ArticleBMC bioinformatics2009
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family.BMC medical genomics · 2019Article
- Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease.Nature genetics · 2019Article
- Atypical Familial Amyotrophic Lateral Sclerosis with Slowly Progressing Lower Extremities-predominant Late-onset Muscular Weakness and Atrophy.Internal medicine (Tokyo, Japan) · 2019Article
- Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy.Nature genetics · 2018Article
- A Homozygous LAMA2 Mutation of c.818G>A Caused Partial Merosin Deficiency in a Japanese Patient.Internal medicine (Tokyo, Japan) · 2018Article
- Partial duplication ofAnnals of clinical and translational neurology · 2017Article
- A de novo mutation of the MYH7 gene in a large Chinese family with autosomal dominant myopathy.Human genome variation · 2015Article
- ERBB4 mutations that disrupt the neuregulin-ErbB4 pathway cause amyotrophic lateral sclerosis type 19.American journal of human genetics · 2013Article
- A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees.Bioinformatics (Oxford, England) · 2013Article
- The TRK-fused gene is mutated in hereditary motor and sensory neuropathy with proximal dominant involvement.American journal of human genetics · 2012Article
- Posterior column ataxia with retinitis pigmentosa in a Japanese family with a novel mutation in FLVCR1.Neurogenetics · 2011Article
- Dominant mutations in RP1L1 are responsible for occult macular dystrophy.American journal of human genetics · 2010Article
- Genetics of neurodegenerative diseases: insights from high-throughput resequencing.Human molecular genetics · 2010Review
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10 authors.
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Abstract
backgroundDuring this recent decade, microarray-based single nucleotide polymorphism (SNP) data are becoming more widely used as markers for linkage analysis in the identification of loci for disease-associated genes. Although microarray-based SNP analyses have markedly reduced genotyping time and cost compared with microsatellite-based analyses, applying these enormous data to linkage analysis programs is a time-consuming step, thus, necessitating a high-throughput platform.
resultsWe have developed SNP HiTLink (SNP High Throughput Linkage analysis system). In this system, SNP chip data of the Affymetrix Mapping 100 k/500 k array set and Genome-Wide Human SNP array 5.0/6.0 can be directly imported and passed to parametric or model-free linkage analysis programs; MLINK, Superlink, Merlin and Allegro. Various marker-selecting functions are implemented to avoid the effect of typing-error data, markers in linkage equilibrium or to select informative data.
conclusionThe results using the 100 k SNP dataset were comparable or even superior to those obtained from analyses using microsatellite markers in terms of LOD scores obtained. General personal computers are sufficient to execute the process, as runtime for whole-genome analysis was less than a few hours. This system can be widely applied to linkage analysis using microarray-based SNP data and with which one can expect high-throughput and reliable linkage analysis.
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