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Bioinformatics. 2013 Jan 15;29(2):197-205. doi: 10.1093/bioinformatics/bts658. Epub 2012 Nov 18.

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

Author information

1
Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.

Erratum in

  • Bioinformatics.2013 Mar 1;29(5):669.

Abstract

MOTIVATION:

The use of dense single nucleotide polymorphism (SNP) data in genetic linkage analysis of 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 linkage analysis of SNP data. It features a fully integrated flexible processing workflow comprising both well-known and novel data analysis tools, including SNP clustering, erroneous data filtering, exact and approximate LOD calculations and maximum-likelihood haplotyping. The system draws its power from thousands of CPUs, performing data analysis tasks orders of magnitude faster than a single computer. By providing an intuitive interface to sophisticated state-of-the-art analysis tools coupled with high computing capacity, Superlink-Online SNP helps geneticists unleash the potential of SNP data for detecting disease genes.

RESULTS:

Computations performed by Superlink-Online SNP are automatically parallelized using novel paradigms, and executed on unlimited number of private or public CPUs. One novel service is large-scale approximate Markov Chain-Monte Carlo (MCMC) analysis. The accuracy of the results is reliably estimated by running the same computation on multiple CPUs and evaluating the Gelman-Rubin Score to set aside unreliable results. Another service within the workflow is a novel parallelized exact algorithm for inferring maximum-likelihood haplotyping. The reported system enables genetic analyses that were previously infeasible. We demonstrate the system capabilities through a study of a large complex pedigree affected with metabolic syndrome.

AVAILABILITY:

Superlink-Online SNP is freely available for researchers at http://cbl-hap.cs.technion.ac.il/superlink-snp. The system source code can also be downloaded from the system website.

CONTACT:

omerw@cs.technion.ac.il

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23162081
PMCID:
PMC3546794
DOI:
10.1093/bioinformatics/bts658
[Indexed for MEDLINE]
Free PMC Article

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