2021-11-11T07:48:08-06:00 2020-12-31 135565207 KPMG LLP 1305 WALT WHITMAN ROAD MELVILLE NY 11747 990 2020-01-01 800631734 NEW YORK GENOME CENTER INC NEWY 6469777000 101 AVENUE OF THE AMERICAS 7TH FL NEW YORK NY 10013 MARIA JOANTA CHIEF FINANCIAL OFFICER 6469777000 2021-11-10 1 MARIA JOANTA 999009999 ROBERT A ROBINSON P00741489 2127589700 2021-11-09 3 AAL1 IAL1 2020 2022-09-23 18:48:47Z TOM MANIATIS 101 AVENUE OF THE AMERICAS NEW YORK NY 10013 64191532 0 X WWW.NYGENOME.ORG X 2010 DE ADVANCING GENOMIC RESEARCH TO DRIVE NOVEL BIOMEDICAL DISCOVERIES TO IMPROVE HUMAN HEALTH 25 23 172 23 1507216 0 32878926 51639109 9402354 8497659 174909 90496 -211744 556725 42244445 60783989 1899777 1010263 0 0 28935750 28728885 129829 2325 900402 49234412 42564807 80199768 72306280 -37955323 -11522291 97126046 83547232 49651789 47595266 47474257 35951966 X OPERATE A STATE-OF-THE-ART, WORLD CLASS GENOMIC RESEARCH CENTER THAT CREATES AND USES ADVANCED GENOMICS TO UNDERSTAND THE GENETIC BASIS OF DISEASE. FOR MORE INFORMATION, SEE SCHEDULE O. 0 0 53028623 1010110 5514656 RESEARCH AND RESEARCH SEQUENCING: NYGC'S RESEARCH SCIENTISTS AND FACULTY CONDUCT RESEARCH INTO THE GENETIC FACTORS THAT CONTRIBUTE TO HUMAN DISEASE, BOTH IN THEIR OWN PROJECTS AND THROUGH COLLABORATIONS. NYGC RESEARCHERS HAVE PROJECTS UNDERWAY IN CANCER, INCLUDING LUNG, LIVER, BREAST AND MELANOMA, A MULTISITE VERY RARE CANCER PROJECT AND A LARGE COLLABORATIVE PROJECT STUDYING CANCER IN UNDERSERVED POPULATIONS IN NYC; NEURODEGENERATIVE DISEASES, INCLUDING ALS AND DEMENTIA AND NEUROPSYCHIATRIC DISEASES, FOCUSING ON AUTISM, AMONG OTHERS. IN 2020, NYGC SEQUENCED OVER 8,300 WHOLE GENOME SAMPLES, COMPLETED 396 PROJECTS, AND COLLABORATED WITH 82 INVESTIGATORS FROM 41 INSTITUTIONS WORLDWIDE. FOR MORE INFORMATION SEE SCHEDULE O. 4471789 1475787 CLINICAL SEQUENCING: NYGC IS AUTHORIZED BY THE NEW YORK STATE DEPARTMENT OF HEALTH TO OFFER THE FOLLOWING APPROVED CLINICAL TESTS THROUGH ITS CLEP/CLIA CERTIFIED CLINICAL LABORATORY: CONSTITUTIONAL WHOLE GENOME SEQUENCING FOR UNDIAGNOSED DISEASE, CONSTITUTIONAL WHOLE GENOME SEQUENCING FOR PREDISPOSITIONAL GENETIC SCREENING, ONCOLOGY WHOLE GENOME AND TRANSCRIPTOME SEQUENCING, CONSTITUTIONAL WHOLE EXOME SEQUENCING, TARGETED VARIANT TESTING USING SANGER SEQUENCING, ONCOLOGY WHOLE EXOME AND TRANSCRIPTOME SEQUENCING, AND THE SMASH GENOMIC ASSAY. 57500412 1 1 0 1 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 57 0 1 172 1 1 1 0 0 0 0 0 0 0 0 0 1 0 X 25 23 0 0 0 0 1 1 0 1 1 0 0 1 1 1 1 1 1 1 1 0 AL AK AR CA CO CT FL GA HI IL KS KY LA ME MD MA MI MN MS MO NH NJ NM NY NC ND OH OK OR PA RI SC TN UT VA WA WV WI NY NY X X NANCY KONG 6469777154 101 AVENUE OF THE AMERICAS 7TH FL NEW YORK NY 10013 X CHERYL A MOORE PRESIDENT & COO 40.00 X X 1429739 0 22317 TOM MANIATIS PHD SCIENTIFIC DIRECTOR & CEO 40.00 X X 488963 0 149133 DAFNA BAR-SAGI PHD DIRECTOR 1.00 X 0 0 0 RUSSELL L CARSON MBA DIRECTOR & CO-CHAIR 4.00 X X 0 0 0 ELI CASDIN DIRECTOR 1.00 X 0 0 0 DENNIS S CHARNEY MD DIRECTOR 1.00 X 0 0 0 AUGUSTINE MK CHOI MD DIRECTOR 1.00 X 0 0 0 NICHOLAS DONOFRIO DIRECTOR 1.00 X 0 0 0 JOHN B EHRENKRANZ DIRECTOR 1.00 X 0 0 0 ANTHONY B EVNIN PHD DIRECTOR 1.00 X 0 0 0 LEE GOLDMAN MD MPH DIRECTOR 1.00 X 0 0 0 WESLIE R JANEWAY DIRECTOR 1.00 X 0 0 0 KENNETH KAUSHANSKY MD DIRECTOR 1.00 X 0 0 0 RICHARD P LIFTON MD PHD DIRECTOR 1.00 X 0 0 0 EDISON T LIU MD DIRECTOR 1.00 X 0 0 0 HERB PARDES MD DIRECTOR & VICE CHAIR 1.00 X 0 0 0 FRANK E RICHARDSON MA JD DIRECTOR 1.00 X 0 0 0 IVAN G SEIDENBERG MBA DIRECTOR & CO-CHAIR 4.00 X X 0 0 0 FRANK V SICA DIRECTOR & COMMITTEE CHAIR 1.00 X 0 0 0 JIM SIMONS PHD DIRECTOR 1.00 X 0 0 0 STEVEN D SINGER ESQ DIRECTOR 1.00 X 0 0 0 BRUCE STILLMAN PHD DIRECTOR 1.00 X 0 0 0 CRAIG B THOMPSON MD DIRECTOR 1.00 X 0 0 0 GORDON F TOMASELLI MD DIRECTOR 1.00 X 0 0 0 KEVIN J TRACEY MD DIRECTOR 1.00 X 0 0 0 ELIZABETH BROOKS O'BRIEN VP & GENERAL COUNSEL 40.00 X 428773 0 46210 ANA LUCIA BASTIANI-POSNER SVP, FIN & ADMIN (THROUGH 6/20) 40.00 X 281437 0 17802 THOMAS LEHNER SCI DIR, NEURO DIS GEN (AS OF 1/20) 40.00 X 460831 0 32248 SOREN GERMER SVP, GENOME TECHNOLOGIES 40.00 X 422326 0 33088 CAROL ASHE CHIEF BUSINESS OFFICER 40.00 X 414579 0 17217 KATHLEEN MCGOVERN KEARNS VP, DEV'T & CO (THROUGH 11/20) 40.00 X 357657 0 31771 CHARLES GAGNON SENIOR DIR, IT INFRASTRUCTURE 40.00 X 324054 0 44932 MICHAEL CHARLES ZODY SCIENTIFIC DIR, COMP BIOLOGY 40.00 X 198743 0 18441 SHAILAJA GARGEYA SENIOR DIR, SOFTWARE ENGINEER 40.00 X 317700 0 18567 DAYNA M OSCHWALD CHIEF OF STAFF 40.00 X 263782 0 30448 CHRISTOPHER PHIFER BLACK DIRECTOR, RESEARCH COMPUTING 40.00 X 212125 0 42313 MELISSA PROBER SENIOR ASSOCIATE COUNSEL 40.00 X 236753 0 14889 NICOLAS ROBINE COMPUTATIONAL BIOLOGY 40.00 X 209092 0 35908 6046554 0 555284 79 0 1 0 PJ MECHANICAL SERVICE & MAINTENANCE CO 55 BROAD STREET NEW YORK NY 10004 ENGINEERING SERVICES 885590 GUARDIAN SERVICE INDUSTRIES INC 88005 EXPEDITE WAY CHICAGO IL 60695 CLEANING SERVICES 411466 TEC SYSTEMS INC 47-25 34TH STREET 4TH FLOOR LONG ISLAND CITY NY 11101 MAINTENANCE SERVICES 208871 STOECKIUS RIGHTS AB MARIA PRASTGARDSGATA 28 APT 1401 STOCKHOLM SW 11852 CONSULTING SERVICES 164905 HAROLD VARMUS 450 WEST END AVE 17A NEW YORK NY 10024 CONSULTING SERVICES 150000 7 3060000 12907064 35672045 386423 51639109 RESEARCH SEQUENCING 541700 7021872 5514656 1507216 CLINICAL SEQUENCING 541700 1475787 1475787 8497659 90496 90496 878878 878878 2343308 3407543 -1064235 -1064235 -1064235 OTHER MISC REVENUE 900099 742082 742082 742082 60783989 6990443 1507216 647221 981757 981757 28506 28506 6629835 2961706 3278702 389427 112969 112969 17631050 12445884 4879642 305524 1156157 781519 363311 11327 1247693 1101307 142149 4237 1951181 1450058 487640 13483 312871 312871 144638 144638 2325 2325 2842691 2768019 74672 302467 94848 205985 1634 2454834 2150989 303845 268140 268140 13746760 11221311 2406317 119132 83962 71420 10993 1549 34967 24179 9803 985 461726 255030 203479 3217 7805926 7307825 459831 38270 391158 391158 DIRECT COST OF SEQUENCI 10746255 10746255 RESEARCH 2510045 2510045 OTHER 346283 142560 194431 9292 RECRUITMENT 112084 76085 35999 72306280 57500412 13905466 900402 11828949 9393791 6037230 4575195 5125099 4431588 2964323 1246622 3956650 3918628 131310735 80043514 57671401 51267221 9542394 8714187 97126046 83547232 6109365 6075510 10610221 11521530 2144347 71442 4820000 4820000 25967856 25106784 49651789 47595266 X 40350629 27915254 7123628 8036712 47474257 35951966 97126046 83547232 -11522291 0 X 0 1 X 1 1 1 X 94901046 70723214 115038771 32878926 51639109 365181066 94901046 70723214 115038771 32878926 51639109 365181066 161309349 203871717 302728 378725 2090669 3205975 3312682 9290779 58024 95299 104653 38049 742082 1038107 375509952 91868129 0.54290 0.56490 X RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED 0 1 0 1 509 0 0 0 0 1 1500 2009 0 PART II-B, LINE 1: SCHEDULE C, PART II-B, LINES 1G & 1I THROUGH ITS LEGISLATIVE CONSULTANTS, NYGC ADVOCATES AT THE STATE AND LOCAL LEVEL FOR GOVERNMENT FUNDS TO SUPPORT CURRENT OPERATIONS AND/OR EXPAND RESEARCH OPPORTUNITIES AT NYGC. IN 2020, THE NYGC RECEIVED DONATED LOBBYING SERVICES TO ENGAGE WITH NEW YORK STATE GOVERNMENT AGENCIES. NYGC ALSO MAINTAINS MEMBERSHIPS IN IRC SECTION 501(C)(6) ORGANIZATIONS THAT REPRESENT THE INTERESTS OF THE MEDICAL RESEARCH COMMUNITY; $1,500 OF THE DUES THAT NYGC PAID TO THESE ASSOCIATIONS WERE ATTRIBUTABLE TO LOBBYING IN 2020. ADDITIONALLY, NYGC STAFF MAY, FROM TIME TO TIME, CONTACT FEDERAL LEGISLATORS OR THEIR STAFF TO ENCOURAGE THEIR SUPPORT FOR MATTERS OF CONCERN TO THE ACADEMIC MEDICAL RESEARCH COMMUNITY. SUCH CONTACT MAY INCLUDE WRITING LETTERS OR OCCASIONAL MEETINGS WITH PUBLIC OFFICIALS. THE APPROXIMATE COST ASSOCIATED WITH NYGC'S COMMUNICATIONS WITH THE FEDERAL GOVERNMENT IN 2020 IS $509. 71040084 22750883 48289201 58774557 55797955 2976602 1496094 1494676 1418 51267221 SECURITY DEPOSITS 8255470 DEFERRED COMPENSATION 458717 8714187 DEFERRED RENT 25106784 25106784 X 64191532 0 64191532 -3407543 -3407543 60783989 75713823 3407543 3407543 72306280 0 72306280 PART X, LINE 2: NYGC IS SUBJECT TO THE PROVISIONS OF THE FASB ASC SECTION 740-10-05, INCOME TAXES - OVERALL, RELATING TO ACCOUNTING AND REPORTING FOR UNCERTAINTY IN INCOME TAXES. NYGC RECOGNIZES THE EFFECT OF INCOME TAX POSITIONS ONLY IF THOSE POSITIONS ARE MORE LIKELY THAN NOT OF BEING SUSTAINED AND HAS DETERMINED IT DID NOT HAVE ANY EXPOSURE TO UNCERTAIN TAX POSITIONS DURING 2020 AND 2019. PART XI, LINE 4B - OTHER ADJUSTMENTS: RENTAL EXPENSE -3,407,543. PART XII, LINE 2D - OTHER ADJUSTMENTS: RENTAL EXPENSE 3,407,543. 1 ASIA 1 PROGRAM SERVICES RESEARCH 499 EUROPE 12 PROGRAM SERVICES RESEARCH 365582 EUROPE 1 PROGRAM SERVICES COLLABORATION 28506 NORTH AMERICA 4 PROGRAM SERVICES RESEARCH 120223 0 18 0 0 0 18 514810 0 514810 EUROPE RESEARCH SUBAWARD 28506 WIRE 1 0 0 0 0 0 0 0 PART I, LINE 2: NYGC MONITORS THE USE OF GRANT FUNDS FOLLOWING THE UNIFORM GUIDANCE FOR FEDERAL AWARDS. GRANT RECIPIENTS ARE REQUIRED TO PROVIDE PROGRESS REPORTS. COSTS ARE REVIEWED FOR ALLOWABILITY WITH REGARD TO RELEVANT COST PRINCIPLES, BUDGETARY RESTRICTIONS, AND TERMS AND CONDITIONS OF THE AWARD BEFORE PAYMENT. PART I, LINE 3: THE PROGRAM EXPENDITURES ARE REPORTED ON THE ACCRUAL METHOD. PART III ACCOUNTING METHOD: 0 UNIVERSITY OF WASHINGTON 129 SCHMITZ HALL 355870 SEATTLE WA 98195 916001537 WA 180007 RESEARCH SUBAWARD WEILL CORNELL MEDICAL COLLEGE 1300 YORK AVENUE NEW YORK NY 10065 150532082 501(C) (3) 177332 RESEARCH SUBAWARD COLD SPRING HARBOR LABORATORY ONE BUNGTOWN ROAD COLD SPRING HARBOR NY 11724 112013303 501(C)(3) 148428 RESEARCH SUBAWARD ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI ONE GUSTAVE L LEVY PLACE NEW YORK NY 10029 136171197 501(C) (3) 100743 RESEARCH SUBAWARD COLUMBIA UNIVERSITY 615 WEST 131ST STREET NEW YORK NY 10027 135598093 501(C) (3) 93023 RESEARCH SUBAWARD WASHINGTON UNIVERSITY SCHOOL OF MEDICINE 700 ROSEDALE AVENUE CB 1034 ST LOUIS MO 63112 430653611 501(C) (3) 78871 RESEARCH SUBAWARD MGH RESEARCH 399 REVOLUTION DRIVE SOMERVILLE MA 02145 042697983 501(C) (3) 67059 RESEARCH SUBAWARD THE BROAD INSTITUTE INC 415 MAIN STREET CAMBRIDGE MA 02142 263428781 501(C) (3) 63648 RESEARCH SUBAWARD JOHNS HOPKINS UNIVERSITY 3910 KESWICK ROAD BALTIMORE MD 21211 520595110 501(C) (3) 47759 RESEARCH SUBAWARD NEW YORK UNIVERSITY 105 E 17TH STREET NEW YORK NY 10003 135562308 501(C) (3) 13278 RESEARCH SUBAWARD MEMORIAL SLOAN KETTERING CANCER CENTER 1275 YORK AVENUE NEW YORK NY 10065 131924236 501(C) (3) 11608 RESEARCH SUBAWARD 11 0 PART I, LINE 2: NYGC MONITORS THE USE OF GRANT FUNDS FOLLOWING THE UNIFORM GUIDANCE FOR FEDERAL AWARDS. GRANT RECIPIENTS ARE REQUIRED TO PROVIDE PROGRESS REPORTS. COSTS ARE REVIEWED FOR ALLOWABILITY WITH REGARD TO RELEVANT COST PRINCIPLES, BUDGETARY RESTRICTIONS, AND TERMS AND CONDITIONS OF THE AWARD BEFORE PAYMENT. X X 1 1 X 0 0 0 0 0 0 0 0 0 CHERYL A MOORE PRESIDENT & COO 922497 0 223725 0 283517 0 17100 0 5217 0 1452056 0 0 0 TOM MANIATIS PHD SCIENTIFIC DIRECTOR & CEO 488963 0 0 0 0 0 0 0 149133 0 638096 0 0 0 THOMAS LEHNER SCI DIR, NEURO DIS GEN (AS OF 1/20) 370780 0 50000 0 40051 0 17006 0 15242 0 493079 0 0 0 ELIZABETH BROOKS O'BRIEN VP & GENERAL COUNSEL 428773 0 0 0 0 0 17100 0 29110 0 474983 0 0 0 SOREN GERMER SVP, GENOME TECHNOLOGIES 390826 0 31500 0 0 0 17100 0 15988 0 455414 0 0 0 CAROL ASHE CHIEF BUSINESS OFFICER 414579 0 0 0 0 0 17100 0 117 0 431796 0 0 0 KATHLEEN MCGOVERN KEARNS VP, DEV'T & CO (THROUGH 11/20) 333954 0 0 0 23703 0 17100 0 14671 0 389428 0 0 0 CHARLES GAGNON SENIOR DIR, IT INFRASTRUCTURE 281505 0 42549 0 0 0 16642 0 28290 0 368986 0 0 0 SHAILAJA GARGEYA SENIOR DIR, SOFTWARE ENGINEER 309918 0 7782 0 0 0 17100 0 1467 0 336267 0 0 0 ANA LUCIA BASTIANI-POSNER SVP, FIN & ADMIN (THROUGH 6/20) 216108 0 40300 0 25029 0 16935 0 867 0 299239 0 0 0 DAYNA M OSCHWALD CHIEF OF STAFF 248782 0 15000 0 0 0 14460 0 15988 0 294230 0 0 0 CHRISTOPHER PHIFER BLACK DIRECTOR, RESEARCH COMPUTING 212125 0 0 0 0 0 13298 0 29015 0 254438 0 0 0 MELISSA PROBER SENIOR ASSOCIATE COUNSEL 236753 0 0 0 0 0 14237 0 652 0 251642 0 0 0 NICOLAS ROBINE COMPUTATIONAL BIOLOGY 209092 0 0 0 0 0 12823 0 23085 0 245000 0 0 0 MICHAEL CHARLES ZODY SCIENTIFIC DIR, COMP BIOLOGY 198743 0 0 0 0 0 9998 0 8443 0 217184 0 0 0 PART I, LINE 1A TAX INDEMNIFICATION AND GROSS-UP PAYMENTS NYGC PAID TAXES ON BEHALF OF ITS PRESIDENT & CHIEF OPERATING OFFICER (COO) VIA A PAYROLL TAX GROSS UP FOR LIFE INSURANCE, DISABILITY AND LONG-TERM CARE BENEFITS PURSUANT TO HER OFFER LETTER. AN EXECUTIVE COMPENSATION COMMITTEE OF INDEPENDENT BOARD MEMBERS WAS RESPONSIBLE FOR ESTABLISHING HER COMPENSATION PACKAGE, WHICH WAS THEN APPROVED BY THE BOARD OF DIRECTORS. HOUSING ALLOWANCE OR RESIDENCE FOR PERSONAL USE NYGC SELECTIVELY OFFERS HOUSING ALLOWANCES TO EMPLOYEES, PRINCIPALLY AS A RECRUITING TOOL FOR NEW FACULTY AND POSTDOCTORAL FELLOWS. SUBSIDIZED HOUSING OR HOUSING ALLOWANCES ARE COMMONLY OFFERED BY PEER ACADEMIC INSTITUTIONS IN NEW YORK CITY TO HELP FACULTY AND OTHER RESEARCHERS DEFRAY THE HIGH COST OF HOUSING. THE VALUE OF THIS ASSISTANCE WAS TREATED AS TAXABLE COMPENSATION TO THE EMPLOYEE. PART I, LINE 3 IN 2020, NYGC'S SCIENTIFIC DIRECTOR & CEO WAS EMPLOYED BY AN UNRELATED ENTITY AND LEASED TO NYGC TO DEVOTE 80% OF HIS TIME AND EFFORT TO SERVING AS NYGC'S SCIENTIFIC DIRECTOR & CEO, AN OFFICER OF THE CORPORATION AND AS A SENIOR ASSOCIATE MEMBER OF NYGC'S FACULTY. HE OVERSAW NYGC'S RESEARCH PROGRAM AND UNDERTOOK OTHER ACTIVITIES AS NYGC'S BOARD OF DIRECTORS REQUESTED FROM TIME TO TIME. THE SCIENTIFIC DIRECTOR & CEO DEVOTED 20% OF HIS TIME TO HIS DUTIES AT THE UNRELATED ENTITY, WHERE HE MAINTAINS A LABORATORY AND CONDUCTS INDEPENDENT, INVESTIGATOR-INITIATED RESEARCH PROJECTS. IN LATE 2019, NYGC HIRED AN INDEPENDENT COMPENSATION CONSULTANT TO PERFORM AN EXECUTIVE TOTAL COMPENSATION STUDY OF SENIOR MANAGEMENT'S COMPENSATION, INCLUDING THE SCIENTIFIC DIRECTOR & CEO. RESULTS OF THIS STUDY WERE PROVIDED TO THE AD-HOC COMPENSATION COMMITTEE IN EARLY 2020 AND THE COMMITTEE DISCUSSED THEM. THE REVIEW SHOWED THAT THE COMPENSATION PAID TO ALL MEMBERS OF SENIOR MANAGEMENT, INCLUDING THE SCIENTIFIC DIRECTOR & CEO, WAS REASONABLE. SILAS MANIATIS FAMILY MEMBER OF DIRECTOR 112696 SALARY 0 X 1 386423 0 0 0 PART I, COLUMN (B): THE NUMBER REPORTED IN PART I, COLUMN B REPRESENTS THE NUMBER OF CONTRIBUTIONS. FORM 990, PART I, LINE 1 & PART III, LINE 1: NYGC IS ORGANIZED AND OPERATED AS AN INDEPENDENT, NON-PROFIT CORPORATION, DEDICATED TO STATE-OF-THE-ART, WORLD-CLASS GENOMIC RESEARCH, SEQUENCING AND BIOINFORMATICS, WHOSE MEMBERS INCLUDE LEADING ACADEMIC, MEDICAL AND RESEARCH INSTITUTIONS. NYGC ADVANCES GENOMICS THROUGH THE DEVELOPMENT OF COMPUTATIONAL AND EXPERIMENTAL METHODS AND THE APPLICATION OF THESE METHODS TO DISEASE-FOCUSED RESEARCH TO ENHANCE OUR UNDERSTANDING OF THE GENETIC BASIS OF CANCER, NEURODEGENERATIVE DISEASE AND NEUROPSYCHIATRIC DISEASE. NYGC HAS THE FOLLOWING KEY OBJECTIVES: (I) LEADING AND CONTRIBUTING TO INTELLECTUALLY VIBRANT RESEARCH COLLABORATIONS IN THE ACADEMIC AND SCIENTIFIC COMMUNITY IN NEW YORK CITY, ACROSS THE COUNTRY AND AROUND THE WORLD. (II) RECRUITING AND RETAINING WORLD-CLASS SCIENTIFIC TALENT TO LEAD THE ORGANIZATION'S RESEARCH AND TECHNOLOGY DEVELOPMENT PROGRAMS; (III) SUPPORTING RESEARCH CONDUCTED BY THE INSTITUTIONAL FOUNDING MEMBERS, OTHER ACADEMIC, RESEARCH AND MEDICAL INSTITUTIONS AND THE BIOTECHNOLOGY/PHARMACEUTICAL INDUSTRY TO ADVANCE NYGC'S SCIENTIFIC RESEARCH PROGRAMS; (IV) DEVELOPING INNOVATIVE EXPERIMENTAL AND COMPUTATIONAL GENOMIC METHODS BASED UPON THE RESEARCH AND SEQUENCING ACTIVITIES CONDUCTED AT THE ORGANIZATION'S FACILITY, FOR THE BROADER BENEFIT OF THE RESEARCH COMMUNITY; (V) ADVANCING GENOMIC RESEARCH TO DRIVE NOVEL BIOMEDICAL DISCOVERIES TO IMPROVE HUMAN HEALTH; (VI) STRIVING TO MAXIMIZE THE BENEFITS OF OUR RESEARCH AND INNOVATION FOR DIVERSE COMMUNITIES; (VII) PROVIDING TRAINING TO THE ACADEMIC, RESEARCH AND TECHNOLOGY COMMUNITIES; (VIII) CREATING A WORKPLACE ENVIRONMENT THAT IS WELCOMING AND FAIR TO ALL REGARDLESS OF RACE, ETHNICITY, GENDER, SEXUAL ORIENTATION, PHYSICAL DISABILITY, AGE, OR RELIGION, AND (IX) CONDUCTING ACTIVITIES ANCILLARY TO THESE OBJECTIVES. FORM 990, PART III, LINE 4A & LINE 4B NYGC IS AN INDEPENDENT, NONPROFIT ACADEMIC RESEARCH INSTITUTION WITH THE MISSION OF IMPROVING HUMAN HEALTH THROUGH TRANSFORMATIVE GENOMIC RESEARCH. NYGC'S WORK BUILDS ON THE EXPERTISE AND EXPERIENCE THAT NYGC HAS DEVELOPED SINCE ITS FOUNDING IN 2011 AND AUGMENTS RESEARCH BEING CONDUCTED BY NYGC MEMBER INSTITUTIONS. COLLABORATING WITH PREMIER ACADEMIC, MEDICAL AND INDUSTRY LEADERS ACROSS THE GLOBE, NYGC IS CONDUCTING DISEASE-BASED GENOMIC RESEARCH IN AREAS WHERE IT HAS DEVELOPED A STRONG AND SUCCESSFUL TRACK RECORD, PARTICULARLY IN NEURODEGENERATIVE DISEASES, SUCH AS ALS; NEUROPSYCHIATRIC DISEASES, PRINCIPALLY IN AUTISM; AND CANCER, FOCUSING ON UNDERSERVED POPULATIONS AND RARE CANCERS, AMONG OTHERS. IN 2020 AND 2021, THE NYGC ALSO HAS EXPANDED ITS EXPERTISE TO COVID-19 RESEARCH. EARLY ON IN THE PANDEMIC, NYGC QUICKLY PIVOTED TO ADDRESSING THE URGENCY OF THE CORONAVIRUS OUTBREAK, WITH OUR FACULTY AND STAFF SCIENTISTS CONDUCTING COVID-19 GENOMICS RESEARCH AND SARS-COV-2 VIRUS TESTING WHILE CONTINUING TO MAKE STRIDES IN OUR CORE RESEARCH AREAS. THROUGH INNOVATIVE RESEARCH AND GENOMIC DISCOVERY, NYGC SERVES AS A VITAL COLLABORATIVE HUB FOR GENOMIC SCIENCE. NYGC, ITS MEMBER INSTITUTIONS AND PARTNERS ARE UNITED IN AN UNPRECEDENTED CLOSE COLLABORATION OF TECHNOLOGY, SCIENCE AND MEDICINE, DESIGNED TO HARNESS THE POWER OF INNOVATION AND GENOMICS TO MAKE GROUNDBREAKING NEW DISCOVERIES IN OUR CORE DISEASE RESEARCH AREAS. THEIR SHARED OBJECTIVE IS THE ACCELERATION OF TRANSLATIONAL MEDICAL GENOMICS TO BENEFIT PATIENTS AROUND THE WORLD. NYGC'S SCIENTIFIC MISSION BUILDS ON THE COLLABORATIVE RESEARCH PROJECTS AMONG NYGC FACULTY MEMBERS AND STAFF SCIENTISTS WITH RESEARCHERS AND CLINICIANS FROM MEMBER INSTITUTIONS, AN AFFILIATE MEMBERSHIP PROGRAM, DISEASE AND TECHNOLOGY-CENTERED WORKING GROUPS AND INDUSTRY PARTNERS. RESEARCH AND FACULTY --------------------- SINCE ITS INCEPTION, NYGC HAS ATTRACTED WORLD-CLASS SCIENTISTS WHOSE GENOMIC EXPERTISE - INCLUDING SINGLE CELL GENOMICS, GENOME ENGINEERING, POPULATION, FUNCTIONAL AND EVOLUTIONARY GENOMICS, TECHNOLOGY AND METHODS DEVELOPMENT, STATISTICS, COMPUTATIONAL BIOLOGY, EPIGENETICS, MACHINE LEARNING AND BIOENGINEERING - ENABLES A MULTIDISCIPLINARY AND IN-DEPTH APPROACH TO THE EVOLVING FIELD OF GENOMICS. NYGC'S FACULTY SUPPORT NYGC'S SCIENTIFIC VISION THROUGH THE ADVANCEMENT OF TECHNOLOGY DEVELOPMENT AND GENOMIC MEDICINE. FACULTY MEMBERS HAVE JOINT APPOINTMENTS AT THE NYGC'S INSTITUTIONAL FOUNDING MEMBERS TO PROMOTE COLLABORATION, STRENGTHEN RESEARCH CAPABILITIES, ADVANCE ACADEMIC LEADERSHIP, AND ENHANCE OUR ABILITY TO UNDERSTAND AND HELP TREAT HUMAN DISEASE. IN 2020, NYGC MANAGED 68 GRANTS INCLUDING FUNDING FROM THE NATIONAL INSTITUTES OF HEALTH (NIH). NYGC'S RESEARCHERS ARE WORKING WITH ITS MEMBER INSTITUTIONS AND COLLABORATIVE PARTNERS TO ADDRESS THE FUNDAMENTAL CHALLENGE IN PRECISION MEDICINE: UNDERSTANDING THE RELATIONSHIP BETWEEN DNA SEQUENCE VARIATION AND MECHANISMS OF HUMAN DISEASE, RANGING FROM CANCER TO AUTISM TO NEURODEGENERATIVE DISEASE. NYGC RESEARCHERS PUBLISHED MORE THAN 50 STUDIES IN LEADING SCIENTIFIC JOURNALS. ACCOMPLISHMENTS IN 2020 INCLUDE: ADVANCING COVID-19 RESEARCH -------------------- IN MARCH OF 2020, THE NYGC LAUNCHED THE COVID-19 GENOMICS RESEARCH NETWORK (CGRN), A NEW MULTIDISCIPLINARY CONSORTIUM WITH THE GOAL OF DEVELOPING COLLABORATIVE RESEARCH PROJECTS WITH THE SCIENTIFIC COMMUNITY TO UNDERSTAND HOW THE SARS-COV-2 VIRUS SPREADS, HOW THE IMMUNE SYSTEM RESPONDS, WHY SOME PEOPLE ARE MINIMALLY AFFECTED WHILE OTHERS ARE SEVERELY IMPACTED, AND WHICH PHARMACEUTICAL STRATEGIES MIGHT OPTIMALLY HELP REDUCE THE SPREAD AND ALLEVIATE SYMPTOMS. A CHIEF GOAL OF THE CGRN IS TO COMBINE CLINICAL AND GENOMIC DATA GENERATED FROM PATIENTS IN AN NYGC-HOSTED DATA COMMONS FOR PARTICIPATING PHYSICIANS AND SCIENTISTS. THIS RESOURCE WILL HELP SUPPORT ONGOING EFFORTS TO IMPROVE TREATMENT OF PATIENTS AND FURTHER STUDIES TO UNDERSTAND THE DISEASE, EVOLUTION OF THE VIRUS, AND LONG-TERM IMPACT ON POPULATION HEALTH. CGRN MEETINGS HAVE BECOME A CRITICAL INFOMRATION-SHARING FORUM FOR THE WORLDWIDE COVID-19 GENOMICS COMMUNITY, WITH UP TO 250 RESEARCHERS AND CLINICIANS FROM AROUND THE GLOBE REGULARLY ATTENDING THESE VIRTUAL MEETINGS. AS PART OF THE CGRN, NYGC IS SEQUENCING COVID VIRAL AND HOST SAMPLES FOR SEVERAL COLLABORATIVE COVID-19 RESEARCH PROJECTS WITH OUR INSTITUTIONAL MEMBERS. IN MAY 2020, A UNIQUE PARTNERSHIP WAS LAUNCHED BETWEEN THE NY STATE DEPARTMENT OF HEALTH, THE NYGC, AND THE ROCKEFELLER UNIVERSITY TO BETTER UNDERSTAND COVID-19 RELATED ILLNESS IN CHILDREN. THE NYGC IS ALSO ONE OF 50 SEQUENCING HUBS INVOLVED IN THE INTERNATIONAL COVID HUMAN GENETIC EFFORT, LED BY JEAN-LAURENT CASANOVA, MD, PHD, AT THE ROCKEFELLER UNIVERSITY AND HELEN SU, MD, PHD, AT THE NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASE. NYGC'S FACULTY QUICKLY PIVOTED TO FOCUS THEIR EXPERTISE ON SARS-COV-2 RESEARCH IN ADDITION TO THEIR PRIMARY AREAS OF EXPERTISE. NYGC CORE FACULTY MEMBER NEVILLE SANJANA, PHD, AND HIS COLLEAGUES USED HIGH-THROUGHPUT CRISPR GENE-EDITING TOOLS IN A STUDY TO IDENTIFY WHICH KEY HUMAN GENES ARE REQUIRED BY THE SARS-COV-2 VIRUS TO BETTER UNDERSTAND HOW THE VIRUS DEPENDS ON ITS HOST AND WHETHER THERE ARE EXISTING DRUGS TO TARGET THOSE CRITICAL DEPENDENCIES. THIS STUDY WAS PUBLISHED IN CELL IN OCTOBER OF 2020. IN CLOSE COLLABORATION WITH THE LAB OF BEN TENOEVER, PHD AT MT. SINAI, THE STUDY TEAM PERFORMED A GENOME-SCALE, LOSS-OF-FUNCTION CRISPR SCREEN TO SYSTEMATICALLY KNOCK OUT ALL THE GENES IN THE HUMAN GENOME, IDENTIFYING THE GENES AND THUS POTENTIAL DRUG TARGETS THAT PROTECT AGAINST SARS-COV-2 INFECTION. THE RESEARCHERS USED A BROAD RANGE OF ANALYTICAL AND EXPERIMENTAL METHODS TO VALIDATE THEIR RESULTS, INCLUDING REPURPOSING EXISTING FDA-APPROVED DRUGS TO COMBAT THE VIRUS. CONTRIBUTORS TO THIS INTEGRATIVE STUDY INCLUDE SCIENTISTS FROM NYGC'S TECHNOLOGY INNOVATION LAB, AND THE CENTER FOR GENOMICS OF NEURODEGENERATIVE DISEASES. FORM 990, PART III, LINE 4A NEURODEGENERATIVE DISEASE --------------------- THE NYGC'S ALS CONSORTIUM, A GLOBAL COLLABORATION OF CLINICIANS, SCIENTISTS, GENETICISTS, AND COMPUTATIONAL BIOLOGISTS ORGANIZED BY NYGC'S CENTER FOR GENOMICS OF NEURODEGENERATIVE DISEASE (CGND), ADDED SIX NEW MEMBERS TO THE CONSORTIUM'S 40 MEMBERS WORLDWIDE. THE MEMBERS THAT JOINED IN 2020 INCLUDE: BROAD INSTITUTE, KOREA ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY, NORTHWELL HEALTH, TEL AVIV SOURASKY MEDICAL CENTER, THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTE (TGEN), AND THE UNIVERSITY OF CALIFORNIA SAN DIEGO. THROUGH THE DATA-SHARING REPOSITORY MAINTAINED BY THE CGND, THE ALS CONSORTIUM IS DEVELOPING AN EVER-GROWING RESOURCE OF GENOMIC SEQUENCING AND CLINICAL DATA. BY YEAR-END 2020, 3,637 WHOLE GENOMES AND ALMOST 2,000 RNA SAMPLES FROM ALS PATIENTS WERE SEQUENCED AND ANALYZED, MAKING THIS DATASET AVAILABLE TO ALL ALS RESEARCHERS, ONE OF THE LARGEST ALS COHORTS IN THE WORLD. IN DECEMBER, THE MEDICAL RESEARCH FOUNDATION, TARGET ALS, WHICH PROVIDES SUPPORT TO THE CGND AND CONTRIBUTES ALS PATIENT SAMPLES TO ITS REPOSITORY, LAUNCHED THE TARGET ALS DIAGNOSIS INITIATIVE, THE FIRST-EVER COMPREHENSIVE EFFORT TO DISCOVER ALS BIOMARKERS. THIS NEW PROGRAM INCLUDES DEVELOPING AN INTEGRATED BIOFLUID AND GENOMICS CORE MADE POSSIBLE THROUGH EXISTING ALLIANCES BETWEEN TARGET ALS, THE ALS ASSOCIATION AND THE TOW FOUNDATION. THE LAB OF NYGC CORE FACULTY MEMBER DAVID KNOWLES, PHD, WHO JOINED NYGC, WITH A JOINT APPOINTMENT AT COLUMBIA UNIVERSITY IN 2019, DEVELOPED A NEW STATISTICAL TOOL TO IMPROVE ANALYSIS OF BIOBANKS AND USING MACHINE LEARNING TO UNCOVER NOVEL THERAPEUTIC TARGETS FOR ALZHEIMER'S DISEASE. THE NEW METHOD IMPROVES THE ABILITY TO INFER SPARSE NETWORKS OF DIRECT CAUSAL EFFECTS FROM PHENOME-SCALE GWAS SUMMARY STATISTICS. IN AUGUST, DR. KNOWLES AND COLLABORATOR TOWFIQUE RAJ, PHD, A CORE FACULTY MEMBER AT MT. SINAI'S RONALD M. LOEB CENTER FOR ALZHEIMER'S DISEASE, WERE AWARDED A UO1 GRANT FROM THE NATIONAL INSTITUTES OF HEALTH FOR THEIR PROJECT "LEARNING THE REGULATORY CODE OF ALZHEIMER'S DISEASE." THE TEAM WILL USE MACHINE LEARNING ALGORITHMS AND BUILD COMPUTATIONAL MODELS TO UNCOVER WHICH GENES, PATHWAYS, AND MOLECULAR MECHANISMS ARE INVOLVED IN ALZEHIEMER'S THAT WILL PROVIDE NOVEL THERAPEUTIC TARGETS FOR PATIENTS. NEUROPSYCHIATRIC DISEASE --------------------- THROUGH A $40 MILLION GRANT AWARD FROM THE NATIONAL HUMAN GENOME RESEARCH INSTITUTE, A DIVISION OF NIH, IN 2015 THE NYGC CREATED A CENTER FOR COMMON DISEASE GENOMICS, ENGAGED IN LARGE-SCALE WHOLE GENOME SEQUENCING STUDIES OF AUTISM AND OTHER COMPLEX DISEASES. NYGC RESEARCHERS ARE INVOLVED IN SFARI (SIMONS FOUNDATION AUTISM RESEARCH INITIATIVE) AND SPARK (SIMONS FOUNDATION POWERING AUTISM RESEARCH FOR KNOWLEDGE) AND LEAD OR CONTRIBUTE TO AN ARRAY OF OTHER COLLABORATIVE NEUROPSYCHIATRIC DISEASE-RELATED GENOMIC STUDIES. BY YEAR-END OF 2020, THE NYGC ALSO REACHED A SIGNIFICANT MILESTONE IN ITS NEUROPSYCHIATRIC AND NEURODEVELOPMENTAL DISEASE RESEARCH. NYGC TEAMS HAVE NOW SEQUENCED AND ANALYZED OVER 41,000 GENOMES, PRIMARILY OF AUTISM PATIENTS AND THEIR FAMILIES, AS PART OF THE CENTERS FOR COMMON DISEASE GENOMICS PROGRAM. IN JANUARY OF 2020, THOMAS LEHNER PHD, MPH, JOINED THE NYGC AS SCIENTIFIC DIRECTOR OF NEUROPSYCHIATRIC DISEASE GENOMICS TO LEAD THE EXPANSION OF THE NYGC'S NEUROPSYCHIATRIC DISEASE RESEARCH PROGRAM, FOCUSED ON THE GENETIC ARCHITECTURE OF AUTISM, SCHIZOPHRENIA, AND BIPOLAR DISORDER. DR. LEHNER IS PURSUING NEW COLLABORATIVE OPPORTUNITIES BOTH NATIONALLY AND GLOBALLY. HE IS HOSTING A SERIES OF SEMINARS WITH POTENTIAL COLLABORATORS REPRESENTING THE BREADTH OF NEUROPSYCHIATRIC DISEASE GENOMICS. DR. LEHNER, WHO CAME TO THE NYGC FROM A DISTINGUISHED 15-YEAR CAREER AT THE NATIONAL INSTITUTE OF MENTAL HEALTH (NIMH), HOSTED A VIRTUAL VISIT BY NIMH DIRECTOR JOSHUA A. GORDON, MD, PHD, TO ENGAGE WITH NYGC FACULTY AND STAFF SCIENTISTS AND DISCUSS OPPORTUNITIES FOR COLLABORATION. DR. LEHNER ALSO LEADS NYGC'S NEUROPSYCHIATRIC DISEASE SCIENTIFIC WORKING GROUP. ONE OF THE SIGNATURE PROJECTS OF THIS GROUP IS THE DEVELOPMENT OF A NEW YORK-WIDE PRECISION PSYCHIATRY COHORT THAT WILL INTEGRATE DIAGNOSTIC, DEMOGRAPHIC, AND PATIENT CARE DATA AND OTHER MEDICAL RECORDS TO PROVIDE A PLATFORM FOR SCIENTIFIC DISCORBY, CLINICAL VALIDATIONS, AND TRANSLATIONAL IMPLEMENTATION. CANCER -------------------- GENOMICS-CENTERED INITIATIVES TO ADDRESS CANCER CARE CHALLENGES ARE A KEY FOCUS OF THE GENOME CENTER CANCER GROUP (GCCG), LED BY NOBEL LAUREATE HAROLD VARMUS, MD, SENIOR ASSOCIATE CORE MEMBER, NYGC, AND LEWIS THOMAS UNIVERSITY PROFESSOR OF MEDICINE, WEILL CORNELL MEDICINE, AND CHARLES SAWYERS, MD, CHAIR, HUMAN ONCOLOGY AND PATHOGENESIS PROGRAM, MARIE-JOSE AND HENRY R. KRAVIS CHAIR, MEMORIAL SLOAN KETTERING CANCER CENTER, AND AFFILIATE MEMBER, NYGC. WITHIN THE LAST THREE YEARS, THE GCCG, COMPOSED OF CLINICIANS AND CANCER RESEARCHERS FROM NYGC'S MEMBER INSTITUTIONS, INCLUDING SEVEN NCI-DESIGNATED CANCER CENTERS, HAS DEVELOPED TWO MAJOR MULTI-INSTITUTIONAL COLLABORATIONS. IN 2018, THE GROUP BEGAN WORK ON ITS POLYETHNIC-1000 PROJECT TO STUDY CANCER GENOMES OF UNDERSERVED, ETHNICALLY DIVERSE POPULATIONS. IN 2019, THE GCCG LAUNCHED THE VERY RARE CANCER CONSORTIUM, A NEW COLLABORATION TO HELP ADVANCE CLINICAL CARE FOR PATIENTS AFFECTED BY VERY RARE TUMOR TYPES. THESE PROJECTS ACHIEVED THE FOLLOWING PROGRESS MILESTONES IN 2020: POLYETHNIC-1000 (P-1000), WAS AWARDED ADDITIONAL GRANT FUNDING IN 2020 TO SUPPORT THE PROGRAM, INCLUDING SEVEN NEW MULTI-INSTITUTIONAL CANCER PROJECTS FOCUSED ON UNDERSERVED POPULATIONS. THE AWARD-WINNING NEW PROJECTS WILL INVESTIGATE A VARIETY OF CANCERS INCLUDING PANCREATIC, COLORECTAL, AND ENDOMETRIAL CANCER IN AFRICAN AMERICANS; LUNG CANCER IN ASIAN AMERICAN PATIENTS; BREAST AND PROSTATE CANCER IN PATIENTS OF AFRICAN ANCESTRY; MULTIPLE MYELOMA IN IN AFRICAN AMERICANS; AND THE ROLE OF ETHNICITY IN BLADDER CANCER. THE VERY RARE CANCER CONSORTIUM (VRCC) VIRTUALLY CONVENED ITS MULTI-INSTITUTIONAL MOLECULAR TUMOR BOARD WHERE ONCOLOGISTS, HEMATOLOGISTS, SCIENTISTS, PATHOLOGISTS, COMPUTATIONAL BIOLOGISTS, AND OTHER MEMBERS OF THE CANCER GENOMICS COMMUNITY ON A REGULAR BASIS. CLINICIANS FROM PARTICIPATING HOSPITALS REPORT CASE CONFERENCES TO THE TUMOR BOARD TO DETERMINE THE MOST EFFECTIVE TREATMENT FOR PATIENTS WITH VERY RARE CANCERS. NYGC CORE FACULTY MEMBER MARCIN IMIELINSI, MD, PHD, PUBLISHED A STUDY IN CELL, THAT IDENTIFIED THREE NEW DISTINCT CLASSES OF STRUCTURAL VARIATIONS IN THE DNA OF THOUSANDS OF CANCER SAMPLES ACROSS MULTIPLE CANCER TYPES. THESE DISCOVERIES HELP EXPLAIN DIFFERENT MECHANISMS THAT ENABLE CANCER CELLS TO EXPAND AND GROW RAPIDLY WHILE SIMULTANEOUSLY EVADING NATURAL DEFENSE MECHANISMS AND TREATMENT. THE RESEARCH TEAM IS CONTINUING TO APPLY TO STRUCTURAL VARIANT DETECTION STRATEGY TO CANCER CASES AND EXPECTS THE APPROACH TO BECOME MORE WIDESPREAD IN CLINICS AND IN RESEARCH LABS IN THE FUTURE. NYGC CORE FACULTY MEMBER DAN LANDAU, MD, PHD, AND HIS RESEARCH TEAM HAVE DEVELOPED A WHOLE-GENOME SEQUENCING TECHNOLOGY POWERED BY MACHINE LEARNING THAT IS ABLE TO IDENTIFY VERY LOW LEVELS OF TUMOR DNA IN BLOOD SAMPLES TO ENABLE THE EARLY DETECTION OF CANCER RECURRENCE AFTER SURGERY OR TREATMENT. THE PROOF-OF-CONCEPT DATA OF THIS LANDMARK LIQUID-BIOPSY METHOD WAS PUBLISHED IN NATURE MEDICINE IN JUNE 2020, WITH NYGC COMPUTATIONAL BIOLOGY TEAM MEMBERS ARE AMONG THE CO-AUTHORS. FORM 990, PART III, LINE 4A TECHNOLOGY INNOVATION -------------------- IN 2020, THE CENTER FOR INTEGRATED CELLULAR ANALYSIS WAS ESTABLISHED AT THE NYGC. FUNDED THROUGH THE CENTERS OF EXCELLENCE IN GENOMIC SCIENCE PROGRAM OF THE NATIONAL HUMAN GENOME RESEARCH INSTITUTE, THE MISSION OF THE CENTER IS TO DEVELOP A COMPREHENSIVE SUITE OF TECHNOLOGIES AND ANALYTICAL METHODS TO MEASURE AND INTEGRATE THE MOLECULAR AND ENVIRONMENTAL DETERMINANTS OF CELLULAR IDENTITY. THIS WILL ADDRESS CRITICAL CHALLENGES IN DATA INTEGRATION, AND PRODUCE SOFTWARE, PROTOCOLS, AND SOFTWARE THAT WILL BE APPLICABLE TO DIVERSE BIOLOGICAL SYSTEMS. IN LINE WITH THE CENTER'S PRIMARY GOALS, RESEARCHERS AT NYGC ALSO CONTINUED TO DEVELOP AND DEPLOY PIONEERING MULTIMODAL SINGLE-CELL TECHNOLOGIES: - THE SATIJA LAB ISSUED VERSION 4.0 OF SEURAT, ITS OPEN-SOURCE SOFTWARE TOOLKIT THAT HARMONIZES AND INTEGRATES MULTIPLE SINGLE-CELL DATASETS. - CITE-SEQ, THE MULTI-DIMENSIONAL RNA SINGLE-CELL ANALYSIS TOOL DEVELOPED AT NYGC, IS WIDELY USED BY THE SCIENTIFIC COMMUNITY AND CONTINUES TO BE EXPANDED UPON. - ECCITE-SEQ, THE EXTENSION OF CITE-SEQ FOR USE WITH CRISPR SCREENS, DEVELOPED IN 2019 BY THE SATIJA LAB AND THE NYGC TECHNOLOGY INNOVATION LAB IN COLLABORATION WITH THE SANJANA LAB IS ONE OF THE KEY TOOLS USED IN CRISPR COVID-19 SCREEN STUDY CO-LED BY THE SANAJA LAB AND PUBLISHED IN CELL IN 2020. - NYGC'S TECHNOLOGY INNOVATION LAB RELEASED ASAP-SEQ, WHICH EXTENDS THE TOOL FOR USE IN SINGLE-CELL ATAC-SEQ, A TECHNIQUE USED IN MOLECULAR BIOLOGY TO ASSESS GENOME-WIDE CHROMATIN ACCESSIBILITY. IN 2020, NYGC CORE FACULTY MEMBER, DR. DAN LANDAU, WAS NAMED A VALLEE SCHOLAR AND RECEIVED A SONTAG FOUNDATION DISTINGUISHED SCIENTIST GRANT, BOTH AWARDS IN SUPPORT OF RESEARCH THAT USES SINGLE-CELL ANALYSIS TECHNOLOGIES. ONE OF THE TOOLS THAT HIS STUDY TEAM DEPLOYS IN THIS RESEARCH IS GENOTYPING OF TRANSCRIPTOMICS, A METHOD DEVELOPED IN 2019 IN A RESEARCH COLLABORATION JOINTLY SUPERVISED AT THE NYGC. EARLY IN 2020, NYGC'S CLINICAL LAB RECEIVED APPROVAL FROM THE NY STATE DEPARTMENT OF HEALTH (NYSDOH) TO RUN ITS CLINICAL CONSTITUTIONAL WHOLE GENOME SEQUENCING (WGS) TESTING ON THE ILLUMINA NOVASEQ PLATFORM. IN DECEMBER, IT WAS ANNOUNCED THAT THE NYGC WILL SEQUENCE THE WHOLE GENOMES OF THOUSANDS OF PATIENTS RECEIVING CARE AT WEILL CORNELL MEDICINE (WCM) AND NEW YORK-PRESBYTERIAN (NYP), MAKING THIS ONE OF THE LARGEST CLINICAL WHOLE GENOME SEQUENCING PROGRAMS IN THE COUNTRY. THE NYGC CLINICAL LAB'S BOARD-CERTIFIED MOLECULAR GENETICISTS WILL INTERPRET AND RETURN THE RESULTS TO PHYSICIANS, WHO MAY THEN SHARE THEM WITH THEIR PATIENTS. THE INITIATIVE, WHICH ALSO INCLUDES A PARTNERSHIP BETWEEN WCM, NYP, AND ILLUMINA, HAS BEEN ESTABLISHED TO STUDY THE FEASIBILITY AND VIABILITY OF A LARGE-SCALE IMPLEMENTATION OF WHOLE-GENOME SEQUENCING WITHIN A MAJOR METROPOLITAN HEALTH CARE SYSTEM IN THE UNITED STATES. THE NYGC WAS THE FIRST SEQUENCING CENTER IN THE COUNTRY TO OBTAIN REGULATORY APPROVAL FOR CLINICAL WHOLE GENOME SEQUENCING TESTS FOR GENETIC DISEASES AND CANCER FROM THE NYGS OOH , WHICH HAS BEEN ACTIVE SINCE 2018. RESEARCH SEQUENCING ------------------- NYGC HAS ONE OF THE LARGEST VOLUME WHOLE GENOME SEQUENCING PROGRAMS IN NEW YORK. IN THE PAST SIX YEARS, NYGC'S SEQUENCING LABORATORY HAS SEQUENCED OVER 77,000 WHOLE GENOME SAMPLES. NYGC HAS FIVE NOVASEQ SYSTEMS SEQUENCERS, WITH THE CAPACITY TO SEQUENCE OVER 40,000 GENOMES A YEAR. THIS STATE-OF-THE-ART SEQUENCING TECHNOLOGY ENABLES NYGC TO CONDUCT LARGE-SCALE GENOMICS PROJECTS WITH GREAT SPEED AND SAMPLE VOLUMES, AND TO EXPLORE THE GENOME IN MORE DEPTH WITH GREATER EFFICIENCY. NYGC'S RESEARCH SEQUENCING LAB, LED BY SOREN GERMER, PHD, SENIOR VICE PRESIDENT OF GENOME TECHNOLOGIES, PROCESSED MORE THAN 11,000 SAMPLES IN 2020, INCLUDING 8,171 WHOLE GENOME SEQUENCING SAMPLES (GERMLINE AND CANCER), 356 EXOME SEQUENCING SAMPLES, AND 2,390 TRANSCRIPTOME (RNA) SEQUENCING SAMPLES. AMONG OTHER LARGE COLLABORATIVE PROJECTS, SINCE 2016 NYGC HAS BEEN AWARDED $48 MILLION FROM THE NHGRI AS ONE OF THE CENTERS FOR COMMON DISEASE GENOMICS (CCDG) FOR WHOLE GENOME SEQUENCING. THROUGH THIS AWARD, ALONG WITH THE GENEROUS PHILANTHROPIC CONTRIBUTIONS FROM OUR DONORS, THE NYGC HAS TAKEN ADVANTAGE OF ITS CLINICALLY FOCUSED, COLLABORATIVE STRUCTURE WITH THE GOAL OF ACHIEVING A COMPREHENSIVE UNDERSTANDING OF DIFFERENT TYPES OF COMMON DISEASES, WITH A CENTER-SPECIFIC FOCUS ON AUTISM. AS A MEMBER OF THIS MULTI-INSTITUTIONAL CONSORTIUM, THE NYGC LEADS AND ENABLES COLLABORATION, COMMUNICATION, AND ANALYSIS BETWEEN CENTERS AND PRINCIPAL INVESTIGATORS, PARTICIPATING IN NUMEROUS WORKING GROUPS, STEERING COMMITTEES, AND CONFERENCES AS WELL AS LEADING THE NEUROPSYCHIATRIC WORKING GROUP WHICH SPANS THREE INSTITUTIONS AND SEVERAL DISORDERS. IN 2020 NYGC COMPLETED THE SEQUENCING PORTION OF THIS PROJECT, HAVING COMPLETED MORE THAN 41,000 GENOMES AND MADE THE DATA PUBLICLY AVAILABLE. THE PROJECT DATA GENERATED BY NYGC HAS ALREADY BEEN THE SOURCE FOR A LARGE NUMBER OF PUBLICATIONS. IN ADDITION, WITH AN AWARD OF SUPPLEMENTAL FUNDS NYGC IN 2020 ALSO PERFORMED WHOLE GENOME SEQUENCING OF 3,202 GENOMES FROM THE 10000 GENOMES PROJECT, CREATING A LARGE HIGH QUALITY OPEN-SOURCE DATASET OF THESE ANCESTRALLY DIVERSE REFERENCE SAMPLES FREELY AVAILABLE TO THE GENOMICS RESEARCH COMMUNITY. IN 2020 NYGC CONTINUED TO EXPAND OUR OPERATIONAL FOCUS ON SINGLE-CELL GENOMICS, MAKING AVAILABLE TO THE RESEARCH COMMUNITY THROUGH FUNCTIONAL GENOMIC COLLABORATIONS NEW CUTTING-EDGE TECHNIQUES INVENTED IN OUR INNOVATION LAB. THESE INCLUDE CITE-SEQ, A TECHNIQUE THAT ALLOWS SIMULTANEOUS MEASUREMENT IN THOUSANDS OF CELLS BOTH RNA ABUNDANCE AND A LARGE NUMBER OF CELL SURFACE PROTEINS. SCIENTIFIC ADVISORY BOARD --------------------- IN 2020, THE NYGC HELD TWO MEETINGS WITH ITS NEW SCIENTIFIC ADVISORY BOARD (SAB), WHICH PROVIDES STRATEGIC ADVICE AND COUNSEL IN SUPPORT OF OUR SCIENTIFIC MISSION. COMPOSED OF LEADING INTERNATIONAL GENOMIC SCIENTISTS, AND CHAIRED BY BARBARA WOLD, PHD, BREN PROFESSOR OF MOLECULAR BIOLOGY AND DIRECTOR OF MERKIN INSTITUTE FOR TRANSLATIONAL RESEARCH AT THE CALIFORNIA INSTITUTE OF TECHNOLOGY, THE 10-MEMBER SAB OFFERS GUIDANCE AND INPUT ON RESEARCH STRATEGY FROM DIVERSE PERSPECTIVES TO THE NYGC. THE WIDE-RANGING EXPERTISE OF THE ADVISORY BOARD INCLUDES QUANTITATIVE HUMAN GENETICS, NEUROGENETICS, FUNCTIONAL GENOMICS, GENOMIC TECHNOLOGY DEVELOPMENT, COMPUTATIONAL BIOLOGY, MACHINE LEARNING, POPULATION GENOMICS, AND CANCER GENOMICS. DIVERSITY, EQUITY, AND INCLUSION --------------------- IN 2020, NYGC LAUNCHED AN ORGANIZATION-WIDE DIVERSITY, EQUITY, AND INCLUSION INITIATIVE, AFFIRMING NYGC'S COMMITMENT TO TAKE ACTIONABLE STEPS TOWARD CREATING A COMMUNITY ENVIRONMENT THAT IS WELCOMING AND INCLUSIVE TO ALL REGARDLESS OF RACE, ETHNICITY, GENDER, SEXUAL ORIENTATION, PHYSICAL ABILITY, AGE, OR RELIGION. NYGC'S CROSS-FUNCTIONAL DIVERSITY, EQUITY AND INCLUSION (DEI) ADVISORY GROUP, WHOSE GOAL IS TO FOSTER AND PROMOTE DIVERSITY, EQUITY AND INCLUSION THROUGHOUT ALL ASPECTS OF NYGC'S WORK AND CULTURE, HAS PROVIDED EDUCATION AND RESOURCES FOR THE NYGC COMMUNITY TO RAISE AWARENESS OF INEQUALITY, BIAS AND ISSUES AND TO ENHANCE CULTURAL COMPETENCY. EXAMPLES INCLUDE BOOK CLUBS, JOURNAL CLUBS, SMALL GROUP DISCUSSIONS AND ORGANIZATION-WIDE TRAINING ON ISSUES RELATED TO DIVERSITY AND INCLUSION. THE GROUP HAS FOSTERED AND CULTIVATED A SUPPORTIVE, WELCOMING AND INCLUSIVE CULTURE AND ENVIRONMENT AT NYGC, FOR EXAMPLE THROUGH SHOWCASING THE WORK AND SKILLS OF DIVERSE EMPLOYEES, STAFF, FACULTY AND TRAINEES, WITH MENTORSHIP CAREER PANELS, AND BY DEVELOPING WEB PAGES, ARTICLES AND COMMUNICATIONS ON DEI-RELATED TOPICS. THEY ARE ALSO WORKING TO PROMOTE AND SUPPORT AN INCLUSIVE RESEARCH AND TRAINING ENVIRONMENT, FOR EXAMPLE BY DEVELOPING AN INTERNSHIP PROGRAM FOR UNDER-REPRESENTED MINORITIES. NYGC IS COMMITTED TO ADDRESSING SYSTEMIC RACISM AND INEQUALITIES IN SCIENCE AND IN THE WORKPLACE AND WILL CONTINUE TO EXPAND ITS WORK IN ALL OF THESE AREAS. FORM 990, PART VI, SECTION A, LINE 6 AS OF DECEMBER 31, 2020, THE CENTER HAD A TOTAL OF 20 MEMBERS, CONSISTING OF 12 INSTITUTIONAL FOUNDING MEMBERS AND EIGHT ASSOCIATE MEMBERS. *THE INSTITUTIONAL FOUNDING MEMBERS ARE THE FOLLOWING RECOGNIZED ACADEMIC, MEDICAL AND RESEARCH INSTITUTIONS: (1) COLD SPRING HARBOR LABORATORY, (2) CORNELL UNIVERSITY/WEILL CORNELL MEDICINE, (3) THE JACKSON LABORATORY, (4) MEMORIAL SLOAN-KETTERING CANCER CENTER, (5) ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI, (6) NEW YORK-PRESBYTERIAN HOSPITAL, (7) NEW YORK UNIVERSITY, SCHOOL OF MEDICINE, (8) NORTHWELL HEALTH, (9) THE RESEARCH FOUNDATION OF STATE UNIVERSITY OF NEW YORK, ON BEHALF OF STONY BROOK UNIVERSITY, (10) THE ROCKEFELLER UNIVERSITY, (11) THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK, AND (12) ALBERT EINSTEIN COLLEGE OF MEDICINE. *ASSOCIATE MEMBERS: (1) AMERICAN MUSEUM OF NATURAL HISTORY, (2) HOSPITAL FOR SPECIAL SURGERY, (3) THE NEW YORK STEM CELL FOUNDATION, (4) ROSWELL PARK CANCER INSTITUTE, (5) PRINCETON UNIVERSITY, (6) HACKENSACK MERIDIAN HEALTH, (7) GEORGETOWN LOMBARDI COMPREHENSIVE CANCER CENTER, AND (8) RUTGERS CANCER INSTITUTE OF NEW JERSEY. FORM 990, PART VI, SECTION A, LINE 7A EACH INSTITUTIONAL FOUNDING MEMBER APPOINTS ONE REPRESENTATIVE TO SERVE ON NYGC'S BOARD OF DIRECTORS. THE BOARD OF DIRECTORS ALSO INCLUDES THE SCIENTIFIC DIRECTOR AND OTHER DESIGNATED DIRECTORS OR INDIVIDUALS APPOINTED BY THE BOARD. DECISIONS REQUIRING BOARD APPROVAL INCLUDE THE ADMISSION OF NEW MEMBERS, CHANGES TO THE MISSION, CERTIFICATE OF INCORPORATION, AND BYLAWS, APPOINTMENT OR REMOVAL OF THE CHAIRPERSON OF THE BOARD AND THE SCIENTIFIC DIRECTOR, AND ADOPTION OF CERTAIN POLICIES AND PROCEDURES. THE BOARD ALSO REVIEWS AND APPROVES THE ANNUAL OPERATING BUDGET. MANAGEMENT HAS THE ABILITY TO ENTER INTO BUSINESS ARRANGEMENTS AND CONTRACTS, INCLUDING FINANCING ARRANGEMENTS AND HAS THE DISCRETION TO MAKE CERTAIN DECISIONS WITHOUT FORMAL BOARD APPROVAL. FORM 990, PART VI, SECTION B, LINE 11B THE FORM 990 IS PREPARED BY AN INDEPENDENT PUBLIC ACCOUNTING FIRM, UTILIZING INFORMATION PROVIDED BY MANAGEMENT. UPON RECEIPT OF THE DRAFT FORM 990, MANAGEMENT, INCLUDING THE CHIEF FINANCIAL OFFICER; DIRECTOR OF FINANCE; GENERAL COUNSEL; AND THE CHIEF SCIENTIFIC DIRECTOR/CEO REVIEW THE FORM. PRIOR TO FILING, MANAGEMENT PRESENTS THE FORM 990 TO THE AUDIT COMMITTEE OF THE BOARD FOR REVIEW AND COMMENT. ALSO PRIOR TO FILING, MANAGEMENT PROVIDES THE FORM 990 TO THE ENTIRE BOARD OF DIRECTORS. FORM 990, PART VI, SECTION B, LINE 12C NYGC REQUIRES ALL INTERESTED PERSONS (DEFINED AS BOARD MEMBERS, PRINCIPAL OFFICERS, OR MEMBERS OF A COMMITTEE TO WHICH THE BOARD HAS DELEGATED POWERS) TO DISCLOSE CONFLICTS OF INTEREST AS REQUIRED BY THE CONFLICT OF INTEREST POLICY. NYGC FOLLOWS A PROCEDURE FOR OBTAINING SUCH DISCLOSURES ANNUALLY. ANY POTENTIAL CONFLICTS OF INTEREST MUST BE REVIEWED BY THE BOARD. IF AN INTERESTED PERSON HAS A POTENTIAL CONFLICT OF INTEREST, HE OR SHE MAY MAKE A PRESENTATION AT THE BOARD OR COMMITTEE MEETING, BUT AFTER SUCH PRESENTATION, HE/SHE SHALL LEAVE THE MEETING DURING THE DISCUSSION OF, AND THE VOTE ON, THE TRANSACTION OR ARRANGEMENT THAT CREATES THE POTENTIAL CONFLICT OF INTEREST. FORM 990, PART VI, SECTION B, LINE 15 FOR THE ORGANIZATION'S TOP MANAGEMENT OFFICIAL, PLEASE REFER TO SCHEDULE J NARRATIVES FOR THE PROCESS OF DETERMINING COMPENSATION. IN LATE 2019 NYGC HIRED AN INDEPENDENT COMPENSATION CONSULTANT TO PERFORM AN EXECUTIVE TOTAL COMPENSATION STUDY OF SENIOR MANAGEMENT'S COMPENSATION. RESULTS OF THIS REVIEW WERE PROVIDED TO THE AD-HOC COMPENSATION COMMITTEE IN EARLY 2020 AND THE COMMITTEE DISCUSSED THEM. THE REVIEW SHOWED THAT THE COMPENSATION PAID TO ALL MEMBERS OF SENIOR MANAGEMENT (CHERYL MOORE, CAROL ASHE, ANA BASTIANI-POSNER, SOREN GERMER, KATHLEEN MCGOVERN KEARNS, ELIZABETH O'BRIEN, MICHAEL ZODY, THOMAS LEHNER AND TOM MANIATIS) WAS REASONABLE. THE AD-HOC COMPENSATION COMMITTEE DISCUSSED SENIOR MANAGEMENT COMPENSATION IN EARLY 2020. SOREN GERMER RECEIVED A SALARY INCREASE IN 2020 TO BRING HIS SALARY TO MARKET LEVELS AT THE RECOMMENDATION OF AN INDEPENDENT COMPENSATION CONSULTANT WHO PERFORMED AN EXECUTIVE TOTAL COMPENSATION STUDY FOR NYGC. THIS SALARY CHANGE WAS REVIEWED BY AN EXECUTIVE COMPENSATION COMMITTEE OF INDEPENDENT BOARD MEMBERS AND APPROVED BY THE BOARD OF DIRECTORS. THE SENIOR MANAGEMENT TEAM DID NOT RECEIVE MERIT INCREASES IN 2020. THE TOTAL COMPENSATION OF THE SENIOR TEAM REMAINED UNCHANGED EXCEPT AS INDICATED ABOVE. FORM 990, PART VI, SECTION C, LINE 19 NYGC'S GOVERNING DOCUMENTS, CONFLICT OF INTEREST POLICY, AND FINANCIAL STATEMENTS ARE AVAILABLE UPON REQUEST. FORM 990, PART VII, SECTION A IN 2020, TOM MANIATIS, PHD, SCIENTIFIC DIRECTOR & CEO, WAS EMPLOYED BY AN UNRELATED ENTITY AND LEASED TO NYGC TO DEVOTE 80% OF HIS TIME AND EFFORT TO SERVING AS NYGC'S SCIENTIFIC DIRECTOR AND CEO, AN OFFICER OF THE CORPORATION, AND AN ASSOCIATE MEMBER OF NYGC'S FACULTY, WITH RESPONSIBILITY FOR OVERSEEING NYGC'S RESEARCH PROGRAM AND FOR UNDERTAKING SUCH OTHER ACTIVITIES AS NYGC'S BOARD OF DIRECTORS REQUESTED FROM TIME TO TIME. DR. MANIATIS DEVOTES 20% OF HIS TIME TO HIS DUTIES AT THE UNRELATED ENTITY, WHERE HE MAINTAINS A LABORATORY AND CONDUCTS INDEPENDENT, INVESTIGATOR-INITIATED RESEARCH PROJECTS.