 2005    |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|4.5            |  | Third Amendment to Rights Agreement between Vermillion, Inc. and Wells Fargo Bank, N.A., dated September 11, 2007                                                                          |  | 8-K                       |  | 000-31617     |  |  | 10.1        |  |  | September 12, 2007 |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|10.1           |  | 1993 Stock Option Plan #                                                                                                                                                                   |  | S-1                       |  | 333-32812     |  |  | 10.3        |  |  | March 20, 2000     |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|10.2           |  | Form of Stock Option Agreement #                                                                                                                                                           |  | S-1/A                     |  | 333-32812     |  |  | 10.4        |  |  | August 24, 2000    |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|10.3           |  | 2000 Stock Plan and related form of Stock Option Agreement #                                                                                                                               |  | S-1/A                     |  | 333-32812     |  |  | 10.5        |  |  | August 4, 2000     |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|10.4           |  | Amended and Restated 2000 Employee Stock Purchase Plan #                                                                                                                                   |  | 10-Q                      |  | 000-31617     |  |  | 10.6        |  |  | November 14, 2007  |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|10.5           |  | Vermillion, Inc. 2010 Stock Incentive Plan #                                                                                                                                               |  | 8-K                       |  | 000-31617     |  |  | 10.1        |  |  | February 12, 2010  |  | 
|               |  |                                                                                                                                                                                            |  |                           |  |              
|10.6           |  | Ciphergen Biosystems, Inc. 401(k) Plan #                                                                                                                                                   |  | 10-K                      |  | 000-31617     |  |  | 10.7        |  |  | March 22, 2005     |  | 



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|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |               |  |  |             |  |  |                    |  | 
|-------------- |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- |  | ------------- |  |  | ----------- |  |  | ------------------ |  | 
|Exhibit Number |  | Exhibit Description                                                                                                                                                                                                                                                         |  | Incorporated by Reference |  | FiledHerewith
|               |  | Form                                                                                                                                                                                                                                                                        |  | File No.                  |  | Exhibit       |  |  | Filing Date | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.7           |  | Securities Purchase Agreement by and among Vermillion, Inc. and the purchasers party thereto dated August 23, 2007                                                                                                                                                          |  | S-1                       |  | 333-146354    |  |  | 10.57       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.8           |  | Form of Warrant                                                                                                                                                                                                                                                             |  | 10-Q                      |  | 000-31617     |  |  | 10.51       |  |  | November 14, 2007  |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.9           |  | Form of Securities Purchase Agreement between Vermillion, Inc. and the purchasers party thereto dated December 24, 2009                                                                                                                                                     |  | 8-K                       |  | 000-31617     |  |  | 10.1        |  |  | December 29, 2009  |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.10          |  | Employment Agreement between Sandra A. Gardiner and Vermillion, Inc. dated April 9, 2010 #                                                                                                                                                                                  |  | 8-K                       |  | 000-31617     |  |  | 10.1        |  |  | April 22, 2010     |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.11          |  | Employment Agreement between Gail S. Page and Vermillion, Inc. dated September 28, 2010 #                                                                                                                                                                                   |  | 8-K                       |  | 000-34810     |  |  | 10.1        |  |  | September 30, 2010 |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.12          |  | Employment Agreement between Eric T. Fung and Vermillion, Inc. dated September 28, 2010 #                                                                                                                                                                                   |  | 8-K                       |  | 000-34810     |  |  | 10.2        |  |  | September 30, 2010 |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.13          |  | Form of Severance Agreement between key executive employees and Vermillion, Inc. #                                                                                                                                                                                          |  | 8-K                       |  | 000-31617     |  |  | 10.1        |  |  | August 29, 2008    |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.14          |  | Form of Proprietary Information Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and certain of its employees #                                                                                                                                     |  | S-1/A                     |  | 333-32812     |  |  | 10.9        |  |  | August 24, 2000    |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.15          |  | Consulting Agreement between Richard G. Taylor and Vermillion, Inc. dated August 26, 2008 #                                                                                                                                                                                 |  | 8-K                       |  | 000-31617     |  |  | 10.1        |  |  | August 29, 2008    |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.16          |  | MAS License Agreement with IllumeSys Pacific, Inc. dated April 7, 1997                                                                                                                                                                                                      |  | S-1/A                     |  | 333-32812     |  |  | 10.23       |  |  | August 24, 2000    |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.17          |  | MAS License Agreement with Ciphergen Technologies, Inc. (formerly ISP Acquisition Corporation) dated April 7, 1997                                                                                                                                                          |  | S-1                       |  | 333-32812     |  |  | 10.24       |  |  | August 24, 2000    |  | 
|               |  |                                                                                                                                                                                                                                                                             |  |                           |  |              
|10.18          |  | Settlement Agreement and Mutual General Release by and among Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.), IllumeSys Pacific, Inc., Ciphergen Technologies, Inc., Molecular
Analytical Systems, Inc., LumiCyte, Inc. and T. William Hutchens dated May 28, 2003  |  | 8-K                       |  | 000-31617     |  |  | 99.2        |  |  | June 11, 2003      |  | 



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|               |  |                                                                                                                                                                                                                                                  |  |                           |  |               |  |  |             |  |  |                    |  | 
|-------------- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |  | ------------------------- |  | ------------- |  |  | ----------- |  |  | ------------------ |  | 
|Exhibit Number |  | Exhibit Description                                                                                                                                                                                                                              |  | Incorporated by Reference |  | FiledHerewith
|               |  | Form                                                                                                                                                                                                                                             |  | File No.                  |  | Exhibit       |  |  | Filing Date | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.19          |  | Assignment Agreement by and among Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.), IllumeSys Pacific, Inc., Ciphergen Technologies, Inc., Molecular Analytical Systems, Inc.,
LumiCyte, Inc. and T. William Hutchens dated May 28, 2003  |  | 8-K                       |  | 000-31617     |  |  | 99.3        |  |  | June 11, 2003      |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.20          |  | License Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Molecular Analytical Systems, Inc. dated May 28, 2003                                                                                                      |  | 8-K                       |  | 000-31617     |  |  | 99.4        |  |  | June 11, 2003      |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.21          |  | Collaborative Research Agreement between University College London, UCL Biomedica plc and Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) dated September 22, 2005
                                                                      |  | 10-K                      |  | 000-31617     |  |  | 10.54       |  |  | March 17, 2006     |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.22          |  | Distribution and Marketing Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Ciphergen Biosystems KK dated March 24, 1999                                                                                             |  | S-1/A                     |  | 333-32812     |  |  | 10.26       |  |  | September 22, 2000 |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.23          |  | Strategic Alliance Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Quest Diagnostics Incorporated dated July 22, 2005                                                                                               |  | 8-K                       |  | 000-31617     |  |  | 10.44       |  |  | July 28, 2005      |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.24          |  | Amendment to Strategic Alliance Agreement between Vermillion, Inc. and Quest Diagnostics Incorporated dated October 7, 2009                                                                                                                      |  | 8-K                       |  | 000-31617     |  |  | 10.2        |  |  | October 21, 2009   |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.25          |  | Amendment to Strategic Alliance Agreement between Vermillion, Inc. and Quest Diagnostics Incorporated dated November 10, 2010                                                                                                                    |  | 8-K                       |  | 000-34810     |  |  | 10.1        |  |  | November 12, 2010  |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.26          |  | Amendment No. 5 to Strategic Alliance Agreement by and among Vermillion, Inc. and Quest Diagnostics Incorporated and Quest Diagnostics India Private Limited, dated
April 2, 2011                                                               |  | 10-Q                      |  | 001-34810     |  |  | 10.1        |  |  | May 10, 2011       |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.27          |  | Stock Purchase Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Quest Diagnostics Incorporated dated July 22, 2005                                                                                                   |  | 8-K                       |  | 000-31617     |  |  | 10.45       |  |  | July 28, 2005      |  | 
|               |  |                                                                                                                                                                                                                                                  |  |                           |  |              
|10.28          |  | Warrant between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Quest Diagnostics Incorporated dated July 22, 2005                                                                                                                    |  | 8-K                       |  | 000-31617     |  |  | 10.46       |  |  | July 22, 2005      |  | 



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|               |  |                                                                                                                                                             |  |                           |  |               |  |  |             |  |  |                    |  | 
|-------------- |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- |  | ------------- |  |  | ----------- |  |  | ------------------ |  | 
|Exhibit Number |  | Exhibit Description                                                                                                                                         |  | Incorporated by Reference |  | FiledHerewith
|               |  | Form                                                                                                                                                        |  | File No.                  |  | Exhibit       |  |  | Filing Date | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.29          |  | Amendment to Warrant between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Quest Diagnostics Incorporated dated August 29, 2007                |  | 8-K                       |  | 000-31617     |  |  | 10.2        |  |  | August 29, 2007    |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.30          |  | Letter Agreement between Vermillion, Inc. and Quest Diagnostics Incorporated dated August 29, 2007                                                          |  | S-1                       |  | 333-146354    |  |  | 10.38       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.31          |  | Credit Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Quest Diagnostics Incorporated dated July 22, 2005                      |  | 8-K                       |  | 000-31617     |  |  | 10.47       |  |  | July 28, 2005      |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.32          |  | Debtor-In-Possession Credit and Security Agreement between Vermillion, Inc. and Quest Diagnostics Incorporated dated October 7, 2009                        |  | 8-K                       |  | 000-31617     |  |  | 10.1        |  |  | October 21, 2009   |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.33          |  | Memorialization Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Quest Diagnostics Incorporated dated January 12, 2006          |  | S-1                       |  | 333-146354    |  |  | 10.40       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.34          |  | Patent Security Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Quest Diagnostics Incorporated dated July 22, 2005             |  | 8-K                       |  | 000-31617     |  |  | 10.48       |  |  | July 28, 2005      |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.35          |  | Asset Purchase Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated August 14, 2006                |  | 14a                       |  | 000-31617     |  |  | Annex A     |  |  | September 12, 2006 |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.36          |  | Amendment to Asset Purchase Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006 |  | S-1                       |  | 333-146354    |  |  | 10.47       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.37          |  | Stock Purchase Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006              |  | S-1                       |  | 333-146354    |  |  | 10.48       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                             |  |                           |  |              
|10.38          |  | Transition Services Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006        |  | S-1/A                     |  | 333-146354    |  |  | 10.53       |  |  | November 27, 2007  |  | 



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|               |  |                                                                                                                                                                    |  |                           |  |               |  |  |             |  |  |                    |  | 
|-------------- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ |  | ------------------------- |  | ------------- |  |  | ----------- |  |  | ------------------ |  | 
|Exhibit Number |  | Exhibit Description                                                                                                                                                |  | Incorporated by Reference |  | FiledHerewith
|               |  | Form                                                                                                                                                               |  | File No.                  |  | Exhibit       |  |  | Filing Date | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.39          |  | Amendment No. 1 to Transition Services Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated May 11,
2007  |  | S-1                       |  | 333-146354    |  |  | 10.50       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.40          |  | Amendment No. 2 to Transition Services Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated June 15,
2007 |  | S-1                       |  | 333-146354    |  |  | 10.51       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.41          |  | Manufacture and Supply Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006            |  | S-1/A                     |  | 333-146354    |  |  | 10.56       |  |  | November 27, 2007  |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.42          |  | Amendment No. 1 to Manufacture and Supply Agreement between Vermillion, Inc. and Bio-Rad Laboratories, Inc. dated August 27, 2007                                  |  | S-1                       |  | 333-146354    |  |  | 10.53       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.43          |  | Cross License Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006                     |  | S-1/A                     |  | 333-146354    |  |  | 10.58       |  |  | November 27, 2007  |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.44          |  | Sublicense Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006                         |  | S-1                       |  | 333-146354    |  |  | 10.13       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.45          |  | Letter Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006                             |  | S-1                       |  | 333-146354    |  |  | 10.55       |  |  | September 27, 2007 |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.46          |  | Sublease Agreement between Vermillion, Inc. (formerly Ciphergen Biosystems, Inc.) and Bio-Rad Laboratories, Inc. dated November 13, 2006                          |  | S-1/A                     |  | 333-146354    |  |  | 10.60       |  |  | November 27, 2007  |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.47          |  | Exclusive Distribution Agreement between Vermillion, Inc. and Pronto Diagnostics Ltd., dated August 1, 2011                                                       |  | 10-Q                      |  | 001-34810     |  |  | 10.1        |  |  | August 9, 2011     |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.48          |  | Consulting Agreement between Vermillion, Inc. and Bruce A. Huebner, dated June 17, 2011#                                                                           |  | 10-Q                      |  | 001-34810     |  |  | 10.2        |  |  | August 9, 2011     |  | 
|               |  |                                                                                                                                                                    |  |                           |  |              
|10.49          |  | Consulting Agreement between Vermillion, Inc. and Eric T. Fung, dated November 4, 2011#                                                                            |  | 10-Q                      |  | 001-34810     |  |  | 10.1        |  |  | November 9, 2011   |  | 



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##### Table of Contents

|               |  |                                                                                                                                                                                    |  |                           |  |               |  |  |             |  |  |                  |  |  |    |  
|-------------- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- |  | ------------- |  |  | ----------- |  |  | ---------------- |  |  | -- | -
|Exhibit Number |  | Exhibit Description                                                                                                                                                                |  | Incorporated by Reference |  | FiledHerewith | 
|               |  | Form                                                                                                                                                                               |  | File No.                  |  | Exhibit       |  |  | Filing Date | 
|               |  |                                                                                                                                                                                    |  |                           |  |              
|10.50          |  | Asset Purchase Agreement between Vermillion, Inc. and Correlogic Systems, Inc., dated November 8, 2011                                                                             |  | 10-K                      |  | 000-34810     |  |  | 10.50       |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|10.51          |  | Settlement Agreement and Release between Vermillion, Inc. and Oppenheimer & Co., Inc., dated February 9, 2012                                                                      |  | 10-K                      |  | 000-34810     |  |  | 10.51       |  |  |                  |  |  | ü  |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|10.52          |  | Employment Agreement between Vermillion, Inc. and Eric J. Schoen, dated April 4, 2012#                                                                                             |  | 8-K                       |  | 000-34810     |  |  | 10.1        |  |  | April 10, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|10.53          |  | Employment Agreement between Vermillion, Inc. and William Creech, dated April 4, 2012#                                                                                             |  | 8-K                       |  | 000-34810     |  |  | 10.2        |  |  | April 10, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|14.1           |  | Code of Ethics                                                                                                                                                                     |  | 8-K                       |  | 001-34810     |  |  | 14.1        |  |  | December 7, 2010 |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|21.0           |  | Subsidiaries of Registrant                                                                                                                                                         |  | 10-K                      |  | 001-34810     |  |  | 21.0        |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|23.1           |  | Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm                                                                                               |  | 10-K                      |  | 001-34810     |  |  | 23.1        |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|31.1           |  | Certification of the Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002                                                                             |  |                           |  |               |  |  |             |  |  |                  |  |  | ü  |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|31.2           |  | Certification of the Chief Accounting Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002                                                                            |  |                           |  |               |  |  |             |  |  |                  |  |  | ü  |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|32.1           |  | Certification of the Chief Executive Officer and Chief Accounting Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of
2002 |  |                           |  |               |  |  |             |  |  |                  |  |  | (1 | )
|               |  |                                                                                                                                                                                    |  |                           |  |              
|101.INS        |  | XBRL Instance Document                                                                                                                                                             |  | 10-K                      |  | 001-34810     |  |  | 101         |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|101.SCH        |  | XBRL Taxonomy Extension Schema Document                                                                                                                                            |  | 10-K                      |  | 001-34810     |  |  | 101         |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|101.CAL        |  | XBRL Taxonomy Extension Calculation Linkbase Document                                                                                                                              |  | 10-K                      |  | 001-34810     |  |  | 101         |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|101.DEF        |  | XBRL Taxonomy Extension Definition Linkbase Document                                                                                                                               |  | 10-K                      |  | 001-34810     |  |  | 101         |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|101.LAB        |  | XBRL Taxonomy Extension Label Linkbase Document                                                                                                                                    |  | 10-K                      |  | 001-34810     |  |  | 101         |  |  | March 27, 2012   |  |  |    |  
|               |  |                                                                                                                                                                                    |  |                           |  |              
|101.PRE        |  | XBRL Taxonomy Extension Presentation Linkbase Document                                                                                                                             |  | 10-K                      |  | 001-34810     |  |  | 101         |  |  | March 27, 2012   |  |  |    |  

Attached as Exhibit 101 to this report are documents formatted in XBRL (Extensible Business Reporting Language).
Users of this data are advised that, pursuant to Rule 406T of Regulation S-T, the interactive data file is deemed not filed or part of a registration statement or prospectus for purposes of Sections 11 or 12 of the Securities Act of
1933, as amended, is deemed not filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and is otherwise not subject to liability under these sections.



|(1) | Furnished herewith
|--- | ------------------



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##### Table of Contents

|# | Management contracts or compensatory plan or arrangement.
|- | ---------------------------------------------------------

| | Confidential treatment has been granted with respect to certain provisions of this agreement. Omitted portions have been filed separately with the Commission.
|- | --------------------------------------------------------------------------------------------------------------------------------------------------------------