Crowdsourced direct-to-consumer genomic analysis of a family quartet

BMC Genomics

Research Article

Huangming Yang¹  Frank Schacherer²  Fiona Nielsen³  Bastian Greshake⁴  Andrew P. Harrison⁵  Pascal Borry⁶  Peter Schols⁷  Federico Moran⁸  Alain Coletta⁹  David Y. Weiss Solís⁹  Alexej Knaus^1,10  Peter N. Robinson^1,11  Peter Krawitz^1,12  Willy Valdivia-Granda^1,13  Mike Cariaso^1,14  Manuel Corpas^1,15  Daniel Swan^1,16  Gustavo Glusman^1,17  Nazareth Torres^1,18 

[1] BGI, Main Building, Beishan Industrial Zone, Yantian District, 518083, Shenzhen, China;BIOBASE, Halchtersche Strasse 33, D-38304, Wolfenbuettel, Germany;DNADigest, Windsor House, Station Court, Station Road, Great Shelford, CB22 5NE, Cambridge, UK;Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany;Department of Mathematical Sciences, University of Essex, Wivenhoe Park, CO4 3SQ, Colchester, Essex, UK;Department of Public Health and Primary Care, Catholic University of Leuven, Leuven, Belgium;Diploid Genomics, Middelweg 129, 3001, Leuven, Belgium;Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain;InSilico Genomics S.A., Avenue Adolphe Buyl, 87, Building C, 5th floor, B-1050, Brussels, Belgium;Institut de Recherches Interdisciplinaires et de Developpements en Intelligence Artificielle, the Computer and Decision Engineering Department, Universite Libre de Bruxelles, 87 av. Adolphe Buyl, 1050, Bruxelles, Belguim;Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany;Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany;Berlin Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, Berlin, Germany;Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany;GeneTalk, Finckensteinallee 84, 12205, Berlin, Germany;Orion Integrated Biosciences Inc., POX 028, 10538, Larchmont, NY, USA;SNPedia, River Road Bio, LLC, 9812 Falls Road #114-237, Potomac, 20854, Maryland, MD, USA;The Genome Analysis Centre, Norwich Research Park, Norwich, UK;The Genome Analysis Centre, Norwich Research Park, Norwich, UK;Oxford Gene Technology, Woodstock Road, Begbroke, OX5 1PF, Oxfordshire, UK;The Institute for Systems Biology, 401 Terry Ave N, 98109, Seattle, WA, USA;Universidad de Navarra, Grupo de Fisiología del Estrés en Plantas (Dpto. de Biología Ambiental), Pamplona, Spain;

关键词: Crowdsourcing;    Personal genomes;    Participatory medicine;    SNPs;    Exome analysis;    Microbiome;    Family genomes;    Direct-to-consumer;    Genetic testing;    Genomics;   

DOI  :  10.1186/s12864-015-1973-7

 received in 2015-01-08, accepted in 2015-10-03,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundWe describe the pioneering experience of a Spanish family pursuing the goal of understanding their own personal genetic data to the fullest possible extent using Direct to Consumer (DTC) tests. With full informed consent from the Corpas family, all genotype, exome and metagenome data from members of this family, are publicly available under a public domain Creative Commons 0 (CC0) license waiver. All scientists or companies analysing these data (“the Corpasome”) were invited to return results to the family.MethodsWe released 5 genotypes, 4 exomes, 1 metagenome from the Corpas family via a blog and figshare under a public domain license, inviting scientists to join the crowdsourcing efforts to analyse the genomes in return for coauthorship or acknowldgement in derived papers. Resulting analysis data were compiled via social media and direct email.ResultsHere we present the results of our investigations, combining the crowdsourced contributions and our own efforts. Four companies offering annotations for genomic variants were applied to four family exomes: BIOBASE, Ingenuity, Diploid, and GeneTalk. Starting from a common VCF file and after selecting for significant results from company reports, we find no overlap among described annotations. We additionally report on a gut microbiome analysis of a member of the Corpas family.ConclusionsThis study presents an analysis of a diverse set of tools and methods offered by four DTC companies. The striking discordance of the results mirrors previous findings with respect to DTC analysis of SNP chip data, and highlights the difficulties of using DTC data for preventive medical care. To our knowledge, the data and analysis results from our crowdsourced study represent the most comprehensive exome and analysis for a family quartet using solely DTC data generation to date.

【 授权许可】

CC BY   
© Corpas et al. 2015