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Sequence variation in the human transcription factor gene POU5F1

Shehnaz K Hussain12*, Reynaldo Sequerra3, Caterina Bertucci4, Noel C Hastings4, Mark Rieder4 and Stephen M Schwartz2

Author Affiliations

1 University of California, Los Angeles, Division of Cancer Prevention and Control Research, School of Public Health and Jonsson Comprehensive Cancer Center, 650 Charles E Young Drive South, Room A2-125 CHS, Box 956900, Los Angeles, CA, 90095-6900, USA

2 Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Box 358080 M4-C308, 1100 Fairview Ave N., Building M, Seattle, WA 98109-1024, USA

3 Agencourt Bioscience Corporation, 500 Cummings Center, Suite 2450, Beverly MA, 01915, USA

4 University of Washington, Department of Genome Sciences, Box 357730, Seattle, WA 98195, USA

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BMC Genetics 2008, 9:15  doi:10.1186/1471-2156-9-15

Published: 6 February 2008



POU5F1 expression is required to maintain stem cell pluripotency and for primordial germ cells to retain proliferative capability in embryonic development. Recent evidence suggests that POU5F1 may also be a testicular germ cell carcinoma (TGCC) oncogene, and POU5F1 variation may influence TGCC risk. As an important first step to a genetic association study, we sought to identify all common sequence variants in an 11.3 kb region containing POU5F1, and to describe the linkage disequilibrium patterns, using DNA from individuals of African-descent (AD) and European-descent (ED).


A higher number of polymorphisms was observed in the AD (n = 102) versus ED (n = 82) population. Among the 41 observed haplotypes, 21 (51%) and 12 (29%) were unique to the AD and ED populations, respectively, while 8 (20%) were observed in both. The number of tagging polymorphisms necessary to explain at least 80% of common variation (minor allele frequency ≥ 0.10) due to the remaining untyped polymorphisms was 17 for an AD and 10 for an ED population, providing a 4.0- and 7.0-fold gain in genotyping efficiency for characterizing nucleotide variation, respectively.


POU5F1 is highly polymorphic, however a smaller subset of polymorphisms can tag the observed genetic variation with little loss of information.