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2.  A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees 
Bioinformatics  2012;29(2):197-205.
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.
doi:10.1093/bioinformatics/bts658
PMCID: PMC3546794  PMID: 23162081
3.  Identification of 11 Novel Mutations in 8 BBS Genes by High-Resolution Homozygosity Mapping 
Journal of medical genetics  2009;47(4):262-267.
Bardet-Biedl syndrome (BBS) is primarily an autosomal recessive disorder characterized by the five cardinal features retinitis pigmentosa, postaxial polydactyly, mental retardation, obesity and hypogenitalism. In addition, renal cysts and other anomalies of the kidney and urinary tract can be present. To date, mutations in 12 BBS genes as well as in MKS1 and CEP290 have been identified as causing BBS. The vast genetic heterogeneity of BBS renders molecular genetic diagnosis difficult in terms of both the time and cost required to screen all 204 coding exons. Here, we report the use of genome-wide homozygosity mapping as a tool to identify homozygous segments at known BBS loci in BBS individuals from inbred and outbred background. In a worldwide cohort of 45 families, we identified, via direct exon sequencing, causative homozygous mutations in 20 families. Eleven of these mutations were novel, thereby increasing the number of known BBS mutations by 5% (11/218). Thus, in the presence of extreme genetic locus heterogeneity, homozygosity mapping provides a valuable approach to the molecular genetic diagnosis of BBS and will facilitate the discovery of novel pathogenic mutations.
doi:10.1136/jmg.2009.071365
PMCID: PMC3017466  PMID: 19797195
Molecular Genetics
5.  Short Stature—Physiology and Pathology 
Western Journal of Medicine  1986;144(6):710-721.
Stature, the quantitative measure of height, varies widely within each ethnic group with a fairly normal distribution. Of the numerous patients whom physicians encounter because of short stature, relatively few are pathologically small in the context of family and ethnic background. Physicians must be able to differentiate pathologic short stature from the lower end of the normal curve before embarking on a complex diagnostic evaluation. There are literally hundreds of different causes of short stature, and the clinical evaluation requires a wide variety of clinical, radiographic, pathologic and biochemical tools. Although specific treatment to promote growth is available only in persons with the endocrinopathies and the acquired nutritional, emotional and chronic disease states, diagnosis of the specific form of short stature can have great importance in being able to prevent complications and to offer accurate prognostic information and genetic counseling.
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PMCID: PMC1306754  PMID: 2873688

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