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Showing papers by "Mark Pinese published in 2021"

Journal Article•DOI•
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data

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André E. Minoche1, André E. Minoche2, Ben Lundie2, Greg B. Peters3, Thomas Ohnesorg2, Mark Pinese1, David Thomas2, David Thomas1, Andreas Zankl2, Andreas Zankl4, Andreas Zankl3, Tony Roscioli, Nicole Schonrock2, Sarah K. Kummerfeld1, Sarah K. Kummerfeld2, Leslie Burnett, Marcel E. Dinger2, Mark J. Cowley •
University of New South Wales1, Garvan Institute of Medical Research2, Children's Hospital at Westmead3, University of Sydney4
25 Feb 2021-Genome Medicine
TL;DR: ClinSV as mentioned in this paper is a WGS-based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs from matched microarrays.
Abstract: Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV, a WGS based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs > 10 kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5–4.5%) and reproducibility high (95–99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35–63% were not detectable by current clinical microarray designs. ClinSV is available at https://github.com/KCCG/ClinSV .

28 citations

Journal Article•DOI•
Childhood acute myeloid leukemia shows a high level of germline predisposition

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Saumya E. Samaraweera1, Paul Po-Shen Wang2, Ka Leung Li1, Debora A. Casolari1, Jinghua Feng, Mark Pinese3, Kyaw Ze Ya Maung1, Paul Leo4, Mark J. Cowley3, Kelly Perkins5, Amanda Smith6, Jonathan Ellis4, Amilia Wee7, Devendra K Hiwase7, Hamish S. Scott1, Andreas W. Schreiber2, Anna L. Brown2, Andrew J. Deans8, David M. Ross1, Andrew S. Moore, Thomas J. Gonda1, Christopher N. Hahn2, Richard J D'Andrea1 •
University of South Australia1, South Australia Pathology2, University of New South Wales3, Queensland University of Technology4, John Radcliffe Hospital5, University of Queensland6, Royal Adelaide Hospital7, St. Vincent's Institute of Medical Research8
14 Sep 2021-Blood
TL;DR: In this paper, the authors performed a comprehensive analysis of rare germline variants in childhood acute myeloid leukemia (AML) using whole genome sequencing (WGS) and whole exome sequence (WES) data available through the TARGET program.

4 citations