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PMID: 16193324 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Allelic imbalance analysis of oral tongue squamous cell carcinoma by high-density single nucleotide polymorphism arrays using whole-genome amplified DNA.

Human genetics ·Vol. 118 ·No. 3-4 ·2005-12-00 ·Pages 504-7

Zhou X, Temam S, Chen Z, Ye H, Mao L, Wong DT

Abstract

Multiple displacement-based whole-genome DNA amplification is a promising tool to obtain sufficient DNA from small tissue specimens for various genetic analyses, such as SNP array-based analysis. Using Affymetrix 10 K and 100 K SNP mapping array, we evaluated the performance of the Phi29 DNA polymerase-based genome amplification. Greater than 99% concordance in genotyping calls were achieved between amplified and non-amplified DNAs for both arrays. By utilizing the Affymetrix GeneChip Chromosome Copy Number Tool, the allelic imbalance profiles for the advanced stage oral tongue squamous cell carcinoma (OTSCC) were generated based on 10 K and 100 K SNP mapping array results. The results from these two array platforms agree closely, but more precise allelic imbalance patterns can be revealed from the 100 K SNP mapping array data. Furthermore, our data suggested a frequent loss at 3p11-p12 for advanced stage OTSCC.

MeSH Terms
Allelic Imbalance Carcinoma, Squamous Cell/genetics Chromosomes, Human, Pair 3 Genotype Humans Nucleic Acid Amplification Techniques Oligonucleotide Array Sequence Analysis Polymorphism, Single Nucleotide Tongue Neoplasms/genetics
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Zhou Xiaofeng
Dental Research Institute, School of Dentistry, University of California at Los Angeles, Los Angeles, CA, USA.
Temam Stephane
Chen Zugen
Ye Hui
Mao Li
Wong David T W
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Article Info
Journal
Human genetics
Abbr.
Hum Genet
ISSN
0340-6717
DOI
10.1007/s00439-005-0069-x
Published
2005-12-00
Epub
2005-00-29
Pages
504-7
Language
English
Region
Germany
NLM ID
7613873
Subset
IM
Grants
NIDCR NIH HHS · K22 DE014847 · United States
NCI NIH HHS · P01 CA106451 · United States
NIDCR NIH HHS · R01 DE015970 · United States
NCI NIH HHS · R03 CA114688 · United States
NIDCR NIH HHS · R03 DE016569 · United States
External Links
PubMed source DOI: 10.1007/s00439-005-0069-x View journal details
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