DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

Scheinin, Ilari; Sie, Daoud; Bengtsson, Henrik; Wiel, Mark A. van de; Olshen, Adam B.; Thuijl, Hinke F. van; Essen, Hendrik F. van; Eijk, Paul P.; Rustenburg, François; Meijer, Gerrit A.; Reijneveld, Jaap C.; Wesseling, Pieter; Pinkel, Daniel; Albertson, Donna G.; Ylstra, Bauke

doi:10.1101/gr.175141.114

articleGenome ResearchSep 18, 2014BRONZE OA

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

ISIlari Scheinin DSDaoud Sie HBHenrik Bengtsson MAMark A. van de Wiel ABAdam B. Olshen

University of Helsinki · Helsinki University Hospital · +9 more institutions

PubMed

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Abstract

Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can…

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Keywords

Biology
Genome
Hybrid genome assembly
Computational biology
Whole genome sequencing
Reference genome
DNA sequencing
Genetics

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