An update on conformation sensitive gel electrophoresis

Ganguly, Arupa

doi:10.1002/humu.10059

Cited by 84 publications

(65 citation statements)

References 25 publications

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“…Unlike conventional CSGE, all PCR amplicons were labeled by fluorescent dye and migrated along the F-CSGE (36 cm) gel (Ganguly, 2002). Prior to the regular application of F-CSGE scanning, 30 samples of each of the 75 fragments were fully analyzed by both F-CSGE and direct sequencing.…”

Section: Discussionmentioning

confidence: 99%

BRCA1 andBRCA2 germline mutations in Korean patients with sporadic breast cancer

et al. 2004

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In order to evaluate the role of BRCA1 and BRCA2 germline mutations in Korean patients with sporadic breast cancer, 97 patients with sporadic breast cancer were analyzed for mutations in the BRCA1 and BRCA2 coding regions, by using a combination of fluorescentconformation sensitive gel electrophoresis (F-CSGE) and direct sequencing. Fifty-five distinct sequence variants were detected, which included three pathogenic truncating mutations, 15 missense mutations, 16 polymorphisms, and 21 intronic variants. Twenty-six of these variants have never been previously reported and may be of Korean-specific origin. Two pathogenic BRCA1 mutations (c.922_924delinsT, c.5445G>A) and one pathogenic BRCA2 mutation (c.2259delT) were observed, and two of these (BRCA1 c.5445G>A and BRCA2 c.2259delT) are novel. The total prevalence of germline pathogenic mutations in BRCA1 and/or BRCA2 in Korean sporadic breast cancer is estimated to be about 3.1%. Considering that the majority of breast cancer cases are sporadic, the present study will be helpful in the evaluation of the need for the genetic screening of germline BRCA mutations in sporadic breast cancer patients. Further study using a larger sample size is required to determine the merits of genetic diagnosis and counseling in breast cancer patients.

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Section: Discussionmentioning

confidence: 99%

BRCA1 andBRCA2 germline mutations in Korean patients with sporadic breast cancer

et al. 2004

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“…The partial genotyping approach can also be applied to any other mutation screening technique that detects heteroduplexes, such as conformation-sensitive gel electrophoresis (Ganguly, 2002). The LD summary measure (Devlin & Risch, 1995) is suitable in the context of this study, since a high value for | | between two SNPs implies that they provide the same power for association mapping (Dunning et al 2000).…”

Section: Prior Estimation Of Snp Frequencies and Ld Relationshipsmentioning

confidence: 99%

Genetic Variation at the Chromosome 16 Chemokine Gene Cluster: Development of a Strategy for Association Studies in Complex Disease

Fisher¹,

Moody²,

Mirza³

et al. 2003

Annals of Human Genetics

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SummaryThe chemokine gene cluster [CCL22, CX3CL1, CCL17] (previously known as [SCYA22, SCYD1, SCYA17]) is a candidate locus for one of the susceptibility genes for inflammatory bowel disease that are located in the peri‐centromeric region of chromosome 16. Screening for sequence variation at this locus led to the detection of 14 single nucleotide polymorphisms (SNPs). An efficient experimental and computational approach was developed to estimate allele frequencies and pairwise linkage disequilibrium relationships between SNPs at this locus, and to test them for association with inflammatory bowel disease. The 12 common SNPs were assigned to 5 distinct linkage disequilibrium groups. Genotyping of one SNP from each linkage disequilibrium group in a large cohort of families with inflammatory bowel disease did not provide convincing evidence of association with either Crohn's disease or ulcerative colitis. We describe an efficient experimental design from SNP screening to association testing. This strategy can be used to test candidate genes for involvement in susceptibility to complex disease.

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“…Primers to amplify the coding sequence and intron-exon boundaries were designed for each gene using primer3 software (http:// www.genome.wi.mit.edu/cgu-bin/primer/primer3, primers and conditions available on request). The genes were screened using Conformation Sensitive Gel Electrophoresis, 13 which we estimate has a 495% sensitivity for the detection of small insertions and deletions and at least 90% sensitivity for base substitutions. The 5 Mb genomic sequence surrounding each gene was downloaded from the UCSC genome browser and scanned for repeat elements.…”

Section: Patientsmentioning

confidence: 99%

Evaluation of NSD2 and NSD3 in overgrowth syndromes

et al. 2004

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Sotos syndrome is an overgrowth condition predominantly caused by truncating mutations, missense mutations restricted to functional domains, or deletions of NSD1. NSD1 is a member of a protein family that includes NSD2 and NSD3, both of which show 70-75% sequence identity with NSD1. This strong sequence similarity suggests that abrogation of NSD2 or NSD3 function may cause non-NSD1 Sotos cases or other overgrowth phenotypes. To evaluate this hypothesis, we mutationally screened NSD2 and NSD3 in 78 overgrowth syndrome cases in which NSD1 mutations and deletions had been excluded. Additionally, we used microsatellite markers within the vicinity of the genes to look for whole gene deletions. No truncating mutations or gene deletions were identified in either gene. We identified two conservative missense NSD2 alterations in two non-Sotos overgrowth cases but neither was within a functional domain. We identified three synonymous and two intronic variants in NSD2 and two synonymous base substitutions in NSD3. Our results suggest that despite strong sequence similarity between NSD1, NSD2 and NSD3, the latter genes are unlikely to be making a substantial contribution to overgrowth phenotypes and thus may operate in distinct functional pathways from NSD1.

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An update on conformation sensitive gel electrophoresis

Abstract: Conformation-sensitive gel electrophoresis (CSGE) was developed as a method of heteroduplex

Cited by 84 publications

References 25 publications

BRCA1 andBRCA2 germline mutations in Korean patients with sporadic breast cancer

BRCA1 andBRCA2 germline mutations in Korean patients with sporadic breast cancer

Genetic Variation at the Chromosome 16 Chemokine Gene Cluster: Development of a Strategy for Association Studies in Complex Disease

Evaluation of NSD2 and NSD3 in overgrowth syndromes

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