title: Pedigree based DNA sequencing pipeline for germline genomes of cancer families.
abstract: BACKGROUND
  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).
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  The 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.
authors: Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany.|Center for Primary Health Care Research, Lund University, Malmö, Sweden.
authors: Asta
authors: A
authors: Försti
authors: Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany.
authors: Abhishek
authors: A
authors: Kumar
authors: Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany.|Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
authors: Nagarajan
authors: N
authors: Paramasivam
authors: Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany.
authors: Matthias
authors: M
authors: Schlesner
authors: Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany.
authors: Calogerina
authors: C
authors: Catalano
authors: Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland.
authors: Dagmara
authors: D
authors: Dymerska
authors: Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland.
authors: Jan
authors: J
authors: Lubinski
authors: Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany.|Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.
authors: Roland
authors: R
authors: Eils
authors: Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany.|Center for Primary Health Care Research, Lund University, Malmö, Sweden.
authors: Kari
authors: K
authors: Hemminki
keywords: Family-based; Genetic risk factors; Germline genetics; Mutation