0001144204-13-009153.txt : 20130214 0001144204-13-009153.hdr.sgml : 20130214 20130214161835 ACCESSION NUMBER: 0001144204-13-009153 CONFORMED SUBMISSION TYPE: 13F-HR PUBLIC DOCUMENT COUNT: 1 CONFORMED PERIOD OF REPORT: 20121231 FILED AS OF DATE: 20130214 DATE AS OF CHANGE: 20130214 EFFECTIVENESS DATE: 20130214 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: 13614137 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 v334885_13f-hr.txt QUARTERLY HOLDINGS REPORT UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 13F FORM 13F COVER PAGE Report for the Calendar Year or Quarter Ended: December 31, 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. February 12, 2013 -------------------------- --------------------------- ------------------- [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: 71 ----------- Form 13F Information Table Entry Value: $3,823,625 ----------- (thousands) List of Other Included Managers: None Baker Brothers Form 13F 12-31-12

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 -------------- ----- ------- ------- --- ---- ---------- -------- ---- ------ ---- Acadia Pharmaceuticals Inc. COM 004225108 72,641 15,621,812 SH SOLE 15,621,812 Aegerion Pharmaceuticals COM 00767E102 15,595 614,485 SH SOLE 614,485 Amicus Therapeutics COM 03152W109 2,050 765,072 SH SOLE 765,072 Anacor Pharmaceuticals COM 32420101 4,038 776,463 SH SOLE 776,463 Aradigm Corp. COM 038505301 13 100,000 SH SOLE 100,000 Ariad Pharmaceuticals Inc. COM 04033A100 40,836 2,129,070 SH SOLE 2,129,070 Arqule Inc. COM 04269E107 3612 1,294,467 SH SOLE 1,294,467 Array Biopharma Inc. COM 04269X105 5,580 1,500,000 SH SOLE 1,500,000 Auxilium COM 05334D107 81,038 4,371,129 SH SOLE 4,371,129 Biocryst Pharmaceuticals Inc. COM 09058V103 7,901 5,563,615 SH SOLE 5,563,615 Biodel Inc. COM 09064M204 1,269 540,000 SH SOLE 540,000 BioDelivery Sciences Intl. Inc. COM 09060J106 9,221 2,139,426 SH SOLE 2,139,426 Biomarin Pharmaceuticals COM 09061G101 9,861 200,432 SH SOLE 200,432 Cerus COM 157085101 6,666 2,109,512 SH SOLE 2,109,512 Chelsea Therapeutics COM 163428105 2,308 3,037,402 SH SOLE 3,037,402 Chemocentryx Inc. COM 16383L106 547 50,000 SH SOLE 50,000 Clovis Oncology COM 189464100 17,843 1,115,182 SH SOLE 1,115,182 Cyclacel Pharmaceuticals Pfd. Conv. Ex 6% PFD CONV EX 23254L207 105 20,979 SH SOLE 20,979 Cytrx Corp. COM 232828509 1,870 1,000,000 SH SOLE 1,000,000 Cubist Pharmaceuticals Inc. COM 229678107 210 5,000 SH SOLE 5,000 Derma Sciences COM 249827502 15,097 1,358,857 SH SOLE 1,358,857 Discovery Laboratories Inc. COM 254668403 1,799 852,617 SH SOLE 852,617 Durata Therapeutics COM 26658A107 1,287 168,486 SH SOLE 168,486 Genomic Health Inc. COM 37244C101 336,681 12,359,827 SH SOLE 12,359,827 Geron Corp. COM 374163103 1,410 1,000,000 SH SOLE 1,000,000 Gilead Sciences Inc. COM 375558103 6,750 91,900 SH SOLE 91,900 Halozyme Therapeutics Inc. COM 40637H109 11,875 1,769,776 SH SOLE 1,769,776 Idera Pharmaceuticals Inc. COM 45168K108 79 88,531 SH SOLE 88,531 Incyte Corp. COM 45337C102 246,003 14,810,559 SH SOLE 14,810,559 Infinity Pharmaceuticals Inc. COM 45665303 41,247 1,178,485 SH SOLE 1,178,485 Insmed Inc. COM 457669307 1,607 240,167 SH SOLE 240,167 Intercept Pharmaceuticals, Inc. COM 45845P108 12,840 375,000 SH SOLE 375,000 Intermune Inc. COM 45884X103 17,054 1,759,926 SH SOLE 1,759,926 Kythera Biopharmaceuticals COM 501570105 5,006 165,000 SH SOLE 165,000 Ligand Pharmaceuticals Inc. CLASS B 53220K207 1,522 73,400 SH SOLE 73,400 Lpath Inc. COM 548910306 1,010 200,000 SH SOLE 200,000 Medivation Inc. COM 58501N101 49,448 966,546 SH SOLE 966,546 MEI Pharma, Inc. COM 55279B103 7,000 1,000,000 SH SOLE 1,000,000 Onyx COM 683399109 12,059 159,652 SH SOLE 159,652 Pharmacyclics Inc. COM 716933106 661,255 11,444,360 SH SOLE 11,444,360 Progenics Pharmaceuticals, Inc. COM 743187106 2,682 900,000 SH SOLE 900,000 QLT, Inc. COM 746927102 11,481 1,460,663 SH SOLE 1,460,663 Repros Therapeutics COM 76028H209 23,595 1,498,089 SH SOLE 1,498,089 Salix Pharmaceuticals, Inc. COM 795435106 2,693 66,536 SH SOLE 66,536 Seattle Genetics Inc. COM 812578102 447,712 19,322,947 SH SOLE 19,322,947 Sequenom Inc. COM 817337405 61 12,900 SH SOLE 12,900 Spectrum COM 84763A108 16,779 1,500,000 SH SOLE 1,500,000 Synageva Biopharma Corp. COM 87159A103 387,145 8,363,462 SH SOLE 8,363,462 Synergy Pharmaceuticals COM 871639308 8,620 1,638,871 SH SOLE 1,638,871 Synta Pharmaceuticals COM 87162T206 13,193 1,462,614 SH SOLE 1,462,614 Threshold Pharma COM 885807107 6,715 1,595,048 SH SOLE 1,595,048 Tranzyme COM 89413J102 2,369 4,386,281 SH SOLE 4,386,281 Vanda Pharmaceuticals, Inc. COM 921659108 1,850 500,000 SH SOLE 500,000 Ventrus Biosciences, Inc. COM 922822101 2,626 1,215,840 SH SOLE 1,215,840 Viropharma Inc. COM 928241108 205,415 9,025,270 SH SOLE 9,025,270 Xenoport COM 98411C100 8,035 1,034,112 SH SOLE 1,034,112 Xoma Corp. COM 98419J107 48,659 20,274,581 SH SOLE 20,274,581 Ziopharm Oncology Inc. COM 98973P101 1,057 254,199 SH SOLE 254,199 Zogenix, Inc. COM 98978L105 2,661 2,001,000 SH SOLE 2,001,000 Biomarin Pharmaceuticals Notes 1.875% 4/23/2017 CONV BONDS 09061GAD3 56,577 22,898,000 PRN SOLE 22,898,000 Exelisis 4.25% 8/15/2019 CONV BONDS 30161QAC8 18,460 19,000,000 PRN SOLE 19,000,000 Gilead 0.625% 5/1/13 CONV BONDS 375558AH6 48,110 25,000,000 PRN SOLE 25,000,000 Gilead 1.625% 5/1/16 CONV BONDS 375558AP8 36,194 21,500,000 PRN SOLE 21,500,000 Incyte Genomics Notes 4.75% 10/1/2015 CONV BONDS 45337CAH5 313,298 157,758,000 PRN SOLE 157,758,000 Intermune Inc Notes 2.5% 9/15/18 CONV BONDS 45884XAE3 12,846 16,500,000 PRN SOLE 16,500,000 Intermune Inc Notes 5% 3/1/15 CONV BONDS 45884XAD5 33,754 33,860,000 PRN SOLE 33,860,000 Medivation 2.625% 4/1/17 CONV BONDS 58501NAA9 31,260 24,500,000 PRN SOLE 24,500,000 Salix 2.75% 5/15/15 CONV BONDS 795435AC0 126,398 110,572,000 PRN SOLE 110,572,000 Salix 144A 1.5% 3/15/19 CONV BONDS 795435AD8 185,100 192,000,000 PRN SOLE 192,000,000 United Therapeutics Notes 1% 9/15/16 144A CONV BONDS 91307CAE2 22,652 18,000,000 PRN SOLE 18,000,000 Vertex Pharmaceuticals Notes 3.35% 10/1/15 CONV BONDS 92532FAN0 31,395 28,000,000 PRN SOLE 28,000,000