title: Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma.
abstract: We present a pipeline to perform integrative analysis of mate-pair (MP) and paired-end (PE) genomic DNA sequencing data. Our pipeline detects structural variations (SVs) by taking aligned sequencing read pairs as input and classifying these reads into properly paired and discordantly paired categories based on their orientation and inferred insert sizes. Recurrent SV was identified from the discordant read pairs. Our pipeline takes into account genomic annotation and genome repetitive element information to increase detection specificity. Application of our pipeline to whole-genome MP and PE sequencing data from three multiple myeloma cell lines (KMS11, MM.1S, and RPMI8226) recovered known SVs, such as heterozygous TRAF3 deletion, as well as a novel experimentally validated SPI1 - ZNF287 inter-chromosomal rearrangement in the RPMI8226 cell line.
authors.affiliation: Department of Biostatics and Bioinformatics, Emory University, Atlanta, GA, USA.
authors.forename: Rendong
authors.initials: R
authors.lastname: Yang
authors.affiliation: Department of Mathematics and Computer Science, Emory University, Atlanta, GA, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Winship Biostatistics and Bioinformatics Shared Resource, Atlanta, GA, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Newman
authors.affiliation: Winship Biostatistics and Bioinformatics Shared Resource, Atlanta, GA, USA.
authors.forename: Khanjan
authors.initials: K
authors.lastname: Gandhi
authors.affiliation: The Emory Integrated Genomics Core, Emory University, Atlanta, GA, USA.
authors.forename: Gregory
authors.initials: G
authors.lastname: Doho
authors.affiliation: Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
authors.forename: Carlos S
authors.initials: CS
authors.lastname: Moreno
authors.affiliation: Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA.
authors.forename: Paula M
authors.initials: PM
authors.lastname: Vertino
authors.affiliation: Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA.
authors.forename: Leon
authors.initials: L
authors.lastname: Bernal-Mizarchi
authors.affiliation: Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA.
authors.forename: Sagar
authors.initials: S
authors.lastname: Lonial
authors.affiliation: Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA.
authors.forename: Lawrence H
authors.initials: LH
authors.lastname: Boise
authors.affiliation: The Emory Integrated Genomics Core, Emory University, Atlanta, GA, USA. ; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Rossi
authors.affiliation: Department of Biostatics and Bioinformatics, Emory University, Atlanta, GA, USA. ; Winship Biostatistics and Bioinformatics Shared Resource, Atlanta, GA, USA.
authors.forename: Jeanne
authors.initials: J
authors.lastname: Kowalski
authors.affiliation: Department of Biostatics and Bioinformatics, Emory University, Atlanta, GA, USA.
authors.forename: Zhaohui S
authors.initials: ZS
authors.lastname: Qin
keywords: multiple myeloma; structural variations; variant detection; whole-genome sequencing