Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2

Min Shi; Diana Caprau; Paul Romitti; Kaare Christensen; Jeffrey C Murray

doi:10.1002/bdra.10076

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Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2

Journal article

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Peer reviewed

Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2

Min Shi, Diana Caprau, Paul Romitti, Kaare Christensen and Jeffrey C Murray

Birth defects research. A Clinical and molecular teratology, Vol.67(8), pp.545-549

08/2003

DOI: 10.1002/bdra.10076

PMID: 14632302

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Abstract

Genetic variation in enzymes involved in vitamin metabolism is a candidate for analysis in studies of how nutritional covariates may impact a disease state. The role of folate pathway genes in birth defects and cardiovascular disease in humans has been widely studied. Since incidence rates for these disorders vary by geographic origins, it is useful to know which variants are the best candidates for studies based on genotype and allele frequency, as well as linkage disequilibrium (LD) in founder populations. Six polymorphisms in five folate metabolism-related genes (MTHFR, MTHFD, MTRR, GCP2, and RFC1) were genotyped on a collection of 1064 DNA samples from populations around the world, which were made available by the Centre d'Etude du Polymorphisme Humain (CEPH) consortium for analysis. In this study we report the genotype frequencies for variants in the MTHFR, MTHFD, MTRR, GCP2, and RFC1 genes, and the LD for two variants (C677T and A1298C) in MTHFR. The rare allele frequency for each of the five genes studied varied widely. LD is strongest in Pakistani and Brazilian populations (D' = 1.0) and weakest in Mexican populations (D' = 0.45). These findings will allow the selection of variants that will provide the most power in studies of folate pathway genes involving different ancestral populations, and contribute to our knowledge of the population distribution of selected nutritional gene variants.

Genetics, Population

Microtubule-Associated Proteins - genetics

Signal Transduction

Membrane Proteins - genetics

Gene Frequency

Humans

Cells, Cultured

Genotype

Linkage Disequilibrium

Carrier Proteins - genetics

Methylenetetrahydrofolate Reductase (NADPH2) - genetics

Ferredoxin-NADP Reductase - genetics

Membrane Transport Proteins

Folic Acid - metabolism

Polymorphism, Single Nucleotide

Methylenetetrahydrofolate Dehydrogenase (NADP) - genetics

Details

Title: Subtitle: Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2
Creators: Min Shi - Biology Department, University of Iowa, Iowa City, Iowa 52242, USA
Diana Caprau
Paul Romitti
Kaare Christensen
Jeffrey C Murray
Resource Type: Journal article
Publication Details: Birth defects research. A Clinical and molecular teratology, Vol.67(8), pp.545-549
DOI: 10.1002/bdra.10076
PMID: 14632302
NLM abbreviation: Birth Defects Res A Clin Mol Teratol
ISSN: 1542-0752
eISSN: 1542-0760
Publisher: Wiley; United States
Grant note: ES10876 / NIEHS NIH HHS DE08559 / NIDCR NIH HHS U50 CCU71328 / ODCDC CDC HHS DE13076 / NIDCR NIH HHS R01 DE 11948 / NIDCR NIH HHS
Language: English
Date published: 08/2003
Academic Unit: Anatomy and Cell Biology; International Programs; Stead Family Department of Pediatrics; Epidemiology; Biostatistics; Pediatric Dentistry; Craniofacial Anomalies Research Center; Nursing; Public Policy Center (Archive); Dental Research
Record Identifier: 9983995180902771

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