Single nucleotide polymorphisms (SNPs) represent an abundant and useful source of genetic markers to understand complex diseases. SNPs in coding regions (cSNPs) of biologically important genes are likely to functionally alter the protein product. We have used pooled DNA sequencing to evaluate the frequency of over 100 polymorphisms in cancer-related genes in Caucasian, African American and Asian populations. This allows the identification of SNPs useful in typing patient cohorts. To perform high throughput genotyping of cancer gene SNPs we have established 5' nuclease (TaqMan) assays for known variants in drug metabolizing enzymes, hormone receptor genes, immune response genes and chemokines and their receptors. These variants have been genotyped on cohorts of African American breast cancer, Caucasian lung cancer and Chinese lung cancer patients. We have developed a cocktail of polymerase and reference dyes for use in genotyping using the 5' nuclease (TaqMan) SNP genoptyping system. This cocktail provides better allele discrimination and is less expensive than the commercial product. We are adapting this method to 384-well plates that will allow a further reduction in cost, increase in throughput and reduced consumption of DNA. For assays that cannot be typed by TaqMan we have established a melt curve-based method that requires only low cost primers. Polymorphisms in several chemokine and chemokine receptor genes have been analyzed in an African American breast cancer cohort. Several significant associations were found that are being analyzed in larger cohorts to attempt to replicate the findings. Using high performance computing on the Cray supercomputer, an exhaustive search for short tandem repeats has been performed in the human genome. This data is in a browser and is searchable by gene or location. Thirty new genes that contain trinucleotide repeats in the coding region were identified that are candidate disease genes.

Agency
National Institute of Health (NIH)
Institute
Division of Basic Sciences - NCI (NCI)
Type
Intramural Research (Z01)
Project #
1Z01BC005652-12
Application #
6558943
Study Section
(LGD)
Project Start
Project End
Budget Start
Budget End
Support Year
12
Fiscal Year
2001
Total Cost
Indirect Cost
Name
Basic Sciences
Department
Type
DUNS #
City
State
Country
United States
Zip Code
Lou, Hong; Villagran, Guillermo; Boland, Joseph F et al. (2015) Genome Analysis of Latin American Cervical Cancer: Frequent Activation of the PIK3CA Pathway. Clin Cancer Res 21:5360-70
Boland, Joseph F; Chung, Charles C; Roberson, David et al. (2013) The new sequencer on the block: comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Hum Genet 132:1153-63
Garrido, Claudia; Santizo, Veronica Giron; Müllers, Petra et al. (2013) Frequency of thiopurine S-methyltransferase mutant alleles in indigenous and admixed Guatemalan patients with acute lymphoblastic leukemia. Med Oncol 30:474
Torimiro, Judith N; Javanbakht, Hassan; Diaz-Griffero, Felipe et al. (2009) A rare null allele potentially encoding a dominant-negative TRIM5alpha protein in Baka pygmies. Virology 391:140-7
Meyer-Lindenberg, A; Kolachana, B; Gold, B et al. (2009) Genetic variants in AVPR1A linked to autism predict amygdala activation and personality traits in healthy humans. Mol Psychiatry 14:968-75
Allikmets, Rando; Dean, Michael (2008) Bringing age-related macular degeneration into focus. Nat Genet 40:820-1
Lou, H; Dean, M (2007) Targeted therapy for cancer stem cells: the patched pathway and ABC transporters. Oncogene 26:1357-60
Remsberg, Jarrett R; Lou, Hong; Tarasov, Sergey G et al. (2007) Structural analogues of smoothened intracellular loops as potent inhibitors of Hedgehog pathway and cancer cell growth. J Med Chem 50:4534-8
O'Brien, Thomas R; Kachapati, Kritika; Zhang, Mingdong et al. (2007) HCV infection clearance with functional or non-functional caspase-12. Scand J Gastroenterol 42:416-7
Li, Xing; Gold, Bert; O'hUigin, Colm et al. (2007) Unique features of TRIM5alpha among closely related human TRIM family members. Virology 360:419-33

Showing the most recent 10 out of 40 publications