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Series GSE45149 Query DataSets for GSE45149
Status Public on Apr 01, 2013
Title The MLH1 c.-27C>A and c.85G>T variants are borne on a European ancestral haplotype which underlies an autosomal dominant form of MLH1 epimutation.
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Lynch syndrome, caused by germline heterozygous mutations of the DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2, or deletions affecting the EPCAM gene upstream of MSH2, is characterized by a predisposition to early-onset colorectal and additional extracolonic cancers. An alternative but rare cause of Lynch syndrome is a constitutional epimutation of MLH1, which is characterized by promoter methylation and transcriptional silencing of a single allele in normal tissues. Worldwide, five families with autosomal dominant transmission of a constitutional MLH1 epimutation linked to an MLH1 haplotype with two single nucleotide variants (c.-27C>A and c.85G>T) have been identified.
Array-based genotyping using Affymetrix SNP 6.0 data in four of these families revealed a shared haplotype extending across a ≤2.6 Mb region of chromosome 3p22 encompassing MLH1 and additional flanking genes, indicating common ancestry.
Overall design Genomic DNA from 5 carriers of the c.-27C>A and c.85G>T variants was hybridized on Affymetrix SNP6.0 array according to manufacturer's procedures
Contributor(s) Kwok C, Vogelaar IP, van Zelst-Stams WA, Mensenkamp AR, Ligtenberg MJ, Rapkins RW, Ward RL, Chun N, Ladabaum U, McKinnon WC, Greenblatt MS, Hitchins MP
Citation(s) 24084575
Submission date Mar 13, 2013
Last update date Oct 23, 2019
Contact name Ingrid Vogelaar
Organization name Radboud University Medical Centre
Department Human Genetics
Street address Geert Grooteplein Zuid 10
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (5)
GSM1098060 F2-II1
GSM1098061 F2-II3
GSM1098062 F1-II2
BioProject PRJNA192973

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45149_RAW.tar 213.0 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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