This project continued to progress well in 2020, with Khalid Mahmood sharing his expertise with the group. Khalid has developed several bioinformatics pipelines for the Colorectal Oncogenomics Group, which are used extensively in the lab. These include somatic variant calling and analysis for targeted tumour/normal sequencing. Another resource under development is a database of tumour and immune features together with somatic mutations for several studies in the lab including the ANGELS study.
Khalid Mahmood continued to co-supervise 3rd year PhD student Philip Harraka with Prof Judy Savidy (RMH).
Publications
Georgeson P, Pope BJ, Rosty C, Clendenning M, Mahmood K, Joo JE, Walker R, Hutchinson RA, Preston S, Como J, Joseland S, Win AK, Macrae FA, Hopper JL, Mouradov D, Gibbs P, Sieber OM, O’Sullivan DE, Brenner DR, Gallinger S, Jenkins MA, Winship IM, Buchanan DD. Evaluating the utility of tumour mutational signatures for identifying hereditary colorectal cancer and polyposis syndrome carriers. Gut. 2021 Jan 7:gutjnl-2019-320462.
Pope BJ, Clendenning M, Rosty C, Mahmood K, Georgeson P, Joo JE, Walker R, Hutchinson RA, Jayasekara H, Joseland S, Como J, Preston S, Spurdle AB, Macrae FA, Win AK, Hopper JL, Jenkins MA, Winship IM, Buchanan DD.
Germline and Tumor Sequencing as a Diagnostic Tool To Resolve Suspected Lynch Syndrome. J Mol Diagn. 2020 Dec 29:S1525-1578(20)30610-3.
Elsayed FA, Grolleman JE, Ragunathan A; NTHL1 study group, Buchanan DD, van Wezel T, de Voer RM. Monoallelic NTHL1 Loss-of-Function Variants and Risk of Polyposis and Colorectal Cancer. Gastroenterology. 2020 Dec;159(6):2241-2243.e6. doi: 10.1053/j.gastro.2020.08.042. Epub 2020 Aug 26. PMID: 32860789.
Nguyen-Dumont T, MacInnis RJ, Steen JA, Theys D, Tsimiklis H, Hammet F, Mahmoodi M, Pope BJ, Park DJ, Mahmood K, Severi G, Bolton D, Milne RL, Giles GG, Southey MC. Rare germline genetic variants and risk of aggressive prostate cancer. Int J Cancer. 2020 Oct 15;147(8):2142-2149. doi: 10.1002/ijc.33024. Epub 2020 May 8. PMID: 32338768.
Publications in preparation
Collaboration with Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) to analyse data from a large GWAS study for colorectal cancer associations. Manuscript in preparation.
Collaboration with the ASPREE project to study genetic colorectal cancer risk factors from more than 15,000 healthy ageing participants. Completing data analysis for manuscript preparation.
Community Engagement
Khalid Mahmood is a committee member of the InSiGHT variant interpretation committee. InSiGHT (International society for gastrointestinal hereditary tumours) is an international multidisciplinary scientific organisation and was on the organising committee member for the Victorian Cancer Bioinformatics Symposium 2020.
Presentations
Jihoon E. Joo, Mark Clendenning, Khalid Mahmood, Christophe Rosty, Ingrid M. Winship, Mark A. Jenkins, Daniel D. Buchanan. Tumor microbiome in subtypes of mismatch repair-deficient colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL.
I have developed several bioinformatics pipelines for the Colorectal Oncogenomics Group used extensively in the lab. These include somatic variant calling and analysis for targeted tumour/normal sequencing. Another resource under development is a database of tumour and immune features together with somatic mutations for several studies in the lab including the ANGELS study.
Overall these projects are supported by significant grants from NHMRC, NIH, Cancer Australia and Cancer Council Victoria.
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Project description
The focus of the Colorectal Oncogenomics Group (COG) led by Assoc Prof Daniel Buchanan includes the identification and investigation of clinically and biologically relevant subtype of colorectal cancers (CRC) in both familial and non-familial settings. The analysis involves a wide range of multi-disciplinary techniques ranging from computational biology, epigenetics and genomics to analyse tumour and pre-malignant lesions in terms of their histopathological features. This very successful collaboration covers a range of colorectal cancer projects including those forming part of the University-hosted NHMRC Centre for Research Excellence in Optimising Screening for Colorectal Cancer, whose vision is to create and implement a personalised approach to colorectal cancer screening to reduce the number of new cases and deaths from this common disease.
Project collaborators
Assoc Prof Daniel Buchanan, University of Melbourne
Assoc Prof Bernie Pope, Melbourne Bioinformatics
Prof Ingrid Winship, Royal Melbourne Hospital & University of Melbourne
Prof Mark Jenkins, University of Melbourne Centre for Cancer Research