Pedigree based DNA sequencing pipeline for germline genomes of cancer families.

Dagmara Dymerska,Nagarajan Paramasivam,Matthias Schlesner,Roland Eils,Jan Lubinski,Kari Hemminki,Calogerina Catalano,Asta Försti,Abhishek Kumar

doi:10.1186/s13053-016-0058-1

Abstract

BackgroundIn the course of our whole-genome sequencing efforts, we have developed a pipeline for analyzing germline genomes from Mendelian types of cancer pedigrees (familial cancer variant prioritization pipeline, FCVPP).ResultsThe variant calling step distinguishes two types of genomic variants: single nucleotide variants (SNVs) and indels, which undergo technical quality control. Mendelian types of variants are assumed to be rare and variants with frequencies higher that 0.1 % are screened out using human 1000 Genomes (Phase 3) and non-TCGA ExAC population data. Segregation in the pedigree allows variants to be present in affected family members and not in old, unaffected ones. The effectiveness of variant segregation depends on the number and relatedness of the family members: if over 5 third-degree (or more distant) relatives are available, the experience has shown that the number of likely variants is reduced from many hundreds to a few tens. These are then subjected to bioinformatics analysis, starting with the combined annotation dependent depletion (CADD) tool, which predicts the likelihood of the variant being deleterious. Different sets of individual tools are used for further evaluation of the deleteriousness of coding variants, 5’ and 3’ untranslated regions (UTRs), and intergenic variants. ConlusionsThe likelihood of success of the present genomic pipeline in finding novel high- or medium-penetrant genes depends on many steps but first and foremost, the pedigree needs to be reasonably large and the assignments and diagnoses among the members need to be correct.

Highlights

In the course of our whole-genome sequencing efforts, we have developed a pipeline for analyzing germline genomes from Mendelian types of cancer pedigrees
We describe a gene identification pipeline for germline mutations in cancer families with the focus on pedigree and functional annotation data, familial cancer variant prioritization pipeline (FCVPP)
The advantage of the pedigree approach is that with a decent number of affected and unaffected family members the number of candidate mutations can be drastically reduced before feeding the data on in the distal pipeline for evaluation of the likelihood for the variant of being deleterious through functional annotation

Summary

Introduction

In the course of our whole-genome sequencing efforts, we have developed a pipeline for analyzing germline genomes from Mendelian types of cancer pedigrees (familial cancer variant prioritization pipeline, FCVPP). Even though NGS would afford an advantageous technology for germline sequencing, no boost in the number of new cancer predisposing genes has been evident. We describe a gene identification pipeline for germline mutations in cancer families with the focus on pedigree and functional annotation data, familial cancer variant prioritization pipeline (FCVPP). The advantage of the pedigree approach is that with a decent number of affected and unaffected family members the number of candidate mutations can be drastically reduced before feeding the data on in the distal pipeline for evaluation of the likelihood for the variant of being deleterious through functional annotation

Methods

Results

Conclusion