Copy number variants in the kallikrein gene cluster

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

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.

Genotyping of common SIRPB1 copy number variant using Paralogue Ratio Test coupled to MALDI-MS quantification

Copy number variant (CNV) regions have been proven to have a significant impact on gene expression. Some of them have been also found to be associated to different human diseases. CNV genotyping is often prone to error and cross-validation with independent methods is frequently required. The platform of choice depends on whether it is a genome-wide discovery screening or a candidate CNV study, the cohort size and the number of CNVs included in the assay and, finally, the budget available. Here we illustrate a affordable approach to determine the CNV genotype using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and based on the quantitative determination of single nucleotide duplicated mismatches (SNDM) mapping the CNV region and a paralogue genomic region that is used as a two-copy reference. We have genotyped nsv436327, a common CNV mapping SIRPB1 intron 1 that has been associated to human personality behavior. SIRP cluster region was subjected to several ancestral duplication events what makes SIRPB1 CNV genotyping technically challenging. We designed three sets of primer pairs that amplified paralogue regions inside and outside the CNV, containing three SNDMs. Post-PCR extension analyses of sequencing oligonucleotides mapping immediately upstream each SNDM allowed us to quantify using MALDI-MS the proportion of PCR products derived from the CNV region versus the external reference. In contrast to other approaches, setting up this genotyping method requires an affordable investment.