title: Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine.
abstract: Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient's genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS.
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. etsai3@partners.org.|Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA. etsai3@partners.org.|Department of Medicine, Harvard Medical School, Boston, MA 02138, USA. etsai3@partners.org.
authors.forename: Ellen A
authors.initials: EA
authors.lastname: Tsai
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. rshakhbatyan@partners.org.
authors.forename: Rimma
authors.initials: R
authors.lastname: Shakbatyan
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. jason.evans@courtagen.com.
authors.forename: Jason
authors.initials: J
authors.lastname: Evans
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. prossetti@partners.org.
authors.forename: Peter
authors.initials: P
authors.lastname: Rossetti
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. cgraham@geneinsight.com.
authors.forename: Chet
authors.initials: C
authors.lastname: Graham
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. hsharma@partners.org.
authors.forename: Himanshu
authors.initials: H
authors.lastname: Sharma
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. cflin@partners.org.|Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA. cflin@partners.org.|Department of Medicine, Harvard Medical School, Boston, MA 02138, USA. cflin@partners.org.
authors.forename: Chiao-Feng
authors.initials: CF
authors.lastname: Lin
authors.affiliation: Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA. mlebo@partners.org.|Department of Pathology, Harvard Medical School, Boston, MA 02138, USA. mlebo@partners.org.|Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA. mlebo@partners.org.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Lebo
keywords: NGS; WGS; bioinformatics; clinical sequencing; next generation sequencing; precision medicine; validation