title: Applicability of next generation sequencing technology in microsatellite instability testing.
abstract: Microsatellite instability (MSI) is a useful marker for risk assessment, prediction of chemotherapy responsiveness and prognosis in patients with colorectal cancer. Here, we describe a next generation sequencing approach for MSI testing using the MiSeq platform. Different from other MSI capturing strategies that are based on targeted gene capture, we utilize "deep resequencing", where we focus the sequencing on only the microsatellite regions of interest. We sequenced a series of 44 colorectal tumours with normal controls for five MSI loci (BAT25, BAT26, BAT34c4, D18S55, D5S346) and a second series of six colorectal tumours (no control) with two mononucleotide loci (BAT25, BAT26). In the first series, we were able to determine 17 MSI-High, 1 MSI-Low and 26 microsatellite stable (MSS) tumours. In the second series, there were three MSI-High and three MSS tumours. Although there was some variation within individual markers, this NGS method produced the same overall MSI status for each tumour, as obtained with the traditional multiplex PCR-based method.
authors: Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia. c.gan3@student.unimelb.edu.au.|Department of Colorectal Medicine and Genetics, Familial Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia. c.gan3@student.unimelb.edu.au.|Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia. c.gan3@student.unimelb.edu.au.
authors: Chun
authors: C
authors: Gan
authors: Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia. clare.love@unimelb.edu.au.
authors: Clare
authors: C
authors: Love
authors: Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, East Melbourne, Victoria 3002, Australia. victoria.beshay@petermac.org.
authors: Victoria
authors: V
authors: Beshay
authors: Department of Colorectal Medicine and Genetics, Familial Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia. finlay.macrae@mh.org.au.|Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia. finlay.macrae@mh.org.au.
authors: Finlay
authors: F
authors: Macrae
authors: Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, East Melbourne, Victoria 3002, Australia. stephen.fox@petermac.org.
authors: Stephen
authors: S
authors: Fox
authors: Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia. pwaring@unimelb.edu.au.
authors: Paul
authors: P
authors: Waring
authors: Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia. graham.taylor@unimelb.edu.au.
authors: Graham
authors: G
authors: Taylor