News

2018

  • PGP-UK: a research and citizen science hybrid project in support of personalized medicine.
    Stephan Beck, Alison M Berner, Graham Bignell, Maggie Bond, Martin J Callanan, Olga Chervova, Lucia Conde, Manuel Corpas, Simone Ecker, Hannah R Elliott, Silvana A Fioramonti, Adrienne M Flanagan, Ricarda Gaentzsch, David Graham, Deirdre Gribbin, Jose Afonso Guerra-Assuncao, Rifat Hamoudi, Vincent Harding, Paul L Harrison, Javier Herrero, Jana Hofmann, Erica Jones, Saif Khan, Jane Kaye, Polly Kerr, Emanuele Libertini, Laura McCormack, Ismail Moghul, Nikolas Pontikos, Sharmini Rajanayagam, Kirti Rana, Momodou Semega-Janneh, Colin P Smith, Louise Strom, Sevgi Urmur, Amy P Webster, Karen Wint, John N Wood. BioRxiv preprint. March 2018. (full text)

  • The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.
    Miriam S. Reuter, Susan Walker, Bhooma Thiruvahindrapuram, Joe Whitney, Iris Cohn, Neal Sondheimer, Ryan K.C. Yuen, Bret.t Trost, Tara A. Paton, Sergio L. Pereira, Jo-Anne Herbrick, Richard F. Wintle, Daniele Merico, Jennifer Howe, Jeffrey R. MacDonald, Chao Lu, Thomas Nalpathamkalam, Wilson W.L. Sung, Zhuozhi Wang, Rohan V. Patel, Giovanna Pellecchia, John Wei, Lisa J. Strug, Sherilyn Bell, Barbara Kellam, Melanie M. Mahtani, Anne S. Bassett, Yvonne Bombard, Rosanna Weksberg, Cheryl Shuman, Ronald D. Cohn, Dimitri J. Stavropoulos, Sarah Bowdin, Matthew R. Hildebrandt, Wei Wei, Asli Romm, Peter Pasceri, James Ellis, Peter Ray, M. Stephen Meyn, Nasim Monfared, S. Mohsen Hosseini, Ann M. Joseph-George, Fred W. Keeley, Ryan A. Cook, Marc Fiume, Hin C. Lee, Christian R. Marshall, Jill Davies, Allison Hazell, Janet A. Buchanan, Michael J. Szego, Stephen W. Scherer CMAJ Feb 2018, 190 (5) E126-E136; DOI: 10.1503/cmaj.171151 (full text)

2017

  • An unbiased index to quantify participant’s phenotypic contribution to an open-access cohort
    Chan Y, Tung M, Garruss AS, Zaranek SW, Chan YK, Lunshof JE, Zaranek AW, Ball MP, Chou MF, Lim ET, Church GM. Sci Rep. 2017 Apr 7. (full text)
  • Association of two synonymous splicing-associated CpG single nucleotide polymorphisms in calpain 10 and solute carrier family 2 member 2 with type 2 diabetes
    Karambataki M, et al. Biomed Rep. Feb 2017. (full text)

2016

  • An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes
    Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Oh TK, Church GM, Bhak J. Nat Commun. 2016 Nov 24. (full text)
  • The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes
    Mao Q, Ciotlos S, Zhang RY, Ball MP, Chin R, Carnevali P, Barua N, Nguyen S, Agarwal MR, Clegg T, Connelly A, Vandewege W, Zaranek AW, Estep PW, Church GM, Drmanac R, Peters BA. Gigascience. 2016 Oct 11. (full text)
  • PALME: PAtients Like My gEnome.
    Wang L, et al. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20. (full text)
  • Extensive sequencing of seven human genomes to characterize benchmark reference materials
    Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M. Sci Data. 2016 Jun 7. (full text)
  • Balancing Benefits and Risks of Immortal Data: Participants’ Views of Open Consent in the Personal Genome Project
    Zarate OA, Brody JG, Brown P, Ramirez-Andreotta MD, Perovich L, Matz J. Hastings Cent Rep. 2016 Jan-Feb. (full text)

2015

  • Privacy Risks from Genomic Data-Sharing Beacons.
    Shringarpure SS, Bustamante CD. Am J Hum Genet. 2015 Nov 5. (full text)
  • Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing
    Zhang W, et al. Pharmacogenomics J. 2015 Aug.

2014

  • A community assessment of privacy preserving techniques for human genomes.
    Jiang X, et al. BMC Med Inform Decis Mak. 2014 Dec 8. (full text)
  • Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population
    Zhang W, et al. BMC Bioinformatics. 2014 Oct 21. (full text)
  • VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants.
    Ho ED, et al. BMC Genomics. 2014 Oct 11. (full text)
  • A probabilistic model to predict clinical phenotypic traits from genome sequencing.
    Chen YC, et al. PLoS Comput Biol. 2014 Sep 4. (full text)
  • Harvard Personal Genome Project: lessons from participatory public research.
    Ball MP, Bobe JR, Chou MF, Clegg T, Estep PW, Lunshof JE, Vandewege W, Zaranek A, Church GM. Genome Med. 2014 Feb 28. (full text)
  • PATH-SCAN: a reporting tool for identifying clinically actionable variants.
    Daneshjou R, Zappala Z, Kukurba K, Boyle SM, Ormond KE, Klein TE, Snyder M, Bustamante CD, Altman RB, Montgomery SB. Pac Symp Biocomput. 2014. (full text)
  • Raw Personal Data: Providing Access
    Lunshof JE, Church GM, Prainsack B. Science. 2014 Jan 24. (full text)

2013

  • Optimization of Scarless Human Stem Cell Genome Editing
    Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. Nucleic Acids Res. 2013 Jul 31. (PDF)

  • Our genomes today: time to be clear
    Jeantine E Lunshof and Madeleine P Ball. Genome Med. 2013 Jun 27;5(6):52. (full text)

  • RNA-guided human genome engineering via Cas9
    Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. Science. 2013 Feb 15;339(6121):823-6. (PDF)

  • Genetic Privacy Needs a More Nuanced Approach
    Misha Angrist, Nature, February 6, 2013.

2012

  • Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells
    Peters BA, Kermani BG, Sparks AB et al. Nature. 2012 Jul 11;487(7406):190-5. (pdf)
  • A Public Resource Facilitating Clinical Use of Genomes
    Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow M, Cano C, Chou MF, Chung WK, Douglas SM, Estep P, Gore A, Hulick P, Labarga A, Lee J, Lunshof J, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters B, Raman AM, Reinhoff HY, Robasky K, Wheeler M, Vandewege W, Vorhaus D, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. PNAS July 13, 2012. (pdf+html).

2011

  • Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
    Greenbaum D, Sboner A, Mu XJ, Gerstein M. PLoS Comput Biol. 2011 Dec;7(12):e1002278. (full text)
  • Neuronal maturation defect in induced pluripotent stem cells from patients with Rett syndrome
    Kim KY, Hysolli E, Park IH. Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14169-74. (full text)

2010

  • Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
    Shoemaker R, Deng J, Wang W, Zhang K. Genome Res. 2010 Jul;20(7):883-9. (full text)
  • Personal genomes in progress: From the Human Genome Project to the Personal Genome Project
    Jeantine Lunshof, Jason Bobe, John Aach, Misha Angrist, Joseph Thakuria, Daniel Vorhaus, Margret Hoehe, George Church. Dialogues in Clinical Neuroscience. 12(1):47-60, 2010. (article)
  • Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays
    Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA. Science. 2010 Jan 1;327(5961):78-81. (Abstract)

2009

  • Targeted and whole-genome methylomics reveals gene-body signatures in human cell lines
    Ball MP, Li JB, Gao Y, Lee J, LeProust E, Park I-H, Xie B, Daley GQ, Church GM. Nature Biotechnol 2009 Apr; 27(4): 361–368. (article)
  • Multiplex padlock capturing and sequencing reveal human hypermutable CpG variations
    Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon J-K, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM. Genome Res 2009 Sep; 19(9): 1606–1615. (PDF)
  • Digital RNA Allelotyping Reveals Tissue-specific and Allele-specific Gene Expression in Human
    Zhang K, Li JB, Gao Y, Egli D, Xie B, Lee JH, Aach J, LeProust E, Eggan K, Church GM (20-Jul-2009) Nature Methods 6, 613 - 618. (abstract)
  • Functional characterization of the antibiotic resistance reservoir in the human microflora
    Sommer MO, Dantas G, Church GM. Science. 2009 Aug 28;325(5944):1128-31. (article)
  • Generation of Functional Human Hepatic Endoderm from Human iPS cells
    Sullivan GJ, Hay DC, Park IH, Fletcher J, Hannoun Z, Payne CM, Dalgetty D, Black JR, Ross J, Samuel K, Wang G, Daley GQ, Lee JH, Church GM, Forbes SJ, Iredale JP, Wilmut I. Hepatology. 2010 Jan;51(1):329-35. (full text)
  • A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells
    Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM. PLoS Genet. 2009 Nov;5(11):e1000718. (full text)

2008

  • From genetic privacy to open consent.
    Lunshof JE, Chadwick R, Vorhaus DB, Church GM (2008) From genetic privacy to open consent. Nat Rev Genet. 2008 May;9(5):406-11. PMID: 18379574 Abstract

2005

  • The Personal Genome Project
    George Church. Molecular Systems Biology, Dec 2005. (full text)