title: cDNA hybrid capture improves transcriptome analysis on low-input and archived samples.
abstract: The use of massively parallel sequencing for studying RNA expression has greatly enhanced our understanding of the transcriptome through the myriad ways these data can be characterized. In particular, clinical samples provide important insights about RNA expression in health and disease, yet these studies can be complicated by RNA degradation that results from the use of formalin as a clinical preservative and by the limited amounts of RNA often available from these precious samples. In this study we describe the combined use of RNA sequencing with an exome capture selection step to enhance the yield of on-exon sequencing read data when compared with RNA sequencing alone. In particular, the exome capture step preserves the dynamic range of expression, permitting differential comparisons and validation of expressed mutations from limited and FFPE preserved samples, while reducing the data generation requirement. We conclude that cDNA hybrid capture has the potential to significantly improve transcriptome analysis from low-yield FFPE material.
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Cabanski
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Vincent
authors.initials: V
authors.lastname: Magrini
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Malachi
authors.initials: M
authors.lastname: Griffith
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Obi L
authors.initials: OL
authors.lastname: Griffith
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Sean
authors.initials: S
authors.lastname: McGrath
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Jason
authors.initials: J
authors.lastname: Walker
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Amy
authors.initials: A
authors.lastname: Ly
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Ryan
authors.initials: R
authors.lastname: Demeter
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Fulton
authors.affiliation: Department of Neurology, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Winnie W
authors.initials: WW
authors.lastname: Pong
authors.affiliation: Department of Neurology, Washington University School of Medicine, St. Louis, Missouri; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: David H
authors.initials: DH
authors.lastname: Gutmann
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Ramaswamy
authors.initials: R
authors.lastname: Govindan
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri.
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri; Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri. Electronic address: cmaher@dom.wustl.edu.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Maher
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D018076:DNA, Complementary / Q000235:genetics*; D059472:Exome; D020869:Gene Expression Profiling / Q000379:methods*; D050939:Gene Fusion; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D018076:DNA, Complementary; D012313:RNA