Centre d'Etude du polymorphisme humain (CEPH): Collaborative genetic mapping of the human genome

Dausset, J; Cann, Howard M.; Cohen, Daniel; Lathrop, Mark; Lalouel, Jean-Marc; White, Ray

doi:10.1016/0888-7543(90)90491-c

Cited by 534 publications

(345 citation statements)

References 9 publications

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“…A sample of CEPH DNA from the Coriell Institute was used as an unmethylated control in pyrosequencing analyses. 25 Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) SALSA MS-MLPA ME011 kit (MRC Holland, Amsterdam) is based on the use of probes that contain a digestion site specific for the methylation-sensitive HhaI enzyme. All reactions were carried out using 100 ng of DNA.…”

Section: Mlh1 Promoter Methylation Analysesmentioning

confidence: 99%

MLH1 methylation screening is effective in identifying epimutation carriers

et al. 2012

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Recently, constitutional MLH1 epimutations have been identified in a subset of Lynch syndrome (LS) cases. The aim of this study was the identification of patients harboring constitutional MLH1 epimutations in a set of 34 patients with a clinical suspicion of LS, MLH1-methylated tumors and non-detected germline mutations in mismatch repair (MMR) genes. MLH1 promoter methylation was analyzed in lymphocyte DNA samples by MS-MLPA (Methylation-specific multiplex ligation-dependent probe amplification). Confirmation of MLH1 constitutional methylation was performed by MS-MCA (Methylation-specific melting curve analysis), bisulfite sequencing and pyrosequencing in different biological samples. Allelic expression was determined using heterozygous polymorphisms. Vertical transmission was evaluated by MS-MLPA and haplotype analyses. MS-MLPA analysis detected constitutional MLH1 methylation in 2 of the 34 individuals whose colorectal cancers showed MLH1 methylation (5.9%). These results were confirmed by bisulfite-based methods. Both epimutation carriers had developed metachronous early-onset LS tumors, with no family history of LS-associated cancers in their first-degree relatives. In one of the cases, the identified MLH1 constitutional methylation was monoallelic and results in MLH1 and EPM2AIP1 allele-specific transcriptional silencing. It was present in normal somatic tissues and absent in spermatozoa. The methylated MLH1 allele was maternally transmitted and methylation was reversed in a daughter who inherited the same allele. MLH1 methylation screening in lymphocyte DNA from patients with early-onset MLH1-methylated LS-associated tumors allows the identification of epimutation carriers. The present study adds further evidence to the emerging entity of soma-wide MLH1 epimutation and its heritability.

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Section: Mlh1 Promoter Methylation Analysesmentioning

confidence: 99%

MLH1 methylation screening is effective in identifying epimutation carriers

et al. 2012

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“…Since not all E coR l frag ments detected by p l3 E -ll can be identified using conventional agarose gels, the polymorphism was scored as a two-or three-allele system. Individuals with only fragments larger than 28 kb were scored as homozygous (1,1) and individuals with a frag ment smaller than 28 kb were scored as heterozy gous (1,2).…”

Section: A T E R Ia L S a N D M E T H O D Smentioning

confidence: 99%

The FSHD-linked locus D4F104S1 (p13E-11) ON 4q35 has a homologue on 10qter

et al. 1995

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Please be advised that this information was generated on 2018-05-08 and may be subject to change.Facioscapulohumeral muscular dystrophy (FSHD) has recently been shown to be associated with deletions that are detectable using probe p13E-11 (D4F104S1). Although these deletions reside within large, highly polymorphic restriction fragments (20-300 kb), the " mutant" fragment is usually shorter than 28 kb and can routinely be detected using conventional agarose gel electrophoresis. Yet, the complete vi sualization of the alleles requires pulsed-field gel electrophoresis (PFGE). Family studies showed that p13E-11 detects two nonallelic loci in this size range, only one of which originates from chromosome 4q35. We have assigned the other p13E-11 locus to chromosome lOqter by linkage analysis in CEPH pedigrees. Knowing the location of both loci improves the diagnostic reliability, as the exact origin of "small" EcoRI fragments can be determined by haplotyping. Since FSHD shows ge netic heterogeneity, this 10qter locus became an interesting candidate to be the second FSHD locus. However, analysis of a large chromosome 4-unlinked FSHD family did not provide evidence for linkage on chro mosome 10qter>

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“…We want to emphasize that this approach is able to generate realistic dependence structures for markers as well as expressions. Real marker data was obtained from the CEPH genotype database (Dausset et al, 1990). Fifteen families from the CEPH/Utah family collection were selected with the family identifiers 1334, 1340, 1345, 1346, 1349, 1350, 1358, 1362, 1375, 1377, 1408, 1418, 1421, 1424 and 1477.…”

Section: Simulationsmentioning

confidence: 99%

Correcting for relatedness in Bayesian models for genomic data association analysis

Pikkuhookana

Sillanpää

2009

Heredity

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For small pedigrees, the issue of correcting for known or estimated relatedness structure in population-based Bayesian multilocus association analysis is considered. Two such relatedness corrections: [1] a random term arising from the infinite polygenic model and [2] a fixed covariate following the class D model of Bonney, are compared with the case of no correction using both simulated and real marker and geneexpression data from lymphoblastoid cell lines from four CEPH families. This comparison is performed with clinical quantitative trait locus (cQTL) models-multilocus association models where marker data and expression levels of gene transcripts as well as possible genotype Â expression interaction terms are jointly used to explain quantitative trait variation. We found out that regardless of having a correction term in the model, the cQTL-models fit a few extra smalleffect components (similar to finite polygenic models) which itself serves as a relatedness correction. For small data and small heritability one may use the covariate model, which clearly outperforms the infinite polygenic model in small data examples.

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Centre d'Etude du polymorphisme humain (CEPH): Collaborative genetic mapping of the human genome

Cited by 534 publications

References 9 publications

MLH1 methylation screening is effective in identifying epimutation carriers

MLH1 methylation screening is effective in identifying epimutation carriers

The FSHD-linked locus D4F104S1 (p13E-11) ON 4q35 has a homologue on 10qter

Correcting for relatedness in Bayesian models for genomic data association analysis

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