A computational analysis of the genetic and transcript diversity at the kallikrein locus

Abstract

Abstract The kallikrein related peptidase gene family (KLKs) comprises 15 genes located between 19q13.3-13.4. KLKs have chymotrypsin and/or trypsin like activity, but the tissue/organ expression profile of each KLK varies considerably. Thus, the role of KLKs in human biology is also very diverse, and the deregulation of their function results in a wide-range of diseases. Here, we have cataloged the transcript (variants and fusions) and genetic (single nucleotide polymorphisms, small insertions/deletions, copy number variations (CNVs), and short tandem repeats) diversity at the KLK locus, providing a data set for researchers to explore the mechanisms through which KLK function may be deregulated. We reveal that the KLK locus hosts 85 fusion transcripts, and 80 variant transcripts. Interestingly, some fusion transcripts comprise up to 6 KLK genes. Our analysis of genetic variations of 2504 individuals from the 1000 Genome Project indicated that the KLK locus is rich in genetic diversity, with some fusion transcripts harboring over 1000 single nucleotide variations. We also found evidence from the literature linking 2387 KLK genetic variants with many types of diseases. Finally, genotyping data from the 131 KLK genetic variants in the NCI-60 cancer cell lines is provided as a resource for the cancer and KLK field.