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

SCHEDULE 13G
(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED
PURSUANT TO RULE 13d-2(b)
 
(Amendment No. 3)1
 

Blueprint Medicines Corporation
 (Name of Issuer)
 
Common Stock, $0.001 par value
 (Title of Class of Securities)
 
09627Y109
 (CUSIP Number)
 
December 31, 2016
 (Date of Event Which Requires Filing of this Statement)
 
 

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:
 
   o  Rule 13d-1(b)
 
   x  Rule 13d-1(c)
 
   o  Rule 13d-1(d)
 
 

_______________
1  The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter the disclosures provided in a prior cover page.
 
      The information required in the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).
 
 
 
 
CUSIP NO. 09627Y109
 
1
NAME OF REPORTING PERSON
 
Biotechnology Value Fund, L.P.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
1,564,734
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
1,564,734
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
1,564,734
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
4.8%
12
TYPE OF REPORTING PERSON
 
PN

 
2
 
CUSIP NO. 09627Y109
 
1
NAME OF REPORTING PERSON
 
Biotechnology Value Fund II, L.P.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
959,457
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
959,457
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
959,457
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
3.0%
12
TYPE OF REPORTING PERSON
 
PN

 
3
 
CUSIP NO. 09627Y109
 
1
NAME OF REPORTING PERSON
 
Biotechnology Value Trading Fund OS LP
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Cayman Islands
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
238,070
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
238,070
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
238,070
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
Less than 1%
12
TYPE OF REPORTING PERSON
 
PN

 
4
 
CUSIP NO. 09627Y109
 
1
NAME OF REPORTING PERSON
 
BVF Partners OS Ltd.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Cayman Islands
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
238,070
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
238,070
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
238,070
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
Less than 1%
12
TYPE OF REPORTING PERSON
 
CO

 
5
 
CUSIP NO. 09627Y109
 
1
NAME OF REPORTING PERSON
 
BVF Partners L.P.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
3,255,280
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
3,255,280
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
3,255,280
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
10.1%
12
TYPE OF REPORTING PERSON
 
PN, IA

 
6
 
CUSIP NO. 09627Y109
 
1
NAME OF REPORTING PERSON
 
BVF Inc.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
3,255,280
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
3,255,280
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
3,255,280
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
10.1%
12
TYPE OF REPORTING PERSON
 
CO

 
7
 
CUSIP NO. 09627Y109
 
1
NAME OF REPORTING PERSON
 
Mark N. Lampert
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
United States
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
3,255,280
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
3,255,280
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
3,255,280
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
10.1%
12
TYPE OF REPORTING PERSON
 
IN

 
8
 
CUSIP NO. 09627Y109
 
Item 1(a).
Name of Issuer:

Blueprint Medicines Corporation, a Delaware corporation (the “Issuer”).

Item 1(b).
Address of Issuer's Principal Executive Offices:

38 Sidney Street, Suite 200
Cambridge, Massachusetts 02139

Item 2(a).
Name of Person Filing
Item 2(b).
Address of Principal Business Office or, if None, Residence
Item 2(c).
Citizenship

Biotechnology Value Fund, L.P. (“BVF”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

Biotechnology Value Fund II, L.P. (“BVF2”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

Biotechnology Value Trading Fund OS LP (“Trading Fund OS”)
PO Box 309 Ugland House
Grand Cayman, KY1-1104
Cayman Islands
Citizenship: Cayman Islands

BVF Partners OS Ltd. (“Partners OS”)
PO Box 309 Ugland House
Grand Cayman, KY1-1104
Cayman Islands
Citizenship: Cayman Islands

BVF Partners L.P. (“Partners”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

BVF Inc.
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

Mark N. Lampert (“Mr. Lampert”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: United States

Each of the foregoing is referred to as a “Reporting Person” and collectively as the “Reporting Persons.”
 
 
9
 
CUSIP NO. 09627Y109

Item 2(d).
Title of Class of Securities:

Common Stock, $0.001 par value (the “Common Stock”)

Item 2(e).
CUSIP Number:

09627Y109

Item 3.
If This Statement is Filed Pursuant to Rule 13d-1(b), or 13d-2(b) or (c), Check Whether the Person Filing is a:

 
/x/
Not applicable.

 
(a)
/ /
Broker or dealer registered under Section 15 of the Exchange Act.

 
(b)
/ /
Bank as defined in Section 3(a)(6) of the Exchange Act.

 
(c)
/ /
Insurance company as defined in Section 3(a)(19) of the Exchange Act.

 
(d)
/ /
Investment company registered under Section 8 of the Investment Company Act.

 
(e)
/ /
An investment adviser in accordance with Rule 13d-1(b)(1)(ii)(E).

 
(f)
/ /
An employee benefit plan or endowment fund in accordance with Rule 13d-1(b)(1)(ii)(F).

 
(g)
/ /
A parent holding company or control person in accordance with Rule 13d-1(b)(1)(ii)(G).

 
(h)
/ /
A savings association as defined in Section 3(b) of the Federal Deposit Insurance Act.

 
(i)
/ /
A church plan that is excluded from the definition of an investment company under Section 3(c)(14) of the Investment Company Act.

 
(j)
/ /
Group, in accordance with Rule 13d-1(b)(1)(ii)(J).

 
(k)
/ /
Group, in accordance with Rule 240.13d-1(b)(1)(ii)(K). If filing as a non-U.S. institution in accordance with Rule 240.13d-1(b)(1)(ii)(J), please specify the type of institution: ____

Item 4.
Ownership

 
(a)
Amount beneficially owned:

 
 
As of the close of business on December 31, 2016 (i) BVF beneficially owned 1,564,734  shares of Common Stock, (ii) BVF2 beneficially owned 959,457 shares of Common Stock, and (iii) Trading Fund OS beneficially owned 238,070 shares of Common Stock.

 
Partners OS as the general partner of Trading Fund OS may be deemed to beneficially own the 238,070 shares of Common Stock beneficially owned by Trading Fund OS.
 
 
10
 
CUSIP NO. 09627Y109
 
 
Partners, as the general partner of BVF, BVF2, the investment manager of Trading Fund OS, and the sole member of Partners OS, may be deemed to beneficially own the 3,255,280 shares of Common Stock beneficially owned in the aggregate by BVF, BVF2, Trading Fund OS, and certain Partners managed accounts (the “Partners Managed Accounts”), including 493,019 shares of Common Stock held in the Partners Managed Accounts.

 
BVF Inc., as the general partner of Partners, may be deemed to beneficially own the 3,255,280 shares of Common Stock beneficially owned by Partners.

 
Mr. Lampert, as a director and officer of BVF Inc., may be deemed to beneficially own the 3,255,280 shares of Common Stock beneficially owned by BVF Inc.

 
The foregoing should not be construed in and of itself as an admission by any Reporting Person as to beneficial ownership of any shares of Common Stock owned by another Reporting Person. Partners OS disclaims beneficial ownership of the shares of Common Stock beneficially owned by Trading Fund OS. Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the shares of Common Stock beneficially owned by BVF, BVF2, Trading Fund OS, and the Partners Managed Accounts, and the filing of this statement shall not be construed as an admission that any such person or entity is the beneficial owner of any such securities.

 
(b)
Percent of class:

 
The following percentages are based on 32,307,556 shares of Common Stock outstanding, as disclosed in the Issuer’s Prospectus filed on Form 424B5 with the Securities and Exchange Commission on December 8, 2016.

 
As of the close of business on December 31, 2016 (i) BVF beneficially owned approximately 4.8% of the outstanding shares of Common Stock, (ii) BVF2 beneficially owned approximately 3.0% of the outstanding shares of Common Stock, (iii) Trading Fund OS beneficially owned less than 1% of the outstanding shares of Common Stock (iv) Partners OS may be deemed to beneficially own less than 1% of the outstanding shares of Common Stock, and (v) each of Partners, BVF Inc. and Mr. Lampert may be deemed to beneficially own approximately 10.1% of the outstanding shares of Common Stock (approximately 1.5% of which is held in the Partners Managed Accounts).

 
(c)
Number of shares as to which such person has:

 
(i)
Sole power to vote or to direct the vote

 
See Cover Pages Items 5-9.

 
(ii)
Shared power to vote or to direct the vote

 
See Cover Pages Items 5-9.

 
(iii)
Sole power to dispose or to direct the disposition of

 
See Cover Pages Items 5-9.

 
(iv)
Shared power to dispose or to direct the disposition of

 
See Cover Pages Items 5-9.
 
 
11
 
CUSIP NO. 09627Y109
 
Item 5.
Ownership of Five Percent or Less of a Class.

Not Applicable.

Item 6.
Ownership of More than Five Percent on Behalf of Another Person.

Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the shares of Common Stock beneficially owned by BVF, BVF2, Trading Fund OS, and the Partners Managed Accounts.

Item 7.
Identification and Classification of the Subsidiary That Acquired the Security Being Reported on by the Parent Holding Company or Control Person.

Not Applicable.

Item 8.
Identification and Classification of Members of the Group.

See Exhibit 99.1 to Amendment No. 1 to the Schedule 13G filed by the Reporting Persons with the Securities and Exchange Commission on February 16, 2016.

Item 9.
Notice of Dissolution of Group.

Not Applicable.

Item 10.
Certifications.

By signing below each of the undersigned certifies that, to the best of its knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.
 
 
12
 
CUSIP NO. 09627Y109

SIGNATURE

After reasonable inquiry and to the best of his knowledge and belief, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

Dated:  February 14, 2017

BIOTECHNOLOGY VALUE FUND, L.P.
    
 
 
    
BVF INC.
By:
BVF Partners L.P., its general partner
    
 
By:
BVF Inc., its general partner
  
By:
/s/ Mark N. Lampert
 
 
    
Mark N. Lampert
By:
/s/ Mark N. Lampert
    
President
 
Mark N. Lampert
      
 
President
    
 
 
 
    
/s/ Mark N. Lampert
 
 
    
MARK N. LAMPERT
BIOTECHNOLOGY VALUE FUND II, L.P.
    
 
 
      
By:
BVF Partners L.P., its general partner
      
By:
BVF Inc., its general partner
      
 
 
      
By:
/s/ Mark N. Lampert
      
 
Mark N. Lampert
      
 
President
      
         
       
         
BVF PARTNERS L.P.
      
         
By:
BVF Inc., its general partner
      
 
 
      
By:
/s/ Mark N. Lampert
      
 
Mark N. Lampert
      
 
President
      


BVF PARTNERS OS LTD.
  
     
By:
BVF Partners L.P., its sole member
  
By:
BVF Inc., its general partner
  
 
 
  
By:
/s/ Mark N. Lampert
  
 
Mark N. Lampert
  
 
President
  
     
     
BIOTECHNOLOGY VALUE TRADING FUND OS LP
  
     
By:
BVF Partners L.P., its investment manager
  
By:
BVF Inc., its general partner
  
 
 
  
By:
/s/ Mark N. Lampert
  
 
Mark N. Lampert
  
 
President
  

 
13