Pei-Yuan Sung1, Yi-Ting Wang1, Ya-Wen Yu2, Ren-Hua Chung2. 1. Institute of Statistics, National Tsing Hua University, Hsin-Chu, Taiwan and. 2. Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan.
Abstract
MOTIVATION: Several efficient gene-gene interaction tests have been developed for unrelated case-control samples in genome-wide association studies (GWAS), making it possible to test tens of billions of interaction pairs of single-nucleotide polymorphisms (SNPs) in a reasonable timeframe. However, current family-based gene-gene interaction tests are computationally expensive and are not applicable to genome-wide interaction analysis. RESULTS: We developed an efficient family-based gene-gene interaction test, GCORE, for trios (i.e. two parents and one affected sib). The GCORE compares interlocus correlations at two SNPs between the transmitted and non-transmitted alleles. We used simulation studies to compare the statistical properties such as type I error rates and power for the GCORE with several other family-based interaction tests under various scenarios. We applied the GCORE to a family-based GWAS for autism consisting of approximately 2000 trios. Testing a total of 22 471 383 013 interaction pairs in the GWAS can be finished in 36 h by the GCORE without large-scale computing resources, demonstrating that the test is practical for genome-wide gene-gene interaction analysis in trios. AVAILABILITY AND IMPLEMENTATION: GCORE is implemented with C ++ and is available at http://gscore.sourceforge.net CONTACT: rchung@nhri.org.tw SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Several efficient gene-gene interaction tests have been developed for unrelated case-control samples in genome-wide association studies (GWAS), making it possible to test tens of billions of interaction pairs of single-nucleotide polymorphisms (SNPs) in a reasonable timeframe. However, current family-based gene-gene interaction tests are computationally expensive and are not applicable to genome-wide interaction analysis. RESULTS: We developed an efficient family-based gene-gene interaction test, GCORE, for trios (i.e. two parents and one affected sib). The GCORE compares interlocus correlations at two SNPs between the transmitted and non-transmitted alleles. We used simulation studies to compare the statistical properties such as type I error rates and power for the GCORE with several other family-based interaction tests under various scenarios. We applied the GCORE to a family-based GWAS for autism consisting of approximately 2000 trios. Testing a total of 22 471 383 013 interaction pairs in the GWAS can be finished in 36 h by the GCORE without large-scale computing resources, demonstrating that the test is practical for genome-wide gene-gene interaction analysis in trios. AVAILABILITY AND IMPLEMENTATION: GCORE is implemented with C ++ and is available at http://gscore.sourceforge.net CONTACT: rchung@nhri.org.tw SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Joseph T Glessner; Kai Wang; Guiqing Cai; Olena Korvatska; Cecilia E Kim; Shawn Wood; Haitao Zhang; Annette Estes; Camille W Brune; Jonathan P Bradfield; Marcin Imielinski; Edward C Frackelton; Jennifer Reichert; Emily L Crawford; Jeffrey Munson; Patrick M A Sleiman; Rosetta Chiavacci; Kiran Annaiah; Kelly Thomas; Cuiping Hou; Wendy Glaberson; James Flory; Frederick Otieno; Maria Garris; Latha Soorya; Lambertus Klei; Joseph Piven; Kacie J Meyer; Evdokia Anagnostou; Takeshi Sakurai; Rachel M Game; Danielle S Rudd; Danielle Zurawiecki; Christopher J McDougle; Lea K Davis; Judith Miller; David J Posey; Shana Michaels; Alexander Kolevzon; Jeremy M Silverman; Raphael Bernier; Susan E Levy; Robert T Schultz; Geraldine Dawson; Thomas Owley; William M McMahon; Thomas H Wassink; John A Sweeney; John I Nurnberger; Hilary Coon; James S Sutcliffe; Nancy J Minshew; Struan F A Grant; Maja Bucan; Edwin H Cook; Joseph D Buxbaum; Bernie Devlin; Gerard D Schellenberg; Hakon Hakonarson Journal: Nature Date: 2009-04-28 Impact factor: 49.962
Authors: Peter Szatmari; Andrew D Paterson; Lonnie Zwaigenbaum; Wendy Roberts; Jessica Brian; Xiao-Qing Liu; John B Vincent; Jennifer L Skaug; Ann P Thompson; Lili Senman; Lars Feuk; Cheng Qian; Susan E Bryson; Marshall B Jones; Christian R Marshall; Stephen W Scherer; Veronica J Vieland; Christopher Bartlett; La Vonne Mangin; Rhinda Goedken; Alberto Segre; Margaret A Pericak-Vance; Michael L Cuccaro; John R Gilbert; Harry H Wright; Ruth K Abramson; Catalina Betancur; Thomas Bourgeron; Christopher Gillberg; Marion Leboyer; Joseph D Buxbaum; Kenneth L Davis; Eric Hollander; Jeremy M Silverman; Joachim Hallmayer; Linda Lotspeich; James S Sutcliffe; Jonathan L Haines; Susan E Folstein; Joseph Piven; Thomas H Wassink; Val Sheffield; Daniel H Geschwind; Maja Bucan; W Ted Brown; Rita M Cantor; John N Constantino; T Conrad Gilliam; Martha Herbert; Clara Lajonchere; David H Ledbetter; Christa Lese-Martin; Janet Miller; Stan Nelson; Carol A Samango-Sprouse; Sarah Spence; Matthew State; Rudolph E Tanzi; Hilary Coon; Geraldine Dawson; Bernie Devlin; Annette Estes; Pamela Flodman; Lambertus Klei; William M McMahon; Nancy Minshew; Jeff Munson; Elena Korvatska; Patricia M Rodier; Gerard D Schellenberg; Moyra Smith; M Anne Spence; Chris Stodgell; Ping Guo Tepper; Ellen M Wijsman; Chang-En Yu; Bernadette Rogé; Carine Mantoulan; Kerstin Wittemeyer; Annemarie Poustka; Bärbel Felder; Sabine M Klauck; Claudia Schuster; Fritz Poustka; Sven Bölte; Sabine Feineis-Matthews; Evelyn Herbrecht; Gabi Schmötzer; John Tsiantis; Katerina Papanikolaou; Elena Maestrini; Elena Bacchelli; Francesca Blasi; Simona Carone; Claudio Toma; Herman Van Engeland; Maretha de Jonge; Chantal Kemner; Frederieke Koop; Frederike Koop; Marjolein Langemeijer; Marjolijn Langemeijer; Channa Hijmans; Channa Hijimans; Wouter G Staal; Gillian Baird; Patrick F Bolton; Michael L Rutter; Emma Weisblatt; Jonathan Green; Catherine Aldred; Julie-Anne Wilkinson; Andrew Pickles; Ann Le Couteur; Tom Berney; Helen McConachie; Anthony J Bailey; Kostas Francis; Gemma Honeyman; Aislinn Hutchinson; Jeremy R Parr; Simon Wallace; Anthony P Monaco; Gabrielle Barnby; Kazuhiro Kobayashi; Janine A Lamb; Ines Sousa; Nuala Sykes; Edwin H Cook; Stephen J Guter; Bennett L Leventhal; Jeff Salt; Catherine Lord; Christina Corsello; Vanessa Hus; Daniel E Weeks; Fred Volkmar; Maïté Tauber; Eric Fombonne; Andy Shih; Kacie J Meyer Journal: Nat Genet Date: 2007-02-18 Impact factor: 38.330