MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

Autor: Marek Cmero, Breon Schmidt, Ian J. Majewski, Paul G. Ekert, Alicia Oshlack, Nadia M. Davidson

Publikováno v: Genome Biology, Vol 22, Iss 1, Pp 1-26 (2021)

Abstract Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline

Externí odkaz: https://doaj.org/article/8f8713914e66485e941f529c5206b3cb

Slinker: Visualising novel splicing events in RNA-Seq data [version 1; peer review: 3 approved]

Autor: Marek Cmero, Breon Schmidt, Nadia Davidson, Paul Ekert, Alicia Oshlack

Publikováno v: F1000Research, Vol 10 (2021)

Visualisation of the transcriptome relative to a reference genome is fraught with sparsity. This is due to RNA sequencing (RNA-Seq) reads being predominantly mapped to exons that account for just under 3% of the human genome. Recently, we have used e

Externí odkaz: https://doaj.org/article/17c1e1c19ae1481ebffd5a68de814978

Using equivalence class counts for fast and accurate testing of differential transcript usage [version 2; peer review: 1 approved, 2 approved with reservations]

Autor: Marek Cmero, Nadia M. Davidson, Alicia Oshlack

Publikováno v: F1000Research, Vol 8 (2019)

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differential gene expression is the most widely used application of this technology, RNA-seq data also has the resolution to inf

Externí odkaz: https://doaj.org/article/56238b11b21b461491b85e841b8f731f

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Autor: Stefan C. Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester, Ignacio Vázquez-García, Kortine Kleinheinz, Dimitri G. Livitz, Salem Malikic, Nilgun Donmez, Subhajit Sengupta, Pavana Anur, Clemency Jolly, Marek Cmero, Daniel Rosebrock, Steven E. Schumacher, Yu Fan, Matthew Fittall, Ruben M. Drews, Xiaotong Yao, Thomas B.K. Watkins, Juhee Lee, Matthias Schlesner, Hongtu Zhu, David J. Adams, Nicholas McGranahan, Charles Swanton, Gad Getz, Paul C. Boutros, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Inigo Martincorena, Florian Markowetz, Ville Mustonen, Ke Yuan, Moritz Gerstung, Paul T. Spellman, Wenyi Wang, Quaid D. Morris, David C. Wedge, Peter Van Loo, Santiago Gonzalez, David D. Bowtell, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Roland Eils, Dale W. Garsed, Gavin Ha, Lara Jerman, Henry Lee-Six, Thomas J. Mitchell, Layla Oesper, Myron Peto, Benjamin J. Raphael, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Lincoln D. Stein, Oliver Spiro, Shankar Vembu, David A. Wheeler, Tsun-Po Yang

Publikováno v: Cell, vol 184, iss 8
PCAWG Evolution and Heterogeneity Working Group, PCAWG Consortium & Wedge, D C 2021, ' Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes ', Cell, vol. 184, no. 8, pp. 2239-2254.e39 . https://doi.org/10.1016/j.cell.2021.03.009
Cell

Summary Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bb531f63564192b68acc8f428aac07cd
http://hdl.handle.net/10138/330238

MSH2-deficient prostate tumours have a distinct immune response and clinical outcome compared to MSH2-deficient colorectal or endometrial cancer

Autor: Izhak Haviv, Michael J Clarkson, Michael Kerger, Ryan Stuchbery, Niall M. Corcoran, Ryan Hutchinson, Andrew M. Ryan, Anthony J. Costello, Marek Cmero, Sebastian Lunke, Geoff Macintyre, Ben Tran, Ken Chow, Stefano Mangiola, Christopher M. Hovens, Patrick Mccoy, Natalie Kurganovs, Peter Georgeson, Matthew K.H. Hong, Bernard J. Pope

Publikováno v: Prostate cancer and prostatic diseases. 24(4)

Recent publications have shown patients with defects in the DNA mismatch repair (MMR) pathway driven by either MSH2 or MSH6 loss experience a significant increase in the incidence of prostate cancer. Moreover, this increased incidence of prostate can

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9983f020d42d6527b6b136a620e9d43b
https://pubmed.ncbi.nlm.nih.gov/34108644