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2020 Journal Article Digital spatial profiling application in breast cancer: a user’s perspectiveMcCart Reed, Amy E., Bennett, James, Kutasovic, Jamie R., Kalaw, Emarene, Ferguson, Kaltin, Yeong, Joe, Simpson, Peter T. and Lakhani, Sunil R. (2020). Digital spatial profiling application in breast cancer: a user’s perspective. Virchows Archiv, 477 (6), 885-890. doi: 10.1007/s00428-020-02821-9 |
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2020 Journal Article Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast CancerKutasovic, Jamie R., McCart Reed, Amy E., Sokolova, Anna, Lakhani, Sunil R. and Simpson, Peter T. (2020). Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer. Cancers, 12 (4) 848, 848. doi: 10.3390/cancers12040848 |
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2020 Journal Article Butler enables rapid cloud-based analysis of thousands of human genomesYakneen, Sergei, Waszak, Sebastian M., Gertz, Michael, Korbel, Jan O., Aminou, Brice, Bartolome, Javier, Boroevich, Keith A., Boyce, Rich, Brooks, Angela N., Buchanan, Alex, Buchhalter, Ivo, Butler, Adam P., Byrne, Niall J., Cafferkey, Andy, Campbell, Peter J., Chen, Zhaohong, Cho, Sunghoon, Choi, Wan, Clapham, Peter, Davis-Dusenbery, Brandi N., De La Vega, Francisco M., Demeulemeester, Jonas, Dow, Michelle T., Dursi, Lewis Jonathan, Eils, Juergen, Eils, Roland, Ellrott, Kyle, Farcas, Claudiu, Favero, Francesco ... von Mering, Christian (2020). Butler enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, 38 (3), 288-292. doi: 10.1038/s41587-019-0360-3 |
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2020 Journal Article Genomic basis for RNA alterations in cancerCalabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang ... von Mering, Christian (2020). Genomic basis for RNA alterations in cancer. Nature, 578 (7793), 129-136. doi: 10.1038/s41586-020-1970-0 |
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2020 Journal Article Pan-cancer analysis of whole genomesCampbell, Peter J., Getz, Gad, Korbel, Jan O., Stuart, Joshua M., Jennings, Jennifer L., Stein, Lincoln D., Perry, Marc D., Nahal-Bose, Hardeep K., Ouellette, B. F. Francis, Li, Constance H., Rheinbay, Esther, Nielsen, G. Petur, Sgroi, Dennis C., Wu, Chin-Lee, Faquin, William C., Deshpande, Vikram, Boutros, Paul C., Lazar, Alexander J., Hoadley, Katherine A., Louis, David N., Dursi, L. Jonathan, Yung, Christina K., Bailey, Matthew H., Saksena, Gordon, Raine, Keiran M., Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun ... Hamdy, Freddie C. (2020). Pan-cancer analysis of whole genomes. Nature, 578 (7793), 82-93. doi: 10.1038/s41586-020-1969-6 |
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2020 Journal Article Comprehensive molecular characterization of mitochondrial genomes in human cancersYuan, Yuan, Ju, Young Seok, Kim, Youngwook, Li, Jun, Wang, Yumeng, Yoon, Christopher J., Yang, Yang, Martincorena, Inigo, Creighton, Chad J., Weinstein, John N., Xu, Yanxun, Han, Leng, Kim, Hyung-Lae, Nakagawa, Hidewaki, Park, Keunchil, Campbell, Peter J., Liang, Han, Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C., Al-Ahmadie, Hikmat ... von Mering, Christian (2020). Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature Genetics, 52 (3), 342-352. doi: 10.1038/s41588-019-0557-x |
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2019 Journal Article Homologous recombination DNA repair defects in PALB2-associated breast cancersLi, Anqi, Geyer, Felipe C., Blecua, Pedro, Lee, Ju Youn, Selenica, Pier, Brown, David N., Pareja, Fresia, Lee, Simon S. K., Kumar, Rahul, Rivera, Barbara, Bi, Rui, Piscuoglio, Salvatore, Wen, Hannah Y., Lozada, John R., Gularte-Mérida, Rodrigo, Cavallone, Luca, Aghmesheh, Morteza, Amor, David, Andrews, Leslie, Antill, Yoland, Balleine, Rosemary, Beesley, Jonathan, Blackburn, Anneke, Bogwitz, Michael, Brown, Melissa, Burgess, Matthew, Burke, Jo, Butow, Phyllis, Caldon, Liz ... Reis-Filho, Jorge S. (2019). Homologous recombination DNA repair defects in PALB2-associated breast cancers. npj Breast Cancer, 5 (1) 23. doi: 10.1038/s41523-019-0115-9 |
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2019 Journal Article Publisher Correction: Homologous recombination DNA repair defects in PALB2-associated breast cancers (npj Breast Cancer, (2019), 5, 1, (23), 10.1038/s41523-019-0115-9)Li, Anqi, Geyer, Felipe C., Blecua, Pedro, Lee, Ju Youn, Selenica, Pier, Brown, David N., Pareja, Fresia, Lee, Simon S. K., Kumar, Rahul, Rivera, Barbara, Bi, Rui, Piscuoglio, Salvatore, Wen, Hannah Y., Lozada, John R., Gularte-Mérida, Rodrigo, Cavallone, Luca, Aghmesheh, Morteza, Amor, David, Andrews, Leslie, Antill, Yoland, Balleine, Rosemary, Beesley, Jonathan, Blackburn, Anneke, Bogwitz, Michael, Brown, Melissa, Burgess, Matthew, Burke, Jo, Butow, Phyllis, Caldon, Liz ... Reis-Filho, Jorge S. (2019). Publisher Correction: Homologous recombination DNA repair defects in PALB2-associated breast cancers (npj Breast Cancer, (2019), 5, 1, (23), 10.1038/s41523-019-0115-9). npj Breast Cancer, 5 (1) 44. doi: 10.1038/s41523-019-0140-8 |
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2019 Journal Article LobSig is a multigene predictor of outcome in invasive lobular carcinomaMcCart Reed, Amy E., Lal, Samir, Kutasovic, Jamie R., Wockner, Leesa, Robertson, Alan, de Luca, Xavier M., Kalita-de Croft, Priyakshi, Dalley, Andrew J., Coorey, Craig P., Kuo, Luyu, Ferguson, Kaltin, Niland, Colleen, Miller, Gregory, Johnson, Julie, Reid, Lynne E., Males, Renique, Saunus, Jodi M., Chenevix-Trench, Georgia, Coin, Lachlan, Lakhani, Sunil R. and Simpson, Peter T. (2019). LobSig is a multigene predictor of outcome in invasive lobular carcinoma. npj Breast Cancer, 5 (1) 18, 18. doi: 10.1038/s41523-019-0113-y |
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2019 Journal Article Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancersNones, K., Johnson, J., Newell, F., Patch, A. M., Thorne, H., Kazakoff, S. H., de Luca, X. M., Parsons, M. T., Ferguson, K., Reid, L. E., McCart Reed, A. E., Srihari, S., Lakis, V., Davidson, A. L., Mukhopadhyay, P., Holmes, O., Xu, Q., Wood, S., Leonard, C., The Kathleen Cuningham Foundation Consortium for Research into Familial Aspects of Breast Cancer (kConFab), The Australian Breast Cancer Tissue Bank (ABCTB), The Brisbane Breast Bank (BBB), Beesley, J., Harris, J. M., Barnes, D., Degasperi, A., Ragan, M. A., Spurdle, A. B., Khanna, K. K. ... Simpson, P. T. (2019). Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Annals of Oncology, 30 (7) mdz132, 1071-1079. doi: 10.1093/annonc/mdz132 |
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2019 Journal Article Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancerFerreira, Manuel A., Gamazon, Eric R., Al-Ejeh, Fares, Aittomaki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arason, Adalgeir, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Asseryanis, Ella, Azzollini, Jacopo, Balmana, Judith, Barnes, Daniel R., Barrowdale, Daniel, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blomqvist, Carl, Bogdanova, Natalia, Bojesen, Stig E., Bolla, Manjeet K., Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Broeks, Annegien, Burwinkel, Barbara ... Yip, Desmond (2019). Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. Nature Communications, 10 (1) 1741. doi: 10.1038/s41467-018-08053-5 |
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2019 Journal Article The circular RNome of primary breast cancerSmid, Marcel, Wilting, Saskia M., Uhr, Katharina, Rodriguez-Gonzalez, F. German, de Weerd, Vanja, Prager-Van der Smissen, Wendy J. C., van der Vlugt-Daane, Michelle, van Galen, Anne, Nik-Zainal, Serena, Butler, Adam, Martin, Sancha, Davies, Helen R., Staaf, Johan, van de Vijver, Marc J., Richardson, Andrea L., MacGrogan, Gaeten, Salgado, Roberto, van den Eynden, Gert G. G. M., Purdie, Colin A., Thompson, Alastair M., Caldas, Carlos, Span, Paul N., Sweep, Fred C. G. J., Simpson, Peter T., Lakhani, Sunil R., Van Laere, Steven, Desmedt, Christine, Paradiso, Angelo, Eyfjord, Jorunn ... Martens, John W. M. (2019). The circular RNome of primary breast cancer. Genome Research, 29 (3), 356-366. doi: 10.1101/gr.238121.118 |
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2019 Journal Article Erratum: Author correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences (Nature (2016) 534 7605 (47-54))Nik-Zainal, Serena, Davies, Helen, Staaf, Johan, Ramakrishna, Manasa, Glodzik, Dominik, Zou, Xueqing, Martincorena, Inigo, Alexandrov, Ludmil B., Martin, Sancha, Wedge, David C., Van Loo, Peter, Ju, Young Seok, Smid, Marcel, Brinkman, Arie B., Morganella, Sandro, Aure, Miriam R., Lingjærde, Ole Christian, Langerød, Anita, Ringnér, Markus, Ahn, Sung-Min, Boyault, Sandrine, Brock, Jane E., Broeks, Annegien, Butler, Adam, Desmedt, Christine, Dirix, Luc, Dronov, Serge, Fatima, Aquila, Foekens, John A. ... Stratton, Michael R. (2019). Erratum: Author correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences (Nature (2016) 534 7605 (47-54)). Nature, 566 (7742), E1-E1. doi: 10.1038/s41586-019-0883-2 |
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2019 Journal Article Diff-Quik cytology smears from endobronchial ultrasound transbronchial needle aspiration lymph node specimens as a source of DNA for next-generation sequencing instead of cell blocksFielding, David, Dalley, Andrew J., Bashirzadeh, Farzad, Singh, Mahendra, Nandakumar, Lakshmy, McCart Reed, Amy E., Black, Debra, Kazakoff, Stephen, Pearson, John V., Nones, Katia, Waddell, Nicola, Lakhani, Sunil R. and Simpson, Peter T. (2019). Diff-Quik cytology smears from endobronchial ultrasound transbronchial needle aspiration lymph node specimens as a source of DNA for next-generation sequencing instead of cell blocks. Respiration, 97 (6), 1-14. doi: 10.1159/000495661 |
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2019 Journal Article Phenotypic and molecular dissection of Metaplastic Breast Cancer and the prognostic implicationsMcCart Reed, Amy Ellen, Kalaw, Emarene, Nones, Katia, Bettington, Mark, Lim, Malcolm, Bennett, James, Johnstone, Kate, Kutasovic, Jamie Rose, Saunus, Jodi Marie, Kazakoff, Stephen, Xu, Qinying, Wood, Scott, Holmes, Oliver, Leonard, Conrad, Reid, Lynne Estelle, Black, Debra, Niland, Colleen, Ferguson, Kaltin, Gresshoff, Irma, Raghavendra, Ashwini, Harvey, Kate, Cooper, Caroline, Liu, Cheng, Kalinowski, Lauren, Reid, Andrew Scott, Davidson, Morgan, Pearson, John V, Pathmanathan, Nirmala, Tse, Gary ... Lakhani, Sunil R. (2019). Phenotypic and molecular dissection of Metaplastic Breast Cancer and the prognostic implications. Journal of Pathology, 247 (2), 214-227. doi: 10.1002/path.5184 |
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2019 Journal Article Breast cancer metastasis to gynaecological organs: a clinico‐pathological and molecular profiling studyKutasovic, Jamie R., McCart Reed, Amy E., Males, Renique, Sim, Sarah, Saunus, Jodi M., Dalley, Andrew, McEvoy, Christopher R., Dedina, Liana, Miller, Gregory, Peyton, Stephen, Reid, Lynne, Lal, Samir, Niland, Colleen, Ferguson, Kaltin, Fellowes, Andrew P., Al-Ejeh, Fares, Lakhani, Sunil R., Cummings, Margaret C. and Simpson, Peter T. (2019). Breast cancer metastasis to gynaecological organs: a clinico‐pathological and molecular profiling study. The Journal of Pathology: Clinical Research, 5 (1), 25-39. doi: 10.1002/cjp2.118 |
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2018 Journal Article Heritable DNA methylation marks associated with susceptibility to breast cancerJoo, Jihoon E., Dowty, James G., Milne, Roger L., Wong, Ee Ming, Dugué, Pierre-Antoine, English, Dallas, Hopper, John L., Goldgar, David E., Giles, Graham G., Southey, Melissa C., kConFab, Sexton, Adrienne, Christian, Alice, Trainer, Alison, Spigelman, Allan, Fellows, Andrew, Shelling, Andrew, De Fazio, Anna, Blackburn, Anneke, Crook, Ashley, Meiser, Bettina, Patterson, Briony, Clarke, Christine, Saunders, Christobel, Hunt, Clare, Scott, Clare, Amor, David, Marsh, Deborah, Edkins, Edward ... Antill, Yoland (2018). Heritable DNA methylation marks associated with susceptibility to breast cancer. Nature Communications, 9 (1) 867. doi: 10.1038/s41467-018-03058-6 |
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2018 Journal Article Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancersGłodzik, D, Purdie, C, Rye, I Hansine, Simpson, P, Staaf, J, Span, P N, Russnes, H and Nik-Zainal, S (2018). Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers. Annals of Oncology, 29 (11), 2223-2231. doi: 10.1093/annonc/mdy404 |
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2018 Journal Article Thioredoxin-interacting protein is an independent risk stratifier for breast ductal carcinoma in situMiligy, Islam M., Gorringe, Kylie L., Toss, Michael S., Al-Kawaz, Abdulbaqi A., Simpson, Peter, Diez-Rodriguez, Maria, Nolan, Christopher C., Ellis, Ian O., Green, Andrew R. and Rakha, Emad A. (2018). Thioredoxin-interacting protein is an independent risk stratifier for breast ductal carcinoma in situ. Modern Pathology, 31 (12), 1-9. doi: 10.1038/s41379-018-0086-7 |
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2018 Journal Article Mixed ductal-lobular carcinomas: evidence for progression from ductal to lobular morphologyMcCart Reed, Amy E., Kutasovic, Jamie R., Nones, Katia, Saunus, Jodi M., Da Silva, Leonard, Newell, Felicity, Kazakoff, Stephen, Melville, Lewis, Jayanthan, Janani, Vargas, Ana Cristina, Reid, Lynne E., Beesley, Jonathan, Chen, Xiao Qing, Patch, Anne Marie, David Clouston, D., Porter, Alan, Evans, Elizabeth, Pearson, John V., Chenevix-Trench, Georgia, Cummings, Margaret C., Waddell, Nic, Lakhani, Sunil R. and Simpson, Peter T. (2018). Mixed ductal-lobular carcinomas: evidence for progression from ductal to lobular morphology. The Journal of Pathology, 244 (4), 460-468. doi: 10.1002/path.5040 |
