Tag SNP selection for association studies

Genetic Epidemiology
Daniel O Stram

Abstract

This report describes current methods for selection of informative single nucleotide polymorphisms (SNPs) using data from a dense network of SNPs that have been genotyped in a relatively small panel of subjects. We discuss the following issues: (1) Optimal selection of SNPs based upon maximizing either the predictability of unmeasured SNPs or the predictability of SNP haplotypes as selection criteria. (2) The dependence of the performance of tag SNP selection methods upon the density of SNP markers genotyped for the purpose of haplotype discovery and tag SNP selection. (3) The likely power of case-control studies to detect the influence upon disease risk of common disease-causing variants in candidate genes in a haplotype-based analysis. We propose a quasi-empirical approach towards evaluating the power of large studies with this calculation based upon the SNP genotype and haplotype frequencies estimated in a haplotype discovery panel. In this calculation, each common SNP in turn is treated as a potential unmeasured causal variant and subjected to a correlation analysis using the remaining SNPs. We use a small portion of the HapMap ENCODE data (488 common SNPs genotyped over approximately a 500 kb region of chromosome 2) as an ...Continue Reading

References

Sep 13, 1996·Science·N Risch, K Merikangas
Jan 16, 1999·Current Opinion in Biotechnology·J D Terwilliger, K M Weiss
Mar 1, 2000·American Journal of Epidemiology·L N KolonelF S Nagamine
May 11, 2001·Nature·D E ReichE S Lander
Oct 5, 2001·Nature Genetics·M J DalyE S Lander
Oct 5, 2001·Nature Genetics·G C JohnsonJ A Todd
Dec 26, 2001·Trends in Genetics : TIG·Kenneth M Weiss, Andrew G Clark
Jan 16, 2002·American Journal of Human Genetics·Daniel J SchaidGregory A Poland
May 25, 2002·Science·Stacey B GabrielDavid Altshuler
May 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Kui ZhangFengzhu Sun
Dec 6, 2002·Genome Research·Penelope E BonnenDavid L Nelson
Jan 23, 2003·Bioinformatics·Xiayi Ke, Lon R Cardon
Aug 14, 2003·American Journal of Human Genetics·Jeffrey D Wall, Jonathan K Pritchard
Aug 29, 2003·Human Molecular Genetics·Christopher A HaimanBrian E Henderson
Dec 19, 2003·American Journal of Human Genetics·Christopher S CarlsonDeborah A Nickerson
Dec 20, 2003·Nature·UNKNOWN International HapMap Consortium
Apr 7, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Alec J JeffreysAdam J Webb
Apr 24, 2004·Science·Gilean A T McVeanPeter Donnelly
Apr 27, 2004·Human Genetics·Stephanie M FullertonKenneth M Weiss
May 22, 2004·Nature Reviews. Genetics·Liisa KauppiScott Keeney

❮ Previous
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Citations

Mar 22, 2006·Human Genetics·Dana C CrawfordDeborah A Nickerson
Sep 28, 2006·Journal of Human Genetics·Aya KuchibaYasuo Ohashi
Sep 28, 2006·Breast Cancer Research and Treatment·Janet E OlsonRichard M Weinshilboum
Nov 19, 2013·Schizophrenia Research·Silviu-Alin BacanuKenneth S Kendler
Nov 6, 2008·European Journal of Human Genetics : EJHG·Zhijun ChenYong Qiu
Oct 29, 2005·Nature·UNKNOWN International HapMap Consortium
Sep 17, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Emrah Kostem, Eleazar Eskin
Sep 19, 2009·American Journal of Epidemiology·Timothy J JorgensenAnthony J Alberg
Sep 29, 2009·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Rosalind J L MartinUNKNOWN Warren 3/UK GoKinD Study Group
Nov 26, 2008·Genome Research·Gary K ChenJeffrey D Wall
Aug 16, 2008·Annals of Human Genetics·B HanE Eskin
Sep 10, 2011·Annals of Human Genetics·Asif JavedPeristera Paschou
Nov 7, 2006·Genes, Brain, and Behavior·I BelferM A Enoch
Aug 30, 2005·Annual Review of Genomics and Human Genetics·Dana C CrawfordDeborah A Nickerson
May 18, 2007·Annual Review of Genomics and Human Genetics·Robert C ElstonGang Zheng
Mar 5, 2009·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Ellen L GoodeThomas A Sellers
Oct 28, 2006·BMC Genetics·Cédric CoulongesJean-François Zagury
Sep 26, 2007·BMC Genetics·Rachid el GaltaJeanine J Houwing-Duistermaat
Jul 12, 2005·Human Genomics·Daniel O Stram
May 10, 2008·BMC Proceedings·Ellen L GoodeSusan L Slager
Mar 15, 2006·PLoS Genetics·Alexandre MontpetitAndres Metspalu
Sep 20, 2007·PloS One·Fabienne LesueurJudith Fischer
May 17, 2006·Genetics·Yeon-Kyeong YooJung-Joo Hwang
Sep 4, 2009·Personalized Medicine·Sharon A Savage
Jun 18, 2009·Pharmacogenomics·Ellen S KosterAnke-Hilse Maitland-van der Zee
May 16, 2015·Scientific Reports·Hao HuThomas F Wienker
Sep 11, 2008·Clinical Endocrinology·Haiyang ZhouMingjun Gu
Apr 6, 2007·Genetic Epidemiology·W James GaudermanDavid V Conti
Feb 14, 2008·Journal of Clinical Periodontology·Luigi NibaliPeter M Brett
Sep 13, 2011·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Q WangY Pan
Mar 25, 2011·Molecular Ecology Resources·J M MillerUNKNOWN International Sheep Genomics Consortium
Nov 26, 2010·Genetic Epidemiology·Y J Hu, D Y Lin

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