New York Genome Center

New York Genome Center
Established 2011 (2011)
Research type Basic (non-clinical), Clinical research and translational research
Field of research
 Genomics, Bioinformatics, DNA sequencing, Whole genome sequencing
President Cheryl A. Moore, President & COO[1]
Director Tom Maniatis, PhD,[2] Scientific Director & CEO
Location New York City, New York, United States
Affiliations
Harold E. Varmus, MD
Website New York Genome Center

The New York Genome Center (NYGC) is a 501(c)(3) nonprofit biomedical research organization in New York, New York.[4] A collaboration of academic, medical and industry leaders in New York and other partners throughout the country, the New York Genome Center focuses on translating genomic research into clinical solutions for serious diseases. NYGC faculty hold joint academic appointments at its member institutions and lead clinically focused genomic studies in a number of disease areas, including pediatric and adult cancer, asthma, autism, Alzheimer’s disease, ALS and other serious neurodegenerative diseases. NYGC scientists bring a multidisciplinary and in-depth approach to the field of genomics, conducting research in a wide range of areas, including single cell genomics, gene engineering, population and evolutionary genomics, technology and methods development, statistics, computational biology and bioengineering.[5] In 2017, co-founder Tom Maniatis was appointed Scientific Director and Chief Executive Officer of the New York Genome Center.[6]

Founding

The Center was legally founded in November 2011 as a collaboration among eleven academic institutions to advance genome research,[7] based on leadership from Tom Maniatis[8] and financial support of $2.5 million from each institution as well as a number of private philanthropists, including then Mayor Michael Bloomberg, James Simons and Russell Carson.[7] One year after its founding, NYGC recruited Robert B. Darnell as President and Scientific Director,[9] and formally opened in a multi-story building at 101 Avenue of the Americas.[10][11] on September 19–20, 2013.[12][13]

The 12 founding institutions (Albert Einstein College of Medicine joined the original 11 institutions on April 2013)[14] were:

Funding

The Center's funding sources include US and New York state governments, a contract with 10 medical institutes for central management of clinical data, and charitable foundations.[10] This includes funds pledged by the Simons Foundation and the Carson Family Charitable Trust of up to $100 million from 2016 to 2019.[15][16]

Government funding has included a $55 million grant from New York State to support genomic medicine [17] and a $40 million grant for establishing a Center for Common Disease Genomics from the National Human Genome Research Institute, the aim of which is to describe a comprehensive list of genes underlying common diseases.[16] Additionally, the Center and Weill Cornell Medicine received a National Cancer Institute grant to support a joint cancer genomics data center for the research and clinical interpretation of tumors, a part of the ongoing development of The Cancer Genome Atlas; the grant provides $490,000 per year for five years.[18] The Center was also awarded a $13.5 million contract to conduct whole genome sequencing and analysis for the National Heart, Lung, and Blood Institute's TOPMed program.[19][lower-alpha 1]

In 2017, New York State committed $17 million in capital improvements for the New York Genome Center to house JLABS@NYC, a life sciences incubator set to open in summer 2018.[20]

Faculty

  • Hemali Phatnani, PhD | Director of the Center for Genomics of Neurodegenerative Disease[21]
  • Greg Hannon, PhD | Senior Associate Core Member & Director of Cancer Genomics[22]
  • Marcin Imielinski, MD, PhD | Core Faculty Member, Assistant Investigator[23]
  • Ivan Iossifov, PhD | Core Faculty Member, Assistant Investigator[22]
  • Dan A. Landau, MD, PhD | Core Faculty Member, Assistant Investigator[24]
  • Tuuli Lappalainen, PhD | Core Faculty Member, Assistant Investigator[25]
  • Joe Pickrell, PhD | Core Faculty Member, Assistant Investigator[26]
  • Neville Sanjana, PhD | Core Faculty Member, Assistant Investigator[27]
  • Rahul Satija, PhD | Core Faculty Member, Assistant Investigator[28]
  • Harold E. Varmus, MD | Senior Associate Core Member[29][30]
  • Michael Wigler, PhD | Senior Associate Core Member[31]
  • David Goldstein, PhD | Associate Member[32]
  • Jerome B. Posner, MD | Clinical Associate Member[33]
  • Simon Tavaré, PhD | Senior Researcher[34]
  • Yaniv Erlich, PhD | Adjunct Core Member[35]

Notes

  1. ↑ NYGC is among several recipients, another being the Broad Institute.

Recent Publications

    • Whole Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Mak AC, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium. Am J Respir Crit Care Med. 2018 Mar 6. doi: 10.1164/rccm.201712-2529OC. PMID 29509491
    • Developmental diversification of cortical inhibitory interneurons. Mayer C, Hafemeister C, Bandler RC, Machold R, Brito RB, Jaglin X, Allaway K, Butler A, Fishell G, Satija R. Nature. 2018 Mar 5. doi: 10.1038/nature25999. PMID 29513653
    • Barrett's esophagus is associated with a distinct oral microbiome. Snider EJ, Compres G, Freedberg DE, Giddins MJ, Khiabanian H, Lightdale CJ, Nobel YR, Toussaint NC, Uhlemann AC, Abrams JA.Clin Transl Gastroenterol. 2018 Feb 20;9(3):135. doi: 10.1038/s41424-018-0005-8. PMID 29491399
    • Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Stephenson W, Donlin LT, Butler A, Rozo C, Bracken B, Rashidfarrokhi A, Goodman SM, Ivashkiv LB, Bykerk VP, Orange DE, Darnell RB, Swerdlow HP, Satija R. Nat Commun. 2018 Feb 23;9(1):791. doi: 10.1038/s41467-017-02659-x. PMID 29476078
    • Machine learning integration of rheumatoid arthritis synovial histology and RNAseq data identifies three disease subtypes. Orange DE, Agius P, DiCarlo EF, Robine N, Geiger H, Szymonifka J, McNamara M, Cummings R, Andersen KM, Mirza S, Figgie M, Ivashkiv L, Pernis AB, Jiang C, Frank M, Darnell R, Lingampali N, William R, Gravallese E, Bykerk VP, Goodman SM, Donlin LT; Accelerating Medicine Partnership: RA/SLE Network. Arthritis Rheumatol. 2018 Feb 22. doi: 10.1002/art.40428. PMID 29468833
    • microRNA expression profiles of scar and normal tissue from patients with posterior urethral stricture caused by pelvic fracture urethral distraction defects. Zhang K, Chen J, Zhang D, Wang L, Zhao W, Lin DY, Chen R, Xie H, Hu X, Fang X, Fu Q. Int J Mol Med. 2018 May;41(5):2733-2743. doi: 10.3892/ijmm.2018.3487. Epub 2018 Feb 12. PMID 29436608
    • Damaging de novo mutations diminish motor skills in children on the autism spectrum. Buja A, Volfovsky N, Krieger AM, Lord C, Lash AE, Wigler M, Iossifov I. Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1859-E1866. doi: 10.1073/pnas.1715427115. Epub 2018 Feb 6. PMID 29434036
    • Asparagine bioavailability governs metastasis in a model of breast cancer. Knott SRV, Wagenblast E, Khan S, Kim SY, Soto M, Wagner M, Turgeon MO, Fish L, Erard N, Gable AL, Maceli AR, Dickopf S, Papachristou EK, D'Santos CS, Carey LA, Wilkinson JE, Harrell JC, Perou CM, Goodarzi H, Poulogiannis G, Hannon GJ. Nature. 2018 Feb 15;554(7692):378-381. doi: 10.1038/nature25465. Epub 2018 Feb 7. PMID29414946
    • Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma. Wrzeszczynski KO, Felice V, Shah M, Rahman S, Emde AK, Jobanputra V, O Frank M, Darnell RB. Methods Mol Biol. 2018;1741:1-29. doi: 10.1007/978-1-4939-7659-1_1. PMID 29392687
    • Strength in numbers from integrated single-cell neuroscience. Satija R. Nat Biotechnol. 2018 Jan 10;36(1):41-42. doi: 10.1038/nbt.4055. No abstract available. PMID 29319686
    • Bakhoum, Samuel F; Landau, Dan A (2017). "Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution". Cold Spring Harbor Perspectives in Medicine. 7 (6). doi:10.1101/cshperspect.a029611. PMID 28213433.
    • Lappalainen, Tuuli; Greally, John M (2017). "Associating cellular epigenetic models with human phenotypes". Nature Reviews Genetics. 18 (7): 441–451. doi:10.1038/nrg.2017.32. PMID 28555657.
    • Henssen, Anton G; Koche, Richard; Zhuang, Jiali; Jiang, Eileen; Reed, Casie; Eisenberg, Amy; Still, Eric; MacArthur, Ian C; Rodríguez-Fos, Elias; Gonzalez, Santiago; Puiggròs, Montserrat; Blackford, Andrew N; Mason, Christopher E; de Stanchina, Elisa; Gönen, Mithat; Emde, Anne-Katrin; Shah, Minita; Arora, Kanika; Reeves, Reeves; Socci, Nicholas D; Perlman, Elizabeth; Antonescu, Cristina R; Roberts, Charles W M; Steen, Hanno; Mullen, Elizabeth; Jackson, Stephen P; Torrents, David; Weng, Zhiping; Armstrong, Scott A; Kentsis, Alex (2017). "PGBD5 promotes site-specific oncogenic mutations in human tumors". Nature Genetics. 49 (10): 1005–1014. doi:10.1038/ng.3866. PMID 28951624.
    • Hodonsky, Chani J; Jain, Deepti; Yuan, Jie; Morrison, Jean V; Brown, Lisa; McHugh, Caitlin P; Schurmann, Claudia; Chen, Diane D; Liu, Yong Mei; Auer, Paul L; Laurie, Cecilia A; Taylor, Kent D; Browning, Brian L; Li, Yun; Papanicolaou, George; Rotter, Jerome I; Kurita, Ryo; Nakamura, Yukio; Browning, Sharon; Loos, Ruth JF; North, Kari E; Laurie, Cathy C; Thornton, Timothy A; Pankratz, Nathan; Bauer, Daniel E; Sofer, Tamar; Reiner, Alex P (2017). "Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos". PLOS Genetics. 13 (4): 590–592. doi:10.1371/journal.pgen.1006760. PMID 28453575.
    • Willems, Thomas; Zielinski, Dina; Yuan, Jie; Gordon, Assaf; Gymrek, Melissa; Erlich, Yaniv (2017). "Genome-wide profiling of heritable and de novo STR variations". Nature Methods. 14 (6): 590–592. doi:10.1038/nmeth.4267. PMID 28436466.
    • Villani, Alexandra-Chloé; Satija, Rahul; Reynolds, Gary; Sarkizova, Siranush; Shekhar, Karthik; Fletcher, James; Griesbeck, Morgane; Butler, Andrew; Zheng, Shiwei; Lazo, Suzan; Jardine, Laura; Dixon, David; Stephenson, Emily; Nilsson, Emil; Grundberg, Ida; McDonald, David; Filby, Andrew; Li, Weibo; De Jager, Philip L.; Rozenblatt-Rosen, Orit; Lane, Andrew A.; Haniffa, Muzlifah; Regev, Aviv; Hacohen, Nir (2017). "Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors". Science. 356 (6335): eaah4573. doi:10.1126/science.aah4573. PMID 28428369.
    • Gierahn, Todd M; Wadsworth, Marc H; Hughes, Travis K; Bryson, Bryan D; Butler, Andrew; Satija, Rahul; Fortune, Sarah; Love, J Christopher; Shalek, Alex K (2017). "Seq-Well: Portable, low-cost RNA sequencing of single cells at high throughput". Nature Methods. 14 (4): 395–398. doi:10.1038/nmeth.4179. PMC 5376227. PMID 28192419.
    • Imielinski, Marcin; Rubin, Mark A. (2017). "Prostate cancer: Clinical hallmarks in whole cancer genomes". Nature Reviews Clinical Oncology. 14 (5): 265–266. doi:10.1038/nrclinonc.2017.45. PMID 28374788.
    • Edelmann, J; Tausch, E; Landau, D A; Robrecht, S; Bahlo, J; Fischer, K; Fink, A M; Bloehdorn, J; Holzmann, K; Böttcher, S; Werner, L; Kneba, M; Gribben, J G; Neuberg, D S; Wu, C J; Hallek, M; Döhner, H; Stilgenbauer, S (2016). "Frequent evolution of copy number alterations in CLL following first-line treatment with FC(R) is enriched with TP53 alterations: Results from the CLL8 trial". Leukemia. 31 (3): 734–738. doi:10.1038/leu.2016.317. PMC 5332302. PMID 27909343.
    • Joung, Julia; Konermann, Silvana; Gootenberg, Jonathan S; Abudayyeh, Omar O; Platt, Randall J; Brigham, Mark D; Sanjana, Neville E; Zhang, Feng (2017). "Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening". Nature Protocols. 12 (4): 828–863. doi:10.1038/nprot.2017.016. PMID 28333914.
    • Curnin, Charles; Gordon, Assaf; Erlich, Yaniv (2017). "DNA Compass: A secure, client-side site for navigating personal genetic information". Bioinformatics. doi:10.1093/bioinformatics/btx135.
    • Erlich, Yaniv; Zielinski, Dina (2017). "DNA Fountain enables a robust and efficient storage architecture". Science. 355 (6328): 950–954. Bibcode:2017Sci...355..950E. doi:10.1126/science.aaj2038. PMID 28254941.
    • Khurana, Vikram; Peng, Jian; Chung, Chee Yeun; Auluck, Pavan K.; Fanning, Saranna; Tardiff, Daniel F.; Bartels, Theresa; Koeva, Martina; Eichhorn, Stephen W.; Benyamini, Hadar; Lou, Yali; Nutter-Upham, Andy; Baru, Valeriya; Freyzon, Yelena; Tuncbag, Nurcan; Costanzo, Michael; San Luis, Bryan-Joseph; Schöndorf, David C.; Barrasa, M. Inmaculada; Ehsani, Sepehr; Sanjana, Neville; Zhong, Quan; Gasser, Thomas; Bartel, David P.; Vidal, Marc; Deleidi, Michela; Boone, Charles; Fraenkel, Ernest; Berger, Bonnie; Lindquist, Susan (2017). "Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways". Cell Systems. 4 (2): 157–170.e14. doi:10.1016/j.cels.2016.12.011. PMC 5388136. PMID 28131822.
    • Manier, Salomon; Salem, Karma Z.; Park, Jihye; Landau, Dan A.; Getz, Gad; Ghobrial, Irene M. (2016). "Genomic complexity of multiple myeloma and its clinical implications". Nature Reviews Clinical Oncology. 14 (2): 100–113. doi:10.1038/nrclinonc.2016.122. PMID 27531699.
    • Jønsson, K. L.; Laustsen, A.; Krapp, C.; Skipper, K. A.; Thavachelvam, K.; Hotter, D.; Egedal, J. H.; Kjolby, M.; Mohammadi, P.; Prabakaran, T.; Sørensen, L. K.; Sun, C.; Jensen, S. B.; Holm, C. K.; Lebbink, R. J.; Johannsen, M.; Nyegaard, M.; Mikkelsen, J. G.; Kirchhoff, F.; Paludan, S. R.; Jakobsen, M. R. (2017). "IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP". Nature Communications. 8: 14391. Bibcode:2017NatCo...814391J. doi:10.1038/ncomms14391. PMC 5309897. PMID 28186168.
    • Velasco, Silvia; Ibrahim, Mahmoud M.; Kakumanu, Akshay; Garipler, Görkem; Aydin, Begüm; Al-Sayegh, Mohamed Ahmed; Hirsekorn, Antje; Abdul-Rahman, Farah; Satija, Rahul; Ohler, Uwe; Mahony, Shaun; Mazzoni, Esteban O. (2017). "A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells". Cell Stem Cell. 20 (2): 205–217.e8. doi:10.1016/j.stem.2016.11.006. PMC 5291817. PMID 27939218.
    • MacIejowski, John; Imielinski, Marcin (2017). "Modeling cancer rearrangement landscapes". Current Opinion in Systems Biology. 1: 54–61. doi:10.1016/j.coisb.2016.12.005.
    • Liu, Jimmy Z; Erlich, Yaniv; Pickrell, Joseph K (2017). "Case–control association mapping by proxy using family history of disease". Nature Genetics. 49 (3): 325–331. doi:10.1038/ng.3766. PMID 28092683.
    • Imielinski, Marcin; Guo, Guangwu; Meyerson, Matthew (2017). "Insertions and Deletions Target Lineage-Defining Genes in Human Cancers". Cell. 168 (3): 460–472.e14. doi:10.1016/j.cell.2016.12.025. PMID 28089356.

    References

    1. ↑ "Cheryl Moore, Hilde Windels, and more". People in the News. genomeweb. 11 September 2015. Retrieved 20 October 2017. (Registration required (help)).
    2. ↑ "Tom Maniatis". People in the News. genomeweb. 18 August 2017. Retrieved 20 October 2017. (Registration required (help)).
    3. ↑ "About Us". New York Genome Center. Our Members.
    4. ↑ Duignan, Christopher (13 August 2015). "Form 990: Return of Organization Exempt From Income Tax" (PDF). GuideStar. p. 1. Retrieved 22 November 2016. (Registration required (help)).
    5. ↑ http://www.nygenome.org/wp-content/uploads/2017/04/AAG_Formatted.pdf%5Bfull+citation+needed%5D
    6. ↑ "Tom Maniatis Andy Page, Brian Caveney, More". People in the News. genomeweb. 25 August 2017. Retrieved 20 October 2017.
    7. 1 2 "New York Genome Center Launches Unprecedented Collaboration of 11 Leading Medical/Research Institutions". newsroom.cumc.columbia.edu. November 3, 2011. Retrieved 26 March 2017.
    8. ↑ "Tom Maniatis' Dream of a NY Genome Center Becomes a Big Apple Reality". www.xconomy.com. Retrieved 26 March 2017.
    9. ↑ "Robert Darnell named President of New York Genome Center". Rockefeller University Newswire. November 28, 2012. Retrieved 26 March 2017.
    10. 1 2 Rosenthal, Eric T. (9 March 2016). "A New 'Manhattan Project': New York Genome Center". MedPage Today. Retrieved 21 November 2016.
    11. ↑ Hargittai, István; Hargittai, Magdolna (2016). New York Scientific: A Culture of Inquiry, Knowledge, and Learning. Oxford, United Kingdom: Oxford University Press. p. 167. ISBN 9780191084683.
    12. ↑ Maher, Brendan (2013). "Biomedical-research hub opens in Manhattan". Nature. doi:10.1038/nature.2013.13740.
    13. ↑ Matheson, Sarah. "Genome Center Opens in New York". Epoch Times. Retrieved 26 March 2017.
    14. ↑ "Einstein joins NYGC as 12th Founding Member". Retrieved 26 March 2017.
    15. ↑ Di Mento, Maria (25 January 2016). "$100 Million for Genome Center and $75 Million for Hospital". Gifts Roundup. The Chronicle of Philanthropy. New York Genome Center. Retrieved 22 November 2016.
    16. 1 2 Lagasse, Jeff (21 January 2016). "New York Genome Center scores $100 million from James Simons, Russell Carson". Healthcare Finance. Retrieved 22 November 2016.
    17. ↑ "Governor Cuomo Announces Partnership between New York Genome Center and IBM Watson Group". Retrieved 27 March 2017.
    18. ↑ "Weill Cornell Medicine and the New York Genome Center Awarded NCI Grant to Create Genomic Data Center". Bio-IT World. 3 November 2016. Retrieved 22 November 2016.
    19. ↑ "NY Genome Center Wins $13.5M from NHLBI Precision Medicine Program". GenomeWeb. 29 October 2015. Retrieved 22 November 2016. (Registration required (help)).
    20. ↑ "J&J, fueled by $17M in state cash, starts work on 30-startup JLABS incubator to address NYC lab shortage | FierceBiotech". www.fiercebiotech.com. Retrieved 2018-03-06.
    21. ↑ http://www.alsa.org/research/our-approach/inspiring-partnerships/strategic-initiatives/new-york-genome-center.html?referrer=https://www.google.com/?referrer=https://en.wikipedia.org/
    22. 1 2 https://www.genomeweb.com/resources/people-news/greg-hannon-ivan-iossifov
    23. ↑ https://news.weill.cornell.edu/news/2016/11/weill-cornell-medicine-and-the-new-york-genome-center-awarded-nci-grant-to-create
    24. ↑ http://vivo.med.cornell.edu/display/cwid-dal3005
    25. ↑ https://systemsbiology.columbia.edu/faculty/tuuli-lappalainen
    26. ↑ https://www.genomeweb.com/business-news/columbia-nygc-researchers-spin-out-new-company-1m-funding
    27. ↑ https://www.crunchbase.com/person/neville-sanjana
    28. ↑ http://engineering.nyu.edu/people/rahul-satija
    29. ↑ https://www.genomeweb.com/cancer/varmus-resigns-nci-director-plans-open-research-lab-weill-cornell-assist-ny-genome-center
    30. ↑ https://www.nature.com/news/harold-varmus-to-resign-as-head-of-us-cancer-institute-1.17063
    31. ↑ http://www.nygenome.org/lab-groups-overview/wigler-lab/
    32. ↑ http://www.columbiamedicinemagazine.org/ps-news/fall-2014/david-goldstein-direct-columbia%E2%80%99s-institute-genomic-medicine
    33. ↑ "Jerome B. Posner, MD, Joins The New York Genome Center as Clinical Member - New York Genome". New York Genome. Retrieved 2017-11-02.
    34. ↑ http://www.nygenome.org/news/simon-tavare-phd-joins-new-york-genome-center-senior-researcher/
    35. ↑ http://www.cs.columbia.edu/2015/erlich-new-prof/
    This article is issued from Wikipedia. The text is licensed under Creative Commons - Attribution - Sharealike. Additional terms may apply for the media files.