Sequence variation in the human transcription factor gene POU5F1.
BACKGROUND
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).


RESULTS
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 > or = 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.


CONCLUSIONS
POU5F1 is highly polymorphic, however a smaller subset of polymorphisms can tag the observed genetic variation with little loss of information.
Hussain
Shehnaz K
SK
University of California, Los Angeles, Division of Cancer Prevention and Control Research, School of Public Health and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095-6900, USA. SKHussain@ucla.edu
Sequerra
Reynaldo
R
Bertucci
Caterina
C
Hastings
Noel C
NC
Rieder
Mark
M
Schwartz
Stephen M
SM
D008040:Genetic Linkage; D014644:Genetic Variation; D023281:Genomics; D006239:Haplotypes; D006801:Humans; D050814:Octamer Transcription Factor-3 / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
D050814:Octamer Transcription Factor-3; C494173:POU5F1 protein, human