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Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects
Author(s) -
Liu Wennuan,
Chang Baoli,
Li Tao,
Dimitrov Latchezar,
Kim Seungchan,
Kim Jin Woo,
Turner Aubrey R.,
Meyers Deborah A.,
Trent Jeffery M.,
Zheng Siqun Lilly,
Isaacs William B.,
Xu Jianfeng
Publication year - 2006
Publication title -
the prostate
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.295
H-Index - 123
eISSN - 1097-0045
pISSN - 0270-4137
DOI - 10.1002/pros.20441
Subject(s) - single nucleotide polymorphism , germline , genotyping , genetics , snp array , biology , snp , snp genotyping , allele , genetic association , copy number variation , genome wide association study , allele frequency , genome , computational biology , genotype , gene
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. Prostate 67:227–233, 2007. © 2006 Wiley‐Liss, Inc.