SNPs in genes with copy number variation: A question of specificity

Sengupta, Mainak; Ray, Ananya; Chaki, Moumita; Maulik, Mahua; Ray, Kunal

doi:10.1007/s12041-008-0014-6

Cited by 2 publications

(1 citation statement)

References 3 publications

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“…The allele frequencies of PTPN22, BANK1, Blk , and FCGR2B were very similar for patients with MMN and controls. The distribution of FCGR2B genotypes was not in Hardy–Weinberg equilibrium due to a higher than expected number of heterozygotes, which may be explained by variation in copy numbers ( Sengupta et al, 2008 ) . Especially, as the FCGR locus evolved through gene copying ( van Sorge et al, 2003 ) .…”

Section: Discussionmentioning

confidence: 91%

Multifocal motor neuropathy is not associated with genetic variation in PTPN22, BANK1, Blk, FCGR2B, CD1A/E, and TAG‐1 genes

Vlam

Cats

Seelen

et al. 2011

J Peripheral Nervous Sys

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The contribution of genetic heterogeneity to the pathogenesis of multifocal motor neuropathy (MMN) has not been elucidated. We investigated frequencies of single nucleotide polymorphisms (SNPs) in the candidate genes protein tyrosine phosphatase, non-receptor type 22 (PTPN22), B-cell scaffold protein with ankyrin repeats (BANK1), B lymphocyte kinase (Blk), and Fc gamma receptor class IIB (FCGR2B), which have been found to be associated with other autoimmune diseases, CD1A and CD1E, important for antigen presentation of glycolipids, and transient axonal glycoprotein 1 (TAG-1), which is associated with responsiveness to intravenous immunoglobulin in patients with chronic inflammatory demyelinating polyneuropathy. SNP frequencies were determined by means of TaqMan SNP genotyping assay and direct sequencing of candidate genes in 92 Dutch patients with MMN and 1152 healthy controls. SNP frequencies did not differ between patients and controls (all p-values >0.15) and disease characteristics were not associated with SNP genotypes. Our results suggest that allelic variation in these genes does not play a major role in determining MMN susceptibility.

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Section: Discussionmentioning

confidence: 91%

Multifocal motor neuropathy is not associated with genetic variation in PTPN22, BANK1, Blk, FCGR2B, CD1A/E, and TAG‐1 genes

Vlam

Cats

Seelen

et al. 2011

J Peripheral Nervous Sys

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dbDNV: a resource of duplicated gene nucleotide variants in human genome

Chen

Lin

2010

Nucleic Acids Research

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Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotide polymorphism (SNP) from individuals. This imperfection is undistinguishable in current genotyping methods. As the next-generation sequencing technologies become more popular for sequence-based association studies, numerous ambiguous SNPs are rapidly accumulated. Thus, analyzing duplication variations in the reference genome to assist in preventing false positive SNPs is imperative. We have identified >10% of human genes associated with duplicated gene loci (DGL). Through meticulous sequence alignments of DGL, we systematically designated 1 236 956 variations as duplicated gene nucleotide variants (DNVs). The DNV database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) has been established to promote more accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304 110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. This is useful while ∼58% of exonic SNPs in DGL are DNV-coupled. Because of high accumulation of ambiguous SNPs, we suggest that annotating SNPs with DNVs possibilities should improve association studies of these variants with human diseases.

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SNPs in genes with copy number variation: A question of specificity

Cited by 2 publications

References 3 publications

Multifocal motor neuropathy is not associated with genetic variation in PTPN22, BANK1, Blk, FCGR2B, CD1A/E, and TAG‐1 genes

Multifocal motor neuropathy is not associated with genetic variation in PTPN22, BANK1, Blk, FCGR2B, CD1A/E, and TAG‐1 genes

dbDNV: a resource of duplicated gene nucleotide variants in human genome

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