High-throughput genotyping of a common deletion polymorphism disrupting the TRY6 gene and its association with breast cancer risk.
BACKGROUND
Copy number polymorphisms caused by genomic rearrangements like deletions, make a significant contribution to the genomic differences between two individuals and may add to disease predisposition. Therefore, genotyping of such deletion polymorphisms in case-control studies could give important insights into risk associations.


RESULTS
We mapped the breakpoints and developed a fluorescent fragment analysis for a deletion disrupting the TRY6 gene to exemplify a quick and cheap genotyping approach for such structural variants. We showed that the deletion is larger than predicted and encompasses also the pseudogene TRY5. We performed a case-control study to test an association of the TRY6 deletion polymorphism with breast cancer using a single nucleotide polymorphism which is in 100% linkage disequilibrium with the deletion. We did not observe an effect of the deletion on breast cancer risk (OR 1.05, 95% CI 0.71-1.56).


CONCLUSIONS
Although we did not observe an association between the TRY6 deletion polymorphism and breast cancer risk, the identification and investigation of further deletions using the present approach may help to elucidate their effect on disease susceptibility.
Wagner
Kerstin
K
Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany. wagner_ke@yahoo.de <wagner_ke@yahoo.de>
Grzybowska
Ewa
E
Butkiewicz
Dorota
D
Pamula-Pilat
Jolanta
J
Pekala
Wioletta
W
Tecza
Karolina
K
Hemminki
Kari
K
Försti
Asta
A
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001943:Breast Neoplasms / Q000235:genetics*; D016022:Case-Control Studies; D017931:DNA Primers; D005260:Female; D017353:Gene Deletion; D005838:Genotype; D006720:Homozygote; D006801:Humans; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D012307:Risk Factors; D016415:Sequence Alignment; D014357:Trypsin; D014362:Trypsinogen / Q000235:genetics*
D017931:DNA Primers; D014362:Trypsinogen; C489303:PRSS1 protein, human; D014357:Trypsin