A resequence analysis of genomic loci on chromosomes 1q32.1, 5p15.33, and 13q22.1 associated with pancreatic cancer risk

Hemang Parikh, Jinping Jia, Xijun Zhang, Charles C. Chung, Kevin B. Jacobs, Meredith Yeager, Joseph Boland, Amy Hutchinson, Laura Burdett, Jason Hoskins, Harvey A. Risch, Rachael Z. Stolzenberg-Solomon, Stephen J. Chanock, Brian M. Wolpin, Gloria M. Petersen, Charles S. Fuchs, Patricia Hartge, Laufey Amundadottir

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

OBJECTIVE: The objective of this study was to fine-map common pancreatic cancer susceptibility regions. METHODS: We conducted targeted Roche-454 resequencing across 428 kb in 3 genomic regions identified in genome-wide association studies (GWAS) of pancreatic cancer, on chromosomes 1q32.1, 5p15.33, and 13q22.1. RESULTS: An analytical pipeline for calling genotypes was developed using HapMap samples sequenced on chr5p15.33. Concordance to 1000 Genomes data for chr5p15.33 was greater than 96%. The concordance for chr1q32.1 and chr13q22.1 with pancreatic cancer GWAS data was greater than 99%. Between 9.2% and 19.0% of variants detected were not present in 1000 Genomes for the respective continental population. The majority of completely novel single-nucleotide polymorphisms (SNPs) were less common (minor allele frequency [MAF], ≤5%) or rare (MAF, ≤2%), illustrating the value of enlarging test sets for discovery of less common variants. Using the data set, we examined haplotype blocks across each region using a tag SNP analysis (r > 0.8 for MAF of ≥5%) and determined that at least 196, 243, and 63 SNPs are required for fine-mapping chr1q32.1, chr5p15.33, and chr13q22.1, respectively, in European populations. CONCLUSIONS: We have characterized germline variation in 3 regions associated with pancreatic cancer risk and show that targeted resequencing leads to the discovery of novel variants and improves the completeness of germline sequence variants for fine-mapping GWAS susceptibility loci.

Original languageEnglish (US)
Pages (from-to)209-215
Number of pages7
JournalPancreas
Volume42
Issue number2
DOIs
StatePublished - Mar 1 2013

Keywords

  • 1000G
  • GWAS
  • SNP
  • pancreatic cancer
  • susceptibility loci
  • targeted resequencing

ASJC Scopus subject areas

  • Internal Medicine
  • Endocrinology, Diabetes and Metabolism
  • Hepatology
  • Endocrinology

Fingerprint Dive into the research topics of 'A resequence analysis of genomic loci on chromosomes 1q32.1, 5p15.33, and 13q22.1 associated with pancreatic cancer risk'. Together they form a unique fingerprint.

  • Cite this

    Parikh, H., Jia, J., Zhang, X., Chung, C. C., Jacobs, K. B., Yeager, M., Boland, J., Hutchinson, A., Burdett, L., Hoskins, J., Risch, H. A., Stolzenberg-Solomon, R. Z., Chanock, S. J., Wolpin, B. M., Petersen, G. M., Fuchs, C. S., Hartge, P., & Amundadottir, L. (2013). A resequence analysis of genomic loci on chromosomes 1q32.1, 5p15.33, and 13q22.1 associated with pancreatic cancer risk. Pancreas, 42(2), 209-215. https://doi.org/10.1097/MPA.0b013e318264cea5