Literature DB >> 22522135

GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations.

Stephen A Stanhope1, Mark Abney.   

Abstract

SUMMARY: Mixed model-based approaches to genome-wide association studies (GWAS) of binary traits in related individuals can account for non-genetic risk factors in an integrated manner. However, they are technically challenging. GLOGS (Genome-wide LOGistic mixed model/Score test) addresses such challenges with efficient statistical procedures and a parallel implementation. GLOGS has high power relative to alternative approaches as risk covariate effects increase, and can complete a GWAS in minutes. AVAILABILITY: Source code and documentation are provided at http://www.bioinformatics.org/~stanhope/GLOGS.

Mesh：

Year:  2012        PMID： 22522135      PMCID： PMC3356846          DOI： 10.1093/bioinformatics/bts190

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  11 in total

1.  A second-generation genomewide screen for asthma-susceptibility alleles in a founder population.

Authors:  C Ober; A Tsalenko; R Parry; N J Cox
Journal:  Am J Hum Genet       Date:  2000-10-05       Impact factor: 11.025

2.  Novel case-control test in a founder population identifies P-selectin as an atopy-susceptibility locus.

Authors:  Catherine Bourgain; Sabine Hoffjan; Raluca Nicolae; Dina Newman; Lori Steiner; Karen Walker; Rebecca Reynolds; Carole Ober; Mary Sara McPeek
Journal:  Am J Hum Genet       Date:  2003-08-15       Impact factor: 11.025

3.  Case-control association testing with related individuals: a more powerful quasi-likelihood score test.

Authors:  Timothy Thornton; Mary Sara McPeek
Journal:  Am J Hum Genet       Date:  2007-07-10       Impact factor: 11.025

4.  A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients.

Authors:  Mark Abney
Journal:  Bioinformatics       Date:  2009-04-09       Impact factor: 6.937

5.  A comparison of strategies for analyzing dichotomous outcomes in genome-wide association studies with general pedigrees.

Authors:  Ming-Huei Chen; Xuan Liu; Fengrong Wei; Martin G Larson; Caroline S Fox; Ramachandran S Vasan; Qiong Yang
Journal:  Genet Epidemiol       Date:  2011-08-04       Impact factor: 2.135

Review 6.  Software engineering the mixed model for genome-wide association studies on large samples.

Authors:  Zhiwu Zhang; Edward S Buckler; Terry M Casstevens; Peter J Bradbury
Journal:  Brief Bioinform       Date:  2009-11       Impact factor: 11.622

7.  Genome-wide search for asthma susceptibility loci in a founder population. The Collaborative Study on the Genetics of Asthma.

Authors:  C Ober; N J Cox; M Abney; A Di Rienzo; E S Lander; B Changyaleket; H Gidley; B Kurtz; J Lee; M Nance; A Pettersson; J Prescott; A Richardson; E Schlenker; E Summerhill; S Willadsen; R Parry
Journal:  Hum Mol Genet       Date:  1998-09       Impact factor: 6.150

8.  Variance component model to account for sample structure in genome-wide association studies.

Authors:  Hyun Min Kang; Jae Hoon Sul; Susan K Service; Noah A Zaitlen; Sit-Yee Kong; Nelson B Freimer; Chiara Sabatti; Eleazar Eskin
Journal:  Nat Genet       Date:  2010-03-07       Impact factor: 38.330

9.  Multipoint quantitative-trait linkage analysis in general pedigrees.

Authors:  L Almasy; J Blangero
Journal:  Am J Hum Genet       Date:  1998-05       Impact factor: 11.025

Review 10.  New approaches to population stratification in genome-wide association studies.

Authors:  Alkes L Price; Noah A Zaitlen; David Reich; Nick Patterson
Journal:  Nat Rev Genet       Date:  2010-07       Impact factor: 53.242
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  4 in total

1.  Leveraging family history in population-based case-control association studies.

Authors:  Arpita Ghosh; Patricia Hartge; Peter Kraft; Amit D Joshi; Regina G Ziegler; Myrto Barrdahl; Stephen J Chanock; Sholom Wacholder; Nilanjan Chatterjee
Journal:  Genet Epidemiol       Date:  2014-01-09       Impact factor: 2.135

Review 2.  Retrospective Association Analysis of Binary Traits: Overcoming Some Limitations of the Additive Polygenic Model.

Authors:  Duo Jiang; Joelle Mbatchou; Mary Sara McPeek
Journal:  Hum Hered       Date:  2016-09-01       Impact factor: 0.444

3.  Fast Genome-Wide QTL Association Mapping on Pedigree and Population Data.

Authors:  Hua Zhou; John Blangero; Thomas D Dyer; Kei-Hang K Chan; Kenneth Lange; Eric M Sobel
Journal:  Genet Epidemiol       Date:  2016-12-12       Impact factor: 2.135

4.  CERAMIC: Case-Control Association Testing in Samples with Related Individuals, Based on Retrospective Mixed Model Analysis with Adjustment for Covariates.

Authors:  Sheng Zhong; Duo Jiang; Mary Sara McPeek
Journal:  PLoS Genet       Date:  2016-10-03       Impact factor: 5.917
  4 in total

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