0001144204-12-062761.txt : 20121115 0001144204-12-062761.hdr.sgml : 20121115 20121114173453 ACCESSION NUMBER: 0001144204-12-062761 CONFORMED SUBMISSION TYPE: 13F-HR PUBLIC DOCUMENT COUNT: 1 CONFORMED PERIOD OF REPORT: 20120930 FILED AS OF DATE: 20121115 DATE AS OF CHANGE: 20121114 EFFECTIVENESS DATE: 20121115 FILER: COMPANY DATA: COMPANY CONFORMED NAME: BAKER BROS ADVISORS LLC CENTRAL INDEX KEY: 0001263508 IRS NUMBER: 134093645 STATE OF INCORPORATION: DE FISCAL YEAR END: 1231 FILING VALUES: FORM TYPE: 13F-HR SEC ACT: 1934 Act SEC FILE NUMBER: 028-10519 FILM NUMBER: 121205822 BUSINESS ADDRESS: STREET 1: 667 MADISON AVE STREET 2: 21ST FLOOR CITY: NEW YORK STATE: NY ZIP: 10065 BUSINESS PHONE: 2123395600 MAIL ADDRESS: STREET 1: 667 MADISON AVE STREET 2: 21ST FLOOR CITY: NEW YORK STATE: NY ZIP: 10065 13F-HR 1 v328378_13f-hr.txt 13F-HR UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 13F FORM 13F COVER PAGE Report for the Calendar Year or Quarter Ended: September 30, 2012 Check here if Amendment [ ]; Amendment Number: _____ This Amendment (Check only one.): [ ] is a restatement. [ ] adds new holdings entries. Institutional Investment Manager Filing this Report: Name: Baker Bros. Advisors, LLC -------------------------------------------- Address: 667 Madison Avenue, 21st Floor -------------------------------------------- New York, NY 10065-8029 -------------------------------------------- Form 13F File Number: 28-10519 The institutional investment manager filing this report and the person by whom it is signed hereby represent that the person signing the report is authorized to submit it, that all information contained herein is true, correct and complete, and that it is understood that all required items, statements, schedules, lists, and tables, are considered integral parts of this form. Person Signing this Report on Behalf of Reporting Manager: Name: Leo Kirby -------------------------------------------- Title: Chief Financial Officer -------------------------------------------- Phone: 212-339-5633 -------------------------------------------- Signature, Place, and Date of Signing: /s/ Leo Kirby New York, N.Y. November 13, 2012 -------------------------- --------------------------- ------------------- [Signature] [City, State] [Date] Report Type (Check only one.): [X] 13F HOLDINGS REPORT. (Check here if all holdings of this reporting manager are reported in this report.) [_] 13F NOTICE. (Check here if no holdings reported are in this report, and all holdings are reported by other reporting manager(s).) [_] 13F COMBINATION REPORT. (Check here if a portion of the holdings for this reporting manager are reported in this report and a portion are reported by other reporting manager(s).) List of Other Managers Reporting for this Manager: None FORM 13F SUMMARY PAGE Report Summary: Number of Other Included Managers: 0 ----------- Form 13F Information Table Entry Total: 70 ----------- Form 13F Information Table Entry Value: $4,537,640 ----------- (thousands) List of Other Included Managers: None Baker Brothers Form 13F 09-30-12

COLUMN 1 COLUMN 2 COLUMN 3 COLUMN 4 COLUMN 5 COLUMN 6 COLUMN 7 COLUMN 8 VALUE SHRS OR SH/ PUT/ INVESTMENT OTHER VOTING AUTHORITY Name of Issuer CUSIP (x1000) PRN AMT PRN CALL DISCRETION MANAGERS SOLE SHARED NONE -------------- ----- ------- ------- --- ---- ---------- -------- ---- ------ ---- 1 Acadia Pharmaceuticals Inc. COM 004225108 13,273 5,246,312 SH SOLE 5,246,312 2 Aegerion Pharmaceuticals COM 00767E102 9,107 614,485 SH SOLE 614,485 3 Alere Inc Preferred PFD CONV EX 01449J204 262 1,293 SH SOLE 1,293 4 Amicus Therapeutics COM 03152W109 3,978 765,072 SH SOLE 765,072 5 Anacor Pharmaceuticals COM 32420101 3,738 568,130 SH SOLE 568,130 6 Anthera Pharmaceuticals COM 03674U102 2,931 2,948,339 SH SOLE 2,948,339 7 Aradigm Corp. COM 038505301 13 100,000 SH SOLE 100,000 8 Ariad Pharmaceuticals Inc. COM 04033A100 134,966 5,574,819 SH SOLE 5,574,819 9 Arqule Inc. COM 04269E107 440 86,167 SH SOLE 86,167 10 Array Biopharma Inc. COM 04269X105 5,845 1,000,000 SH SOLE 1,000,000 11 Auxilium COM 05334D107 152,984 6,254,457 SH SOLE 6,254,457 12 Biocryst Pharmaceuticals Inc. COM 09058V103 23,590 5,563,615 SH SOLE 5,563,615 13 Biodel Inc. COM 09064M204 1,604 540,000 SH SOLE 540,000 14 BioDelivery Sciences Intl. Inc. COM 09060J106 13,521 2,139,426 SH SOLE 2,139,426 15 Biomarin Pharmaceuticals COM 09061G101 8,069 200,432 SH SOLE 200,432 16 Cerus COM 157085101 7,172 2,109,512 SH SOLE 2,109,512 17 Chelsea Therapeutics COM 163428105 3,645 3,037,402 SH SOLE 3,037,402 18 Chemocentryx Inc. COM 16383L106 582 50,000 SH SOLE 50,000 19 Clovis Oncology COM 189464100 33,183 1,622,630 SH SOLE 1,622,630 20 Cyclacel Pharmaceuticals Pfd. Conv. Ex 6% PFD CONV EX 23254L207 67 20,979 SH SOLE 20,979 21 Cubist Pharmaceuticals Inc. COM 229678107 238 5,000 SH SOLE 5,000 22 Cumberland Pharmaceuticals COM 230770109 153 23,627 SH SOLE 23,627 23 Derma Sciences COM 249827502 12,548 1,208,857 SH SOLE 1,208,857 24 Discovery Laboratories Inc. COM 254668403 3,352 1,025,000 SH SOLE 1,025,000 25 Durata Therapeutics COM 26658A107 3,001 319,210 SH SOLE 319,210 26 Exelixis Inc. COM 30161Q104 441 91,368 SH SOLE 91,368 27 Genomic Health Inc. COM 37244C101 388,652 11,203,588 SH SOLE 11,203,588 28 Gilead Sciences Inc. COM 375558103 49,104 740,300 SH SOLE 740,300 29 Halozyme Therapeutics Inc. COM 40637H109 13,438 1,782,228 SH SOLE 1,782,228 30 Idera Pharmaceuticals Inc. COM 45168K108 297 288,252 SH SOLE 288,252 31 Incyte Corp. COM 45337C102 267,331 14,810,559 SH SOLE 14,810,559 32 Infinity Pharmaceuticals Inc. COM 45665303 17,031 724,428 SH SOLE 724,428 33 Intermune Inc. COM 45884X103 7,779 868,181 SH SOLE 868,181 34 Ligand Pharmaceuticals Inc. CLASS B 53220K207 1,259 73,400 SH SOLE 73,400 35 Medivation Inc. COM 58501N101 54,465 966,546 SH SOLE 966,546 36 Onyx COM 683399109 18,129 214,543 SH SOLE 214,543 37 Pharmacyclics Inc. COM 716933106 738,161 11,444,360 SH SOLE 11,444,360 38 QLT, Inc. COM 746927102 7,400 949,937 SH SOLE 949,937 39 Questcor Pharmaceuticals, Inc. COM 74835Y101 4,618 250,000 SH SOLE 250,000 40 Repros Therapeutics COM 76028H209 17,712 1,162,936 SH SOLE 1,162,936 41 Seattle Genetics Inc. COM 812578102 520,560 19,322,947 SH SOLE 19,322,947 42 Sequenom Inc. COM 817337405 46 12,900 SH SOLE 12,900 43 Spectrum COM 84763A108 38,848 3,320,360 SH SOLE 3,320,360 44 Synageva Biopharma Corp. COM 87159A103 446,860 8,363,463 SH SOLE 8,363,463 45 Synergy Pharmaceuticals COM 871639308 7,696 1,610,000 SH SOLE 1,610,000 46 Synta Pharmaceuticals COM 87162T206 10,001 1,312,471 SH SOLE 1,312,471 47 Threshold Pharma COM 885807107 11,041 1,525,048 SH SOLE 1,525,048 48 Tranzyme COM 89413J102 19,563 4,386,281 SH SOLE 4,386,281 49 United Therapeutics, Inc. COM 91307C102 9,204 164,708 SH SOLE 164,708 50 Ventrus Biosciences, Inc. COM 922822101 1,721 480,696 SH SOLE 480,696 51 Vertex Pharmaceuticals, Inc. COM 92532F100 45,315 810,794 SH SOLE 810,794 52 Viropharma Inc. COM 928241108 328,645 10,885,878 SH SOLE 10,885,878 53 Xenoport COM 98411C100 11,842 1,034,112 SH SOLE 1,034,112 54 Xoma Corp. COM 98419J107 57,387 15,551,915 SH SOLE 15,551,915 55 YM Biosciences COM 984238105 5,725 3,111,257 SH SOLE 3,111,257 56 Ziopharm Oncology Inc. COM 98973P101 1,385 254,199 SH SOLE 254,199 57 Zogenix, Inc. COM 98978L105 5,283 2,001,000 SH SOLE 2,001,000 58 Alere Inc. Conv. Notes 3% 5/15/16 CONV BONDS 01449JAA3 4,237 4,482,000 PRN SOLE 4,482,000 59 Biomarin Pharmaceuticals Notes 1.875% 4/23/2017 CONV BONDS 09061GAD3 47,697 22,898,000 PRN SOLE 22,898,000 60 Exelisis 4.25% 8/15/2019 CONV BONDS 30161QAC8 19,796 19,000,000 PRN SOLE 19,000,000 61 Gilead 1.625% 5/1/16 CONV BONDS 375558AP8 33,634 21,500,000 PRN SOLE 21,500,000 62 Incyte Genomics Notes 4.75% 10/1/2015 CONV BONDS 45337CAH5 340,215 157,758,000 PRN SOLE 157,758,000 63 Intermune Inc Notes 2.5% 9/15/18 CONV BONDS 45884XAE3 12,612 16,500,000 PRN SOLE 16,500,000 64 Intermune Inc Notes 5% 3/1/15 CONV BONDS 45884XAD5 33,394 33,860,000 PRN SOLE 33,860,000 65 Medivation 2.625% 4/1/17 CONV BONDS 58501NAA9 32,960 24,500,000 PRN SOLE 24,500,000 66 Salix 5.5% 8/15/28 CONV BONDS 795435AB2 102,363 22,250,000 PRN SOLE 22,250,000 67 Salix 2.75% 5/15/15 CONV BONDS 795435AC0 129,439 110,572,000 PRN SOLE 110,572,000 68 Salix 144A 1.5% 3/15/19 CONV BONDS 795435AD8 214,716 222,000,000 PRN SOLE 222,000,000 69 United Therapeutics Notes 1% 9/15/16 144A CONV BONDS 91307CAE2 5,251 4,000,000 PRN SOLE 4,000,000 70 Vertex Pharmaceuticals Notes 3.35% 10/1/15 CONV BONDS 92532FAN0 16,125 12,500,000 PRN SOLE 12,500,000 ---------- 4,537,640 ==========