Journal article
A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing
K Quek, K Nones, AM Patch, J Lynn Fink, F Newell, N Cloonan, D Miller, MZH Fadlullah, K Kassahn, AN Christ, TJC Bruxner, S Manning, I Harliwong, S Idrisoglu, C Nourse, E Nourbakhsh, S Wani, A Steptoe, M Anderson, O Holmes Show all
Biotechniques | TAYLOR & FRANCIS LTD | Published : 2014
DOI: 10.2144/000114189
Abstract
Somatic rearrangements, which are commonly found in human cancer genomes, contribute to the progression and maintenance of cancers. Conventionally, the verification of somatic rearrangements comprises many manual steps and Sanger sequencing. This is labor intensive when verifying a large number of rearrangements in a large cohort. To increase the verification throughput, we devised a high-throughput workflow that utilizes benchtop next-generation sequencing and in-house bioinformatics tools to link the laboratory processes. In the proposed workflow, primers are automatically designed. PCR and an optional gel electrophoresis step to confirm the somatic nature of the rearrangements are perform..
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Grants
Awarded by National Health and Medical Research Council of Australia (NHMRC)
Awarded by Cancer ouncil NSW
Awarded by Cancer Institute NSW
Funding Acknowledgements
We would like to thank D. Gwynne for central coordination at the Queensland Centre for Medical Genomics. We wish to thank all of the APGI members as well as patients who contribute to APGI. This research has been supported by the National Health and Medical Research Council of Australia (NHMRC: 631701, 535903, 427601, APP1047334); Australian Government: Department of Innovation, Industry, Science and Research (DIISR); Australian Cancer Research Foundation (ACRF); Queensland Government (NI-RAP); University of Queensland; Cancer ouncil NSW: (SRP06-01); Cancer Institute NSW: (10/ECF/2-26; 06/EC F/1-24; 09/C D F/2-40; 07/C D F/1-03; 10/CRF/1-01, 08/RSA/1-15, 07/CDF/1-28, 10/CDF/2-26,10/FRL/2-03, 06/RSA/1-05, 09/RIG/1-02, 10/ TPG/1-04, 11/R EG/1-10, 11/CDF/3-26); Garvan Institute of Medical Research; Avner Nahmani Pancreatic Cancer Research Foundation; R.T. Hall Trust; Petre Foundation; Philip Hemstritch Foundation; Gastroenterological Society of Australia (GESA); American Association for Cancer Research (AACR) Landon Foundation INNOVATOR Award; Royal Australasian College of Surgeons (RACS); Royal Australasian College of Physicians (RACP); Royal College of Pathologists of Australasia (RCPA). S.G. is a recipient of a NHMRC Principal Research Fellowship.