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2024 Journal Article Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 variant curation expert panelParsons, Michael T., de la Hoya, Miguel, Richardson, Marcy E., Tudini, Emma, Anderson, Michael, Berkofsky-Fessler, Windy, Caputo, Sandrine M., Chan, Raymond C., Cline, Melissa S., Feng, Bing-Jian, Fortuno, Cristina, Gomez-Garcia, Encarna, Hadler, Johanna, Hiraki, Susan, Holdren, Megan, Houdayer, Claude, Hruska, Kathleen, James, Paul, Karam, Rachid, Leong, Huei San, Martins, Alexandra, Mensenkamp, Arjen R., Monteiro, Alvaro N., Nathan, Vaishnavi, O'Connor, Robert, Pedersen, Inge Sokilde, Pesaran, Tina, Radice, Paolo, Schmidt, Gunnar ... Spurdle, Amanda B. (2024). Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 variant curation expert panel. The American Journal of Human Genetics, 111 (9), 2044-2058. doi: 10.1016/j.ajhg.2024.07.013 |
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2024 Journal Article Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing datasetDavidson, Aimee L., Michailidou, Kyriaki, Parsons, Michael T., Fortuno, Cristina, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Naven, Marc, Abubakar, Mustapha, Ahearn, Thomas U., Alonso, M. Rosario, Andrulis, Irene L., Antoniou, Antonis C., Auvinen, Päivi, Behrens, Sabine, Bermisheva, Marina A., Bogdanova, Natalia V., Bojesen, Stig E., Brüning, Thomas, Byers, Helen J., Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Cessna, Melissa H., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Sahlberg, Kristine K., Børresen-Dale, Anne-Lise ... kConFab Investigators (2024). Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing dataset. The American Journal of Human Genetics, 111 (9), 2059-2069. doi: 10.1016/j.ajhg.2024.07.004 |
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2024 Journal Article Regional-specific calibration enables application of computational evidence for clinical classification of 5′ cis-regulatory variants in Mendelian diseaseVillani, Rehan M., McKenzie, Maddison E., Davidson, Aimee L. and Spurdle, Amanda B. (2024). Regional-specific calibration enables application of computational evidence for clinical classification of 5′ cis-regulatory variants in Mendelian disease. American Journal of Human Genetics, 111 (7), 1301-1315. doi: 10.1016/j.ajhg.2024.05.002 |
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2024 Journal Article Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelinesFortuno, Cristina, Michailidou, Kyriaki, Parsons, Michael, Dolinsky, Jill S., Pesaran, Tina, Yussuf, Amal, Mester, Jessica L., Hruska, Kathleen S., Hiraki, Susan, O'Connor, Robert, Chan, Raymond C., Kim, Serra, Tavtigian, Sean, Goldgar, David, James, Paul A. and Spurdle, Amanda B. (2024). Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines. Human Molecular Genetics, 33 (8), 724-732. doi: 10.1093/hmg/ddae009 |
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2023 Journal Article The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort studyDavidson, Aimee L., Dressel, Uwe, Norris, Sarah, Canson, Daffodil M., Glubb, Dylan M., Fortuno, Cristina, Hollway, Georgina E., Parsons, Michael T., Vidgen, Miranda E., Holmes, Oliver, Koufariotis, Lambros T., Lakis, Vanessa, Leonard, Conrad, Wood, Scott, Xu, Qinying, McCart Reed, Amy E., Pickett, Hilda A., Al-Shinnag, Mohammad K., Austin, Rachel L., Burke, Jo, Cops, Elisa J., Nichols, Cassandra B., Goodwin, Annabel, Harris, Marion T., Higgins, Megan J., Ip, Emilia L., Kiraly-Borri, Catherine, Lau, Chiyan, Mansour, Julia L. ... Ward, Robyn L. (2023). The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort study. Genome Medicine, 15 (1) 74, 1-16. doi: 10.1186/s13073-023-01223-1 |
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2023 Journal Article Design and quality control of large-scale two-sample Mendelian randomization studiesHaycock, Philip C, Borges, Maria Carolina, Burrows, Kimberley, Lemaitre, Rozenn N, Harrison, Sean, Burgess, Stephen, Chang, Xuling, Westra, Jason, Khankari, Nikhil K, Tsilidis, Kostas K, Gaunt, Tom, Hemani, Gibran, Zheng, Jie, Truong, Therese, O'Mara, Tracy A, Spurdle, Amanda B, Law, Matthew H, Slager, Susan L, Birmann, Brenda M, Saberi Hosnijeh, Fatemeh, Mariosa, Daniela, Amos, Christopher I, Hung, Rayjean J, Zheng, Wei, Gunter, Marc J, Davey Smith, George, Relton, Caroline and Martin, Richard M (2023). Design and quality control of large-scale two-sample Mendelian randomization studies. International Journal of Epidemiology, 52 (5), 1498-1521. doi: 10.1093/ije/dyad018 |
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2023 Journal Article Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing SubgroupWalker, Logan C., Hoya, Miguel de la, Wiggins, George A R, Lindy, Amanda, Vincent, Lisa M., Parsons, Michael T., Canson, Daffodil M., Bis-Brewer, Dana, Cass, Ashley, Tchourbanov, Alexander, Zimmermann, Heather, Byrne, Alicia B., Pesaran, Tina, Karam, Rachid, Harrison, Steven M., Spurdle, Amanda B. and ClinGen Sequence Variant Interpretation Working Group (2023). Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. American Journal of Human Genetics, 110 (7), 1046-1067. doi: 10.1016/j.ajhg.2023.06.002 |
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2023 Journal Article The association between genetically elevated polyunsaturated fatty acids and risk of cancerTintle, Nathan, Rice, Terri, Cheng, Iona, Jenkins, Mark, Gallinger, Steve, Cornish, Alex J., Sud, Amit, Vijayakrishnan, Jayaram, Wrensch, Margaret, Johansson, Mattias, Norman, Aaron D., Klein, Alison, Clay-Gilmour, Alyssa, Franke, Andre, Ardisson Korat, Andres V., Wheeler, Bill, Nilsson, Björn, Smith, Caren, Heng, Chew-Kiat, Song, Ci, Riadi, David, Claus, Elizabeth B., Ellinghaus, Eva, Ostroumova, Evgenia, Hosnijeh,, de Vathaire, Florent, Cugliari, Giovanni, Matullo, Giuseppe, Oi-Lin Ng, Irene ... Martin, Richard M. (2023). The association between genetically elevated polyunsaturated fatty acids and risk of cancer. eBioMedicine, 91 104510. doi: 10.1016/j.ebiom.2023.104510 |
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2023 Journal Article Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genesCanson, Daffodil M., O’Mara, Tracy A., Spurdle, Amanda B. and Glubb, Dylan M. (2023). Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes. Human Genetics and Genomics Advances, 4 (2) 100185, 1-7. doi: 10.1016/j.xhgg.2023.100185 |
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2023 Journal Article SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletionCanson, Daffodil M., Davidson, Aimee L., de la Hoya, Miguel, Parsons, Michael T., Glubb, Dylan M., Kondrashova, Olga and Spurdle, Amanda B. (2023). SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion. Bioinformatics, 39 (4) btad179, 1-3. doi: 10.1093/bioinformatics/btad179 |
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2022 Journal Article Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplarsCanson, Daffodil, Glubb, Dylan and Spurdle, Amanda B. (2022). Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Human Mutation, 43 (12), 2328-2328. doi: 10.1002/humu.24500 |
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2022 Journal Article Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretationTudini, Emma, Andrews, James, Lawrence, David M., King-Smith, Sarah L., Baker, Naomi, Baxter, Leanne, Beilby, John, Bennetts, Bruce, Beshay, Victoria, Black, Michael, Boughtwood, Tiffany F., Brion, Kristian, Cheong, Pak Leng, Christie, Michael, Christodoulou, John, Chong, Belinda, Cox, Kathy, Davis, Mark R., Dejong, Lucas, Dinger, Marcel E., Doig, Kenneth D., Douglas, Evelyn, Dubowsky, Andrew, Ellul, Melissa, Fellowes, Andrew, Fisk, Katrina, Fortuno, Cristina, Friend, Kathryn, Gallagher, Renee L. ... and on behalf of the Shariant Consortium (2022). Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. American Journal of Human Genetics, 109 (11), 1960-1973. doi: 10.1016/j.ajhg.2022.10.006 |
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2022 Journal Article The splicing effect of variants at branchpoint elements in cancer genesCanson, Daffodil M., Dumenil, Troy, Parsons, Michael T., O'Mara, Tracy A., Davidson, Aimee L., Okano, Satomi, Signal, Bethany, Mercer, Tim R., Glubb, Dylan M. and Spurdle, Amanda B. (2022). The splicing effect of variants at branchpoint elements in cancer genes. Genetics in Medicine, 24 (2), 398-409. doi: 10.1016/j.gim.2021.09.020 |
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2021 Journal Article Germline and Tumor Sequencing as a Diagnostic Tool To Resolve Suspected Lynch SyndromePope, Bernard J., Clendenning, Mark, Rosty, Christophe, Mahmood, Khalid, Georgeson, Peter, Joo, Jihoon E., Walker, Romy, Hutchinson, Ryan A., Jayasekara, Harindra, Joseland, Sharelle, Como, Julia, Preston, Susan, Spurdle, Amanda B., Macrae, Finlay A., Win, Aung K., Hopper, John L., Jenkins, Mark A., Winship, Ingrid M. and Buchanan, Daniel D. (2021). Germline and Tumor Sequencing as a Diagnostic Tool To Resolve Suspected Lynch Syndrome. Journal of Molecular Diagnostics, 23 (3), 358-371. doi: 10.1016/j.jmoldx.2020.12.003 |
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2021 Journal Article The Impact of Variants at Branchpoint Splicing Elements in Cancer GenesCanson, Daffodil, Dumenil, Troy, Parsons, Michael, O’Mara, Tracy, Davidson, Aimee , Okano, Satomi , Signal, Bethany , Mercer, Tim, Glubb, Dylan and Spurdle, Amanda (2021). The Impact of Variants at Branchpoint Splicing Elements in Cancer Genes. SSRN Electronic Journal, 24 (2), 398-409. doi: 10.2139/ssrn.3933049 |
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2020 Journal Article Co-existence of leiomyomas, adenomyosis and endometriosis in women with endometrial cancerJohnatty, Sharon E., Stewart, Colin J. R., Smith, Deborah, Nguyen, Anthony, O’ Dwyer, John, O’Mara, Tracy A., Webb, Penelope M. and Spurdle, Amanda B. (2020). Co-existence of leiomyomas, adenomyosis and endometriosis in women with endometrial cancer. Scientific Reports, 10 (1) 3621. doi: 10.1038/s41598-020-59916-1 |
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2020 Journal Article Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplarsCanson, Daffodil, Glubb, Dylan and Spurdle, Amanda B. (2020). Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Human Mutation, 41 (10) humu.24074, 1705-1721. doi: 10.1002/humu.24074 |
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2019 Journal Article A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndromeDrost, Mark, Tiersma, Yvonne, Thompson, Bryony A., Frederiksen, Jane H., Keijzers, Guido, Glubb, Dylan, Kathe, Scott, Osinga, Jan, Westers, Helga, Pappas, Lisa, Boucher, Kenneth M., Molenkamp, Siska, Zonneveld, José B., van Asperen, Christi J., Goldgar, David E., Wallace, Susan S., Sijmons, Rolf H., Spurdle, Amanda B., Rasmussen, Lene J., Greenblatt, Marc S., de Wind, Niels and Tavtigian, Sean V. (2019). A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndrome. Genetics in Medicine, 21 (7), 1486-1496. doi: 10.1038/s41436-018-0372-2 |
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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 Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variantsDadaev, Tokhir, Saunders, Edward J., Newcombe, Paul J., Anokian, Ezequiel, Leongamornlert, Daniel A., Brook, Mark N., Cieza-Borrella, Clara, Mijuskovic, Martina, Wakerell, Sarah, Olama, Ali Amin Al, Schumacher, Fredrick R., Berndt, Sonja I., Benlloch, Sara, Ahmed, Mahbubl, Goh, Chee, Sheng, Xin, Zhang, Zhuo, Muir, Kenneth, Govindasami, Koveela, Lophatananon, Artitaya, Stevens, Victoria L., Gapstur, Susan M., Carter, Brian D., Tangen, Catherine M., Goodman, Phyllis, Thompson, Ian M., Batra, Jyotsna, Chambers, Suzanne, Moya, Leire ... The PRACTICAL (Prostate Cancer Association Group to Investigate Cancer-Associated Alterations in the Genome) Consortium (2018). Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants. Nature Communications, 9 (1) 2256. doi: 10.1038/s41467-018-04109-8 |
