SNP cherry picker: maximizing the chance of finding an association with a disease SNP.
The high cost of genotyping single nucleotide polymorphisms (SNPs) generally prohibits the systematic mapping of entire genetic linkage regions in order to find the polymorphisms associated with increased risk of disease. In practice, SNPs are selected at approximately equal spacing across the linkage region to try to locate a SNP lying in the haplotype block of the disease SNP. The size of the haplotype block may not be known, however, and SNPs taken from public domain sources may not in fact be polymorphic. Our program will choose a subset of the SNPs in a linkage region so as to maximize the expected proportion of the sequence that lies within a given distance of a real SNP.


BACKGROUND
The software is available, free of charge, for academic use on request from the authors.


BACKGROUND
www.oxagen.co.uk
Harris
Mark
M
Oxagen Ltd, 91 Milton Park, Abingdon, Oxon OX14 4RY, UK. SD@oxagen.co.uk
Martin
Jeremy M R
JM
Peden
John F
JF
Rawlings
Christopher J
CJ
D000465:Algorithms; D001483:Base Sequence; D020869:Gene Expression Profiling / Q000379:methods*; D005787:Gene Frequency / Q000235:genetics; D030342:Genetic Diseases, Inborn / Q000175:diagnosis / Q000235:genetics*; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*