Intra- and interpopulation genotype reconstruction from tagging SNPs.
The optimal method to be used for tSNP selection, the applicability of a reference LD map to unassayed populations, and the scalability of these methods to genome-wide analysis, all remain subjects of debate. We propose novel, scalable matrix algorithms that address these issues and we evaluate them on genotypic data from 38 populations and four genomic regions (248 SNPs typed for approximately 2000 individuals). We also evaluate these algorithms on a second data set consisting of genotypes available from the HapMap database (1336 SNPs for four populations) over the same genomic regions. Furthermore, we test these methods in the setting of a real association study using a publicly available family data set. The algorithms we use for tSNP selection and unassayed SNP reconstruction do not require haplotype inference and they are, in principle, scalable even to genome-wide analysis. Moreover, they are greedy variants of recently developed matrix algorithms with provable performance guarantees. Using a small set of carefully selected tSNPs, we achieve very good reconstruction accuracy of "untyped" genotypes for most of the populations studied. Additionally, we demonstrate in a quantitative manner that the chosen tSNPs exhibit substantial transferability, both within and across different geographic regions. Finally, we show that reconstruction can be applied to retrieve significant SNP associations with disease, with important genotyping savings.
Paschou
Peristera
P
Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA. ppaschou@mbg.duth.gr
Mahoney
Michael W
MW
Javed
Asif
A
Kidd
Judith R
JR
Pakstis
Andrew J
AJ
Gu
Sheng
S
Kidd
Kenneth K
KK
Drineas
Petros
P
D000465:Algorithms; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics; D030561:Databases, Nucleic Acid; D005838:Genotype; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium; D009419:Nerve Tissue Proteins; D027362:Organic Anion Transport Protein 1 / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011956:Receptors, Cell Surface; D018013:Receptors, Neuropeptide / Q000235:genetics
D018398:Homeodomain Proteins; D009419:Nerve Tissue Proteins; D027362:Organic Anion Transport Protein 1; D011956:Receptors, Cell Surface; D018013:Receptors, Neuropeptide; C498347:SorCS3 protein, human