Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium.
We compared seven different tagging single-nucleotide polymorphism (SNP) programs in 10 regions with varied amounts of linkage disequilibrium (LD) and physical distance. We used the Collaborative Studies on the Genetics of Alcoholism dataset, part of the Genetic Analysis Workshop 14. We show that in regions with moderate to strong LD these programs are relatively consistent, despite different parameters and methods. In addition, we compared the selected SNPs in a multipoint linkage analysis for one region with strong LD. As the number of selected SNPs increased, the LOD score, mean information content, and type I error also increased.
Duggal
Priya
P
Inherited Disease Research Branch, NHGRI/NIH, Baltimore, MD, USA. pduggal@mail.nih.gov
Gillanders
Elizabeth M
EM
Mathias
Rasika A
RA
Ibay
Grace P
GP
Klein
Alison P
AP
Baffoe-Bonnie
Agnes B
AB
Ou
Liang
L
Dusenberry
Ian P
IP
Tsai
Ya-Yu
YY
Chines
Peter S
PS
Doan
Betty Q
BQ
Bailey-Wilson
Joan E
JE
D002874:Chromosome Mapping; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*