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

A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction

Autor: Joanne M. Hildebrand, Maria Kauppi, Ian J. Majewski, Zikou Liu, Allison J. Cox, Sanae Miyake, Emma J. Petrie, Michael A. Silk, Zhixiu Li, Maria C. Tanzer, Gabriela Brumatti, Samuel N. Young, Cathrine Hall, Sarah E. Garnish, Jason Corbin, Michael D. Stutz, Ladina Di Rago, Pradnya Gangatirkar, Emma C. Josefsson, Kristin Rigbye, Holly Anderton, James A. Rickard, Anne Tripaydonis, Julie Sheridan, Thomas S. Scerri, Victoria E. Jackson, Peter E. Czabotar, Jian-Guo Zhang, Leila Varghese, Cody C. Allison, Marc Pellegrini, Gillian M. Tannahill, Esme C. Hatchell, Tracy A. Willson, Dina Stockwell, Carolyn A. de Graaf, Janelle Collinge, Adrienne Hilton, Natasha Silke, Sukhdeep K. Spall, Diep Chau, Vicki Athanasopoulos, Donald Metcalf, Ronald M. Laxer, Alexander G. Bassuk, Benjamin W. Darbro, Maria A. Fiatarone Singh, Nicole Vlahovich, David Hughes, Maria Kozlovskaia, David B. Ascher, Klaus Warnatz, Nils Venhoff, Jens Thiel, Christine Biben, Stefan Blum, John Reveille, Michael S. Hildebrand, Carola G. Vinuesa, Pamela McCombe, Matthew A. Brown, Benjamin T. Kile, Catriona McLean, Melanie Bahlo, Seth L. Masters, Hiroyasu Nakano, Polly J. Ferguson, James M. Murphy, Warren S. Alexander, John Silke

Publikováno v: Nature Communications, Vol 11, Iss 1, Pp 1-16 (2020)

Necroptosis is a regulated form of inflammatory cell death driven by activated MLKL. Here, the authors identify a mutation in the brace region that confers constitutive activation, leading to lethal inflammation in homozygous mutant mice and providin

Externí odkaz: https://doaj.org/article/eb684694de314067aac5b53c9a7c86cd

SuperFreq: Integrated mutation detection and clonal tracking in cancer.

Autor: Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J Majewski

Publikováno v: PLoS Computational Biology, Vol 16, Iss 2, p e1007603 (2020)

Analysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves. Monitoring the expansion and contraction of distinct clones helps to reveal the mutations that initiate the disease and those that driv

Externí odkaz: https://doaj.org/article/d340fd5794ea4940b93de0376ed72bed

The BRCA1ness signature is associated significantly with response to PARP inhibitor treatment versus control in the I-SPY 2 randomized neoadjuvant setting

Autor: Tesa M. Severson, Denise M. Wolf, Christina Yau, Justine Peeters, Diederik Wehkam, Philip C. Schouten, Suet-Feung Chin, Ian J. Majewski, Magali Michaut, Astrid Bosma, Bernard Pereira, Tycho Bismeijer, Lodewyk Wessels, Carlos Caldas, René Bernards, Iris M. Simon, Annuska M. Glas, Sabine Linn, Laura van ‘t Veer

Publikováno v: Breast Cancer Research, Vol 19, Iss 1, Pp 1-9 (2017)

Abstract Background Patients with BRCA1-like tumors correlate with improved response to DNA double-strand break-inducing therapy. A gene expression-based classifier was developed to distinguish between BRCA1-like and non-BRCA1-like tumors. We hypothe

Externí odkaz: https://doaj.org/article/f9d39320e8404ffdb7196315ea5646b3

Germline MBD4 deficiency causes a multi-tumor predisposition syndrome

Autor: Claire Palles, Hannah D. West, Edward Chew, Sara Galavotti, Christoffer Flensburg, Judith E. Grolleman, Erik A.M. Jansen, Helen Curley, Laura Chegwidden, Edward H. Arbe-Barnes, Nicola Lander, Rebekah Truscott, Judith Pagan, Ashish Bajel, Kitty Sherwood, Lynn Martin, Huw Thomas, Demetra Georgiou, Florentia Fostira, Yael Goldberg, David J. Adams, Simone A.M. van der Biezen, Michael Christie, Mark Clendenning, Laura E. Thomas, Constantinos Deltas, Aleksandar J. Dimovski, Dagmara Dymerska, Jan Lubinski, Khalid Mahmood, Rachel S. van der Post, Mathijs Sanders, Jürgen Weitz, Jenny C. Taylor, Clare Turnbull, Lilian Vreede, Tom van Wezel, Celina Whalley, Claudia Arnedo-Pac, Giulio Caravagna, William Cross, Daniel Chubb, Anna Frangou, Andreas J. Gruber, Ben Kinnersley, Boris Noyvert, David Church, Trevor Graham, Richard Houlston, Nuria Lopez-Bigas, Andrea Sottoriva, David Wedge, Mark A. Jenkins, Roland P. Kuiper, Andrew W. Roberts, Jeremy P. Cheadle, Marjolijn J.L. Ligtenberg, Nicoline Hoogerbrugge, Viktor H. Koelzer, Andres Dacal Rivas, Ingrid M. Winship, Clara Ruiz Ponte, Daniel D. Buchanan, Derek G. Power, Andrew Green, Ian P.M. Tomlinson, Julian R. Sampson, Ian J. Majewski, Richarda M. de Voer

Publikováno v: American Journal of Human Genetics, 109(5), 953-960. Cell Press
Palles, C, West, H, Chew, E, Galavotti, S, Flensburg, C, Grolleman, J, Jansen, E, Curley, H, Chedwiggen, L, Arbe-Barnes, E, Lander, N, Truscot, R, Pagan, J, Bajel, A, Sherwood, K, Martin, L, Thomas, H, Georgiou, D, Fostira, F, Goldberg, Y, Adams, D, van der Biezen, S, Christie, M, Clendenning, M, Thomas, L, Deltas, C, Dimovski, A, Dymerska, D, Lubinski, J, Mahmood, K, van der Post, R, Sanders, M, Weitz, J, Taylor, J, Turnbull, C, Vreede, L, van Wezel, T, Whalley, C, Arnedo, C, Caravagna, G, Cross, W, Chubb, D, Frangou, A, Gruber, A, Kinnersley, B, Noyvert, B, Church, D, Graham, T, Houlston, R, Lopez, N, Sottoriva, A, Wedge, D, Jenkins, M, Kuiper, R, Roberts, A, Cheadle, J, Ligtenberg, M, Hoogerbrugge, N, Koelzer, V, Dacal Rivas, A, Winship, I, Ruiz Ponte, C, Buchanan, D, Power, D, Green, A, Tomlinson, I P M, Sampson, J, Majewski, I & M. de Voer, R 2022, ' Germline MBD4-deficiency causes a multi-tumor predisposition syndrome ', American Journal of Human Genetics, vol. 109, no. 5, pp. 953-960 . https://doi.org/10.1016/j.ajhg.2022.03.018
American Journal of Human Genetics, 109, 953-960
American Journal of Human Genetics, 109, 5, pp. 953-960

Contains fulltext : 251996.pdf (Publisher’s version ) (Open Access) We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f57bab222db11593a33cdeea1ce5674f
https://doi.org/10.1016/j.ajhg.2022.03.018