A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees

• DOI: 10.1093/bioinformatics/bts658
• Publication Date: 2012-11-19T01:40:30Z
• Authors: Mark Silberstein; Omer Weissbrod; Lars Otten; Anna Tzemach; Andrei Anisenia; Oren Shtark; Dvir Tuberg; Eddie Galfrin; Irena Gannon; Adel Shalata; Zvi U. Borochowitz; Rina Dechter; Elizabeth Thompson; Dan Geiger
• Keywords: Tag SNP; SNP; Linkage (software); Pedigree chart

Abstract Motivation: The use of dense single nucleotide polymorphism (SNP) data in genetic linkage analysis large pedigrees is impeded by significant technical, methodological and computational challenges. Here we describe Superlink-Online SNP, a new powerful online system that streamlines the SNP data. It features fully integrated flexible processing workflow comprising both well-known novel tools, including clustering, erroneous filtering, exact approximate LOD calculations maximum-likelihood haplotyping. draws its power from thousands CPUs, performing tasks orders magnitude faster than computer. By providing an intuitive interface to sophisticated state-of-the-art tools coupled with high computing capacity, helps geneticists unleash potential for detecting disease genes. Results: Computations performed are automatically parallelized using paradigms, executed on unlimited number private or public CPUs. One service large-scale Markov Chain–Monte Carlo (MCMC) analysis. accuracy results reliably estimated running same computation multiple CPUs evaluating Gelman–Rubin Score set aside unreliable results. Another within algorithm inferring reported enables analyses were previously infeasible. We demonstrate capabilities through study complex pedigree affected metabolic syndrome. Availability: freely available researchers at http://cbl-hap.cs.technion.ac.il/superlink-snp. source code can also be downloaded website. Contact: [e-mail] Supplementary information: Bioinformatics online.