SEC FORM 3

SEC Form 3

FORM 3

UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

INITIAL STATEMENT OF BENEFICIAL OWNERSHIP OF SECURITIES

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934
or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person^*

AFEYAN NOUBAR

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

2. Date of Event Requiring Statement (Month/Day/Year)
02/03/2011

3. Issuer Name and Ticker or Trading Symbol
BG Medicine, Inc. [ BGMD ]

4. Relationship of Reporting Person(s) to Issuer
(Check all applicable)

X	Director	X	10% Owner
	Officer (give title below)		Other (specify below)

5. If Amendment, Date of Original Filed (Month/Day/Year)

6. Individual or Joint/Group Filing (Check Applicable Line)

	Form filed by One Reporting Person
X	Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Beneficially Owned
1. Title of Security (Instr. 4)	2. Amount of Securities Beneficially Owned (Instr. 4)	3. Ownership Form: Direct (D) or Indirect (I) (Instr. 5)	4. Nature of Indirect Beneficial Ownership (Instr. 5)
Common Stock	2,029,865⁽¹⁾	I	See footnotes⁽²⁾⁽³⁾

Table II - Derivative Securities Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 4)	2. Date Exercisable and Expiration Date (Month/Day/Year)		3. Title and Amount of Securities Underlying Derivative Security (Instr. 4)		4. Conversion or Exercise Price of Derivative Security	5. Ownership Form: Direct (D) or Indirect (I) (Instr. 5)	6. Nature of Indirect Beneficial Ownership (Instr. 5)
1. Title of Derivative Security (Instr. 4)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares	4. Conversion or Exercise Price of Derivative Security	5. Ownership Form: Direct (D) or Indirect (I) (Instr. 5)	6. Nature of Indirect Beneficial Ownership (Instr. 5)
Series A Preferred Stock	⁽⁴⁾	⁽⁵⁾	Common Stock	2,816,102	⁽⁶⁾	I	See footnotes⁽³⁾⁽⁷⁾⁽⁸⁾
Series D Preferred Stock	⁽⁴⁾	⁽⁵⁾	Common Stock	469,218	⁽⁹⁾	I	See footnotes⁽³⁾⁽¹⁰⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	07/28/2015	Common Stock	228,445⁽¹²⁾	$0.03⁽¹²⁾	I	See footnotes⁽³⁾⁽¹³⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	09/08/2015	Common Stock	17,834⁽¹²⁾	$0.03⁽¹²⁾	I	See footnotes⁽³⁾⁽¹⁴⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	09/28/2015	Common Stock	17,834⁽¹²⁾	$0.03⁽¹²⁾	I	See footnotes⁽³⁾⁽¹⁵⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	11/14/2015	Common Stock	17,834⁽¹²⁾	$0.03⁽¹²⁾	I	See footnotes⁽³⁾⁽¹⁶⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	12/15/2015	Common Stock	17,834⁽¹²⁾	$0.03⁽¹²⁾	I	See footnotes⁽³⁾⁽¹⁷⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	03/10/2016	Common Stock	35,669⁽¹²⁾	$0.03⁽¹²⁾	I	See footnotes⁽³⁾⁽¹⁸⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	07/10/2016	Common Stock	17,833⁽¹²⁾	$0.03⁽¹²⁾	I	See footnotes⁽³⁾⁽¹⁹⁾
Warrants to Purchase Common Stock	⁽¹¹⁾	03/28/2018	Common Stock	70,465⁽¹²⁾	$0.02⁽¹²⁾	I	See footnotes⁽³⁾⁽²⁰⁾
Warrants to Purchase Common Stock	⁽²¹⁾	03/30/2020	Common Stock	46,142⁽¹²⁾	$0.02⁽¹²⁾	I	See footnotes⁽³⁾⁽²²⁾
Warrants to Purchase Common Stock	⁽²¹⁾	09/27/2020	Common Stock	46,142⁽¹²⁾	$0.02⁽¹²⁾	I	See footnotes⁽³⁾⁽²³⁾
Warrants to Purchase Common Stock	⁽²¹⁾	11/04/2020	Common Stock	46,142⁽¹²⁾	$0.02⁽¹²⁾	I	See footnotes⁽³⁾⁽²⁴⁾
Convertible Promissory Notes	⁽²⁵⁾⁽²⁶⁾	⁽²⁷⁾	Common Stock	111,995	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽²⁵⁾
Convertible Promissory Notes	⁽²⁶⁾⁽²⁸⁾	⁽²⁷⁾	Common Stock	79,884	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽²⁸⁾
Convertible Promissory Notes	⁽²⁶⁾⁽²⁹⁾	⁽²⁷⁾	Common Stock	42,109	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽²⁹⁾
Convertible Promissory Notes	⁽²⁶⁾⁽³⁰⁾	⁽²⁷⁾	Common Stock	11,336	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽³⁰⁾
Convertible Promissory Notes	⁽²⁶⁾⁽³¹⁾	⁽²⁷⁾	Common Stock	45,906	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽³¹⁾
Convertible Promissory Notes	⁽²⁶⁾⁽³²⁾	⁽²⁷⁾	Common Stock	11,304	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽³²⁾
Convertible Promissory Notes	⁽²⁶⁾⁽³³⁾	⁽²⁷⁾	Common Stock	43	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽³³⁾
Convertible Promissory Notes	⁽²⁶⁾⁽³⁴⁾	⁽²⁷⁾	Common Stock	3	$7⁽²⁶⁾	I	See footnotes⁽³⁾⁽³⁴⁾

1. Name and Address of Reporting Person^*

AFEYAN NOUBAR

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

X	Director	X	10% Owner
	Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

KANIA EDWIN M JR

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

Flagship Ventures Management, Inc.

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

NewcoGen Group, Inc.

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

NEWCOGEN GROUP LLC

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

NEWCOGEN EQUITY INVESTORS LLC

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

NewcoGen Elan LLC

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

NewcoGen Long Reign Holding LLC

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

NewcoGen PE LLC

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

1. Name and Address of Reporting Person^*

ST NewcoGen LLC

(Last)

(First)

(Middle)

C/O FLAGSHIP VENTURES

ONE MEMORIAL DRIVE, 7TH FLOOR

(Street)

CAMBRIDGE

02142

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

Explanation of Responses:

1. Reflects the 1-for-1.6667 reverse stock split effected on November 29, 2010.

2. Held by NewcoGen Group LLC.

3. NewcoGen Group, Inc. ("NG") is the manager of each of NewcoGen Group LLC ("NGG"), NewcoGen Equity Investors LLC ("NEI"), NewcoGen-Elan LLC ("NGE"), NewcoGen-Long Reign Holding LLC ("NGLRH"), NewcoGen-PE LLC ("NGP") and ST NewcoGen LLC ("STN", and together with NGG, NEI, NGE, NGLRH and NGP, the "NewcoGen Funds"). NG is also the general partner of AGTC Partners, L.P., which is the general partner of AGTC Advisors Fund, L.P. ("AGTCA") and Applied Genomic Technology Capital Fund L.P. ("AGTCF", and together with AGTCA, the "AGTC Funds"). NG is a wholly-owned subsidiary of Flagship Ventures Management, Inc. ("Flagship"). Noubar Afeyan and Edwin M. Kania, Jr. are directors of Flagship and may be deemed to beneficially own the securities held by the NewcoGen Funds and the AGTC Funds. Each of Messrs. Afeyan and Kania disclaim beneficial ownership of the securities except to the extent of his pecuniary interest therein.

4. These shares are convertible into the Issuer's common stock in accordance with the Issuer's Restated Certificate of Incorporation, as amended, at any time after the issuance of such shares, at the holder's election.

5. Not applicable.

6. The shares of preferred stock shall convert into common stock upon the closing of the Issuer's initial public offering using a calculation defined in the Issuer's Restated Certificate of Incorporation, as amended, based on the initial purchase price and the conversion rate in effect at the time of conversion. The Series A Preferred Stock will convert on a 1-for-0.2804 basis and such conversion rate is reflected in the amount of common stock underlying the security.

7. Consists of the following shares of the Issuer's common stock into which the Series A Preferred Stock held by the following entities are convertible: 371,027 shares by NewcoGen Equity Investors LLC, 223,746 shares by NewcoGen-Elan LLC, 53,864 shares by NewcoGen-Long Reign Holding LLC, 224,224 shares by NewcoGen-PE LLC, 53,741 shares by ST NewcoGen LLC, 102,877 shares by AGTC Advisors Fund, L.P., 1,701,967 shares by Applied Genomic Technology Capital Fund, L.P., 4,232 shares by OneLiberty Advisors Fund 2000 L.P. and 80,424 shares by OneLiberty Ventures 2000 L.P.

8. Noubar Afeyan and Edwin M. Kania, Jr. are managing members of OneLiberty Partners 2000, LLC, which is the general partner of OneLiberty Advisors Fund 2000 L.P. ("OLA") and OneLiberty Ventures 2000 L.P. ("OLV"), and may be deemed to beneficially own the securities held by OLA and OLV. Each of Messrs. Afeyan and Kania disclaim beneficial ownership of the securities except to the extent of his pecuniary interest therein.

9. The shares of preferred stock shall convert into common stock upon the closing of the Issuer's initial public offering using a calculation defined in the Issuer's Restated Certificate of Incorporation, as amended, based on the initial purchase price and the conversion rate in effect at the time of conversion. The Series D Preferred Stock will convert on a 1-for-0.6 basis and such conversion rate is reflected in the amount of common stock underlying the security.

10. Consists of the following shares of the Issuer's common stock into which the Series D Preferred Stock held by the following entities are convertible: 39,876 shares by NewcoGen Equity Investors LLC, 5,658 shares by NewcoGen-Long Reign Holding LLC, 17,183 shares by NewcoGen-PE LLC, 5,645 shares by ST NewcoGen LLC, 22,848 shares by AGTC Advisors Fund, L.P. and 378,008 shares by Applied Genomic Technology Capital Fund, L.P.

11. These warrants are immediately exercisable.

12. Reflects the 1-for-1.6667 reverse stock split effected on November 29, 2010 in connection with the Issuer's initial public offering, pursuant to which (i) the number of shares of common stock underlying the warrants was divided by 1.6667 and (ii) the exercise price of the warrants was multiplied by 1.6667.

13. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 215,425 shares by Applied Genomic Technology Capital Fund, L.P. and 13,020 shares by AGTC Advisors Fund, L.P.

14. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 16,818 shares by Applied Genomic Technology Capital Fund, L.P. and 1,016 shares by AGTC Advisors Fund, L.P.

15. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 16,818 shares by Applied Genomic Technology Capital Fund, L.P. and 1,016 shares by AGTC Advisors Fund, L.P.

16. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 16,818 shares by Applied Genomic Technology Capital Fund, L.P. and 1,016 shares by AGTC Advisors Fund, L.P.

17. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 16,818 shares by Applied Genomic Technology Capital Fund, L.P. and 1,016 shares by AGTC Advisors Fund, L.P.

18. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 33,637 shares by Applied Genomic Technology Capital Fund, L.P. and 2,032 shares by AGTC Advisors Fund, L.P.

19. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 12,021 shares by NewcoGen Equity Investors LLC, 2,353 shares by NewcoGen-Elan LLC, 499 shares by NewcoGen-Long Reign Holding LLC, 2,497 shares by NewcoGen-PE LLC and 463 shares by ST NewcoGen LLC.

20. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 5,988 shares by NewcoGen Equity Investors LLC, 849 shares by NewcoGen-Long Reign Holding LLC, 2,580 shares by NewcoGen-PE LLC, 847 shares by ST NewcoGen LLC, 56,770 shares by Applied Genomic Technology Capital Fund, L.P. and 3,431 shares by AGTC Advisors Fund, L.P.

21. The warrants become exercisable upon the earliest of the closing of the Issuer's initial public offering or another qualified financing, the occurence of a liquidation event or March 30, 2011.

22. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 17,080 shares by NewcoGen Group LLC, 12,182 shares by NewcoGen Equity Investors LLC, 6,422 shares by NewcoGen-Elan LLC, 1,728 shares by NewcoGen-Long Reign Holding LLC, 7,001 shares by NewcoGen-PE LLC, 1,723 shares by ST NewcoGen LLC and 6 shares by Applied Genomic Technology Capital Fund, L.P.

23. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 17,080 shares by NewcoGen Group LLC, 12,182 shares by NewcoGen Equity Investors LLC, 6,422 shares by NewcoGen-Elan LLC, 1,728 shares by NewcoGen-Long Reign Holding LLC, 7,001 shares by NewcoGen-PE LLC, 1,723 shares by ST NewcoGen LLC and 6 shares by Applied Genomic Technology Capital Fund, L.P.

24. Consists of the following shares of the Issuer's common stock underlying the warrants held by the following entities: 17,080 shares by NewcoGen Group LLC, 12,182 shares by NewcoGen Equity Investors LLC, 6,422 shares by NewcoGen-Elan LLC, 1,728 shares by NewcoGen-Long Reign Holding LLC, 7,001 shares by NewcoGen-PE LLC, 1,723 shares by ST NewcoGen LLC and 6 shares by Applied Genomic Technology Capital Fund, L.P.

25. Reflects $740,172.00 aggregate principal amount of convertible promissory notes (the "Convertible Notes") held by NewcoGen Group LLC dated March 30, 2010, September 27, 2010 and November 4, 2010.

26. The outstanding principal and accrued and unpaid interest on the Convertible Notes are automatically convertible into shares of common stock upon the closing of the Issuer's initial public offering at $7.00 per share, the initial public offering price per share.

27. The unpaid principal amount of the Convertible Notes, together with any interest accrued but unpaid thereon, is payable at any time upon the earlier of demand by holders of 66 2/3% of the aggregate principal amount outstanding under the Convertible Notes, acceleration due to an event of default, a liquidation event or March 29, 2011, and if not repaid, will automatically convert upon the closing of the Issuer's initial public offering.

28. Reflects $527,952.00 aggregate principal amount of Convertible Notes held by NewcoGen Equity Investors LLC dated March 30, 2010, September 27, 2010 and November 4, 2010.

29. Reflects $278,307.00 aggregate principal amount of Convertible Notes held by NewcoGen-Elan LLC dated March 30, 2010, September 27, 2010 and November 4, 2010.

30. Reflects $74,928.00 aggregate principal amount of Convertible Notes held by NewcoGen-Long Reign Holding LLC dated March 30, 2010, September 27, 2010 and November 4, 2010.

31. Reflects $303,399.00 aggregate principal amount of Convertible Notes held by NewcoGen-PE LLC dated March 30, 2010, September 27, 2010 and November 4, 2010.

32. Reflects $74,712.00 aggregate principal amount of Convertible Notes held by ST NewcoGen LLC dated March 30, 2010, September 27, 2010 and November 4, 2010.

33. Reflects $300.00 aggregate principal amount of Convertible Notes held by Applied Genomic Technology Capital Fund, L.P. dated March 30, 2010, September 27, 2010 and November 4, 2010.

34. Reflects $30.00 aggregate principal amount of Convertible Notes held by AGTC Advisors Fund, L.P. dated March 30, 2010, September 27, 2010 and November 4, 2010.

Remarks:

An additional Form 3 (the "Additional Form 3") is being filed on the date hereof by AGTC Partners, L.P., Applied Genomic Technology Capital Fund, L.P., and AGTC Advisors Fund, L.P. (the "Additional Reporting Owners") because the number of reporting owners allowed to be included in a joint filing on Form 3 is limited to ten. Please note that the holdings of the Issuer's securities by the Additional Reporting Owners reflected in the Additional Form 3 are also reflected on this Form 3. (1 of 2)

	/s/ John P. Condon, Attorney-in-fact for Noubar Afeyan	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for Edwin M. Kania, Jr.	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for Flagship Ventures Management, Inc.	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for NewcoGen Group, Inc.	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for NewcoGen Group LLC	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for NewcoGen Equity Investors LLC	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for NewcoGen-Elan LLC	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for NewcoGen-Long Reign Holding LLC	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for NewcoGen-PE LLC	02/03/2011
	/s/ John P. Condon, Attorney-in-fact for ST NewcoGen LLC	02/03/2011
	** Signature of Reporting Person	Date
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
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