Population-specific variation in haplotype composition and heterozygosity at the POLB locus

Jennifer Yamtich; William C. Speed; Eva Straka; Judith R. Kidd; Joann B. Sweasy; Kenneth K. Kidd

doi:10.1016/j.dnarep.2008.12.005

Population-specific variation in haplotype composition and heterozygosity at the POLB locus

Jennifer Yamtich, William C. Speed, Eva Straka, Judith R. Kidd, Joann B. Sweasy, Kenneth K. Kidd

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Abstract

DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.

Original language	English (US)
Pages (from-to)	579-584
Number of pages	6
Journal	DNA Repair
Volume	8
Issue number	5
DOIs	https://doi.org/10.1016/j.dnarep.2008.12.005
State	Published - May 1 2009
Externally published	Yes

Keywords

Alleles
Haplotypes
POLB
Population genetics
Single nucleotide polymorphisms
Variation

ASJC Scopus subject areas

Biochemistry
Molecular Biology
Cell Biology

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10.1016/j.dnarep.2008.12.005

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title = "Population-specific variation in haplotype composition and heterozygosity at the POLB locus",

abstract = "DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.",

keywords = "Alleles, Haplotypes, POLB, Population genetics, Single nucleotide polymorphisms, Variation",

author = "Jennifer Yamtich and Speed, {William C.} and Eva Straka and Kidd, {Judith R.} and Sweasy, {Joann B.} and Kidd, {Kenneth K.}",

note = "Funding Information: This work was funded, in part, by National Institute of Health grants GM057672 to Kenneth K. Kidd and NCICA16038 funded to Joann B. Sweasy. None of the authors has any conflicts of interest related to the data presented here. We thank all the colleagues who helped us assemble the population samples, the Corriell Institute for Medical Research (NIGMS Human Genetic Cell Repository), and The National Laboratory for the Genetics of Israeli Populations at Tel-Aviv University. Special thanks are due the many hundreds of individuals from these populations who volunteered to give blood samples for studies such as this.",

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doi = "10.1016/j.dnarep.2008.12.005",

language = "English (US)",

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AU - Yamtich, Jennifer

AU - Speed, William C.

AU - Straka, Eva

AU - Kidd, Judith R.

AU - Sweasy, Joann B.

AU - Kidd, Kenneth K.

N1 - Funding Information: This work was funded, in part, by National Institute of Health grants GM057672 to Kenneth K. Kidd and NCICA16038 funded to Joann B. Sweasy. None of the authors has any conflicts of interest related to the data presented here. We thank all the colleagues who helped us assemble the population samples, the Corriell Institute for Medical Research (NIGMS Human Genetic Cell Repository), and The National Laboratory for the Genetics of Israeli Populations at Tel-Aviv University. Special thanks are due the many hundreds of individuals from these populations who volunteered to give blood samples for studies such as this.

PY - 2009/5/1

Y1 - 2009/5/1

N2 - DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.

AB - DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.

KW - Alleles

KW - Haplotypes

KW - POLB

KW - Population genetics

KW - Single nucleotide polymorphisms

KW - Variation

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Population-specific variation in haplotype composition and heterozygosity at the POLB locus

Abstract

Keywords

ASJC Scopus subject areas

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