title: Assessment of whole genome amplification for sequence capture and massively parallel sequencing.
abstract: Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74%) of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information.
authors.affiliation: Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Johanna
authors.initials: J
authors.lastname: Hasmats
authors.affiliation: Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden ; Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden ; Clinical Pharmacology, Department of Health and Medical Sciences, Linköping University, Linköping, Sweden.
authors.forename: Henrik
authors.initials: H
authors.lastname: Gréen
authors.affiliation: Genomics Unit, Institut Gustave Roussy, Villejuif, France.
authors.forename: Cedric
authors.initials: C
authors.lastname: Orear
authors.affiliation: Department of Pathology, Institut Mutualiste Montsouris, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Validire
authors.affiliation: Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
authors.forename: Mikael
authors.initials: M
authors.lastname: Huss
authors.affiliation: Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Max
authors.initials: M
authors.lastname: Käller
authors.affiliation: Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
mesh_terms: D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics / Q000473:pathology; D005260:Female; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics / Q000473:pathology; D008297:Male; D009154:Mutation; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA