Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects

Wennuan Liu; Baoli Chang; Tao Li; Latchezar Dimitrov; Seungchan Kim; Woo Kim Jin; Aubrey R. Turner; Deborah A. Meyers; Jeffery M. Trent; Siqun Lilly Zheng; William B. Isaacs; Jianfeng Xu

doi:10.1002/pros.20441

Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects

Wennuan Liu, Baoli Chang, Tao Li, Latchezar Dimitrov, Seungchan Kim, Woo Kim Jin, Aubrey R. Turner, Deborah A. Meyers, Jeffery M. Trent, Siqun Lilly Zheng, William B. Isaacs, Jianfeng Xu

School of Medicine

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

3 Scopus citations

Abstract

BACKGROUND. Recent studies using ROMA and Array-CGH suggest that germline copy number polymorphisms (CNPs) involving >100 kb are common in humans. METHODS. In this study, we used the Affymetrix GeneChip 100K single nucleotide polymorphisms (SNP) mapping panel to further examine the type and frequency of germline CNPs in the genome. By utilizing the allele intensity data generated while genotyping ∼116,000 SNPs among 23 subjects from 4 families, we were able to detect multiple CNPs. RESULTS. However, in contrast to several previous studies, we found that CNPs >100 kb are rare in the genome but CNPs involving 100s-1,000s of base pairs are more common. CONCLUSIONS. We have demonstrated the utility of this approach, which has an important advantage over other methods because it is able to simultaneously assess both CNPs and SNPs, and therefore has great potential in genetic association studies of common diseases.

Original language	English (US)
Pages (from-to)	227-233
Number of pages	7
Journal	Prostate
Volume	67
Issue number	3
DOIs	https://doi.org/10.1002/pros.20441
State	Published - Feb 15 2007

Keywords

DNA copy number polymorphisms (CNPs)
Genomewide
Germline

ASJC Scopus subject areas

Oncology
Urology

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10.1002/pros.20441

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title = "Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects",

abstract = "BACKGROUND. Recent studies using ROMA and Array-CGH suggest that germline copy number polymorphisms (CNPs) involving >100 kb are common in humans. METHODS. In this study, we used the Affymetrix GeneChip 100K single nucleotide polymorphisms (SNP) mapping panel to further examine the type and frequency of germline CNPs in the genome. By utilizing the allele intensity data generated while genotyping ∼116,000 SNPs among 23 subjects from 4 families, we were able to detect multiple CNPs. RESULTS. However, in contrast to several previous studies, we found that CNPs >100 kb are rare in the genome but CNPs involving 100s-1,000s of base pairs are more common. CONCLUSIONS. We have demonstrated the utility of this approach, which has an important advantage over other methods because it is able to simultaneously assess both CNPs and SNPs, and therefore has great potential in genetic association studies of common diseases.",

keywords = "DNA copy number polymorphisms (CNPs), Genomewide, Germline",

author = "Wennuan Liu and Baoli Chang and Tao Li and Latchezar Dimitrov and Seungchan Kim and Jin, {Woo Kim} and Turner, {Aubrey R.} and Meyers, {Deborah A.} and Trent, {Jeffery M.} and Zheng, {Siqun Lilly} and Isaacs, {William B.} and Jianfeng Xu",

year = "2007",

month = feb,

day = "15",

doi = "10.1002/pros.20441",

language = "English (US)",

volume = "67",

pages = "227--233",

journal = "Prostate",

issn = "0270-4137",

publisher = "Wiley-Liss Inc.",

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TY - JOUR

T1 - Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects

AU - Liu, Wennuan

AU - Chang, Baoli

AU - Li, Tao

AU - Dimitrov, Latchezar

AU - Kim, Seungchan

AU - Jin, Woo Kim

AU - Turner, Aubrey R.

AU - Meyers, Deborah A.

AU - Trent, Jeffery M.

AU - Zheng, Siqun Lilly

AU - Isaacs, William B.

AU - Xu, Jianfeng

PY - 2007/2/15

Y1 - 2007/2/15

N2 - BACKGROUND. Recent studies using ROMA and Array-CGH suggest that germline copy number polymorphisms (CNPs) involving >100 kb are common in humans. METHODS. In this study, we used the Affymetrix GeneChip 100K single nucleotide polymorphisms (SNP) mapping panel to further examine the type and frequency of germline CNPs in the genome. By utilizing the allele intensity data generated while genotyping ∼116,000 SNPs among 23 subjects from 4 families, we were able to detect multiple CNPs. RESULTS. However, in contrast to several previous studies, we found that CNPs >100 kb are rare in the genome but CNPs involving 100s-1,000s of base pairs are more common. CONCLUSIONS. We have demonstrated the utility of this approach, which has an important advantage over other methods because it is able to simultaneously assess both CNPs and SNPs, and therefore has great potential in genetic association studies of common diseases.

AB - BACKGROUND. Recent studies using ROMA and Array-CGH suggest that germline copy number polymorphisms (CNPs) involving >100 kb are common in humans. METHODS. In this study, we used the Affymetrix GeneChip 100K single nucleotide polymorphisms (SNP) mapping panel to further examine the type and frequency of germline CNPs in the genome. By utilizing the allele intensity data generated while genotyping ∼116,000 SNPs among 23 subjects from 4 families, we were able to detect multiple CNPs. RESULTS. However, in contrast to several previous studies, we found that CNPs >100 kb are rare in the genome but CNPs involving 100s-1,000s of base pairs are more common. CONCLUSIONS. We have demonstrated the utility of this approach, which has an important advantage over other methods because it is able to simultaneously assess both CNPs and SNPs, and therefore has great potential in genetic association studies of common diseases.

KW - DNA copy number polymorphisms (CNPs)

KW - Genomewide

KW - Germline

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DO - 10.1002/pros.20441

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ER -

Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects

Abstract

Keywords

ASJC Scopus subject areas

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