nach oben

BMC Proceedings

Erschienen in:

Open Access 01.10.2016 | Proceedings

Comparing performance of non–tree-based and tree-based association mapping methods

verfasst von: Katherine L. Thompson, David W. Fardo

Erschienen in: BMC Proceedings | Sonderheft 7/2016

Einloggen, um Zugang zu erhalten

Abstract

A central goal in the biomedical and biological sciences is to link variation in quantitative traits to locations along the genome (single nucleotide polymorphisms). Sequencing technology has rapidly advanced in recent decades, along with the statistical methodology to analyze genetic data. Two classes of association mapping methods exist: those that account for the evolutionary relatedness among individuals, and those that ignore the evolutionary relationships among individuals. While the former methods more fully use implicit information in the data, the latter methods are more flexible in the types of data they can handle. This study presents a comparison of the 2 types of association mapping methods when they are applied to simulated data.

Donnelly P. Progress and challenges in genome-wide association studies in humans. Nature. 2008;456(7223):728–31.CrossRefPubMed

McClurg P, Pletcher TM, Wilthsire T, Su AI. Comparative analysis of haplotype association mapping algorithms. BMC Bioinformatics. 2006;7:61.CrossRefPubMedPubMedCentral

Besenbacher S, Mailund T, Schierup MH. Local phylogeny mapping of quantitative traits: higher accuracy and better ranking than single-marker association in genomewide scans. Genetics. 2009;181(2):747–53.CrossRefPubMedPubMedCentral

Pan F, McMillan L, de Villena FPM, Threadgill D, Wang W. TreeQA: quantitative genome wide association mapping using local perfect phylogeny trees. Pac Symp Biocomput. 2009;415–26.

Thompson K, Kubatko L. Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies. BMC Bioinformatics. 2013;14:200.CrossRefPubMedPubMedCentral

Zhang Z, Zhang X, Wang W. HTreeQA: using semi-perfect phylogeny trees in quantitative trait loci study on genotype data. G3 (Bethesda). 2012;2(2):175–89.CrossRef

Zöllner S, Pritchard JK. Coalescent-based association mapping and fine mapping of complex trait loci. Genetics. 2005;169(2):1071–92.CrossRefPubMedPubMedCentral

Blangero J, Teslovich TM, Sim X, Almeida MA, Jun G, Dyer TD, Johnson M, Peralta JM, Manning AK, Wood AR, et al. Omics squared: human genomic, transcriptomic, and phenotypic data for Genetic Analysis Workshop 19. BMC Proc. 2015;9 Suppl 8:S2.

Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Am J Hum Genet. 2007;81(5):1084–97.CrossRefPubMedPubMedCentral

10.

Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, et al. GeneCards Version 3: the human gene integrator. 2010;2010:baq020.

11.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker R, Lunter G, Marth G, Sherry ST, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8.CrossRefPubMedPubMedCentral

12.

Mailund T, Besenbacher S, Schierup MH. Whole genome association mapping by incompatibilities and local phylogenies. BMC Bioinformatics. 2006;7:454.CrossRefPubMedPubMedCentral

13.

Sasieni P. From genotypes to genes: doubling the sample size. Biometrics. 1997;53(4):1253–61.CrossRefPubMed

Titel: Comparing performance of non–tree-based and tree-based association mapping methods
verfasst von: Katherine L. Thompson
David W. Fardo
Publikationsdatum: 01.10.2016
Verlag: BioMed Central
Erschienen in: BMC Proceedings / Ausgabe Sonderheft 7/2016
Elektronische ISSN: 1753-6561
DOI: https://doi.org/10.1186/s12919-016-0063-4

Die Highlights vom Kongress des American College of Cardiology 2024

Springer Medizin

Comparing performance of non–tree-based and tree-based association mapping methods

Abstract

Die Highlights vom Kongress des American College of Cardiology 2024

Springer Medizin

Abstract

Bitte loggen Sie sich ein, um Zugang zu diesem Inhalt zu erhalten

Weitere Artikel der Sonderheft 7/2016

Identity-by-descent mapping for diastolic blood pressure in unrelated Mexican Americans

A combined association test for rare variants using family and case-control data

Prioritization of family member sequencing for the detection of rare variants

Comparison of parametric and machine methods for variable selection in simulated Genetic Analysis Workshop 19 data

A LASSO penalized regression approach for genome-wide association analyses using related individuals: application to the Genetic Analysis Workshop 19 simulated data

Incorporation of protein binding effects into likelihood ratio test for exome sequencing data