ArticleBioinformatics (Oxford, England)2013
A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- A rare 5'UTR variant in SEC24D reveals translational dysfunction in osteogenesis imperfecta: a roadmap for RNA therapeutic rescue.Scientific reports · 2026Article
- Griscelli Syndrome Type 2: Comprehensive Analysis of 149 New and Previously Described Patients with RAB27A Deficiency.Journal of clinical immunology · 2024Article
- Genome-Wide Mapping of Consanguineous Families Confirms Previously Implicated Gene Loci and Suggests New Loci in Specific Language Impairment (SLI).Children (Basel, Switzerland) · 2024Article
- Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities.Nature genetics · 2024Article
- IHH enhancer variant within neighboring NHEJ1 intron causes microphthalmia anophthalmia and coloboma.NPJ genomic medicine · 2023Article
- C-terminal frameshift variant of TDP-43 with pronounced aggregation-propensity causes rimmed vacuole myopathy but not ALS/FTD.Acta neuropathologica · 2023Article
- Familial multiple discoid fibromas is linked to a locus on chromosome 5 including the FNIP1 gene.Journal of human genetics · 2023Article
- PRDM10 directs FLCN expression in a novel disorder overlapping with Birt-Hogg-Dubé syndrome and familial lipomatosis.Human molecular genetics · 2023Article
- Limb girdle muscular disease caused byProceedings of the National Academy of Sciences of the United States of America · 2023Article
- The role of GPD1L, a sodium channel interacting gene, in the pathogenesis of Brugada Syndrome.Frontiers in medicine · 2023Article
- Sonic Hedgehog Intron Variant Associated With an Unusual Pediatric Cortical Cataract.Investigative ophthalmology & visual science · 2022Article
- Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment.Journal of speech, language, and hearing research : JSLHR · 2020Article
- How to Assess Founder Effect in Patients with Congenital Factor XIII Deficiency.International journal of hematology-oncology and stem cell research · 2020Review
- Identification of ADHD risk genes in extended pedigrees by combining linkage analysis and whole-exome sequencing.Molecular psychiatry · 2020Article
- Long-range cis-regulatory elements controlling GDF6 expression are essential for ear development.The Journal of clinical investigation · 2020Article
- Mutations in COMP cause familial carpal tunnel syndrome.Nature communications · 2020Article
- Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma.PLoS genetics · 2020Article
- Loss of ADAMTS19 causes progressive non-syndromic heart valve disease.Nature genetics · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
14 authors.
Funding
Abstract
motivationThe 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.
resultsComputations 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.