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

Research output: Contribution to journalArticle

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 languageEnglish (US)
Pages (from-to)227-233
Number of pages7
JournalProstate
Volume67
Issue number3
DOIs
StatePublished - Feb 15 2007

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DNA Copy Number Variations
Single Nucleotide Polymorphism
Nucleotide Mapping
Genome
Genetic Association Studies
Base Pairing
Alleles

Keywords

  • DNA copy number polymorphisms (CNPs)
  • Genomewide
  • Germline

ASJC Scopus subject areas

  • Urology

Cite this

Liu, W., Chang, B., Li, T., Dimitrov, L., Kim, S., Jin, W. K., ... Xu, J. (2007). Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects. Prostate, 67(3), 227-233. https://doi.org/10.1002/pros.20441

Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects. / Liu, Wennuan; Chang, Baoli; Li, Tao; Dimitrov, Latchezar; Kim, Seungchan; Jin, Woo Kim; Turner, Aubrey R.; Meyers, Deborah A.; Trent, Jeffery M.; Zheng, Siqun Lilly; Isaacs, William B; Xu, Jianfeng.

In: Prostate, Vol. 67, No. 3, 15.02.2007, p. 227-233.

Research output: Contribution to journalArticle

Liu, W, Chang, B, Li, T, Dimitrov, L, Kim, S, Jin, WK, Turner, AR, Meyers, DA, Trent, JM, Zheng, SL, Isaacs, WB & Xu, J 2007, 'Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects', Prostate, vol. 67, no. 3, pp. 227-233. https://doi.org/10.1002/pros.20441
Liu, Wennuan ; Chang, Baoli ; Li, Tao ; Dimitrov, Latchezar ; Kim, Seungchan ; Jin, Woo Kim ; Turner, Aubrey R. ; Meyers, Deborah A. ; Trent, Jeffery M. ; Zheng, Siqun Lilly ; Isaacs, William B ; Xu, Jianfeng. / Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects. In: Prostate. 2007 ; Vol. 67, No. 3. pp. 227-233.
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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

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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.

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