Lichtenstein P, Holm NV, Verkasalo PK, Iliadou A, Kaprio J, Koskenvuo M, et al. Environmental and heritable factors in the causation of cancer–analyses of cohorts of twins from Sweden, Denmark, and Finland. N Engl J Med. 2000;343(2):78–85.
Article CAS PubMed Google Scholar
Rahman N. Realizing the promise of cancer predisposition genes. Nature. 2014;505(7483):302–8.
Article CAS PubMed PubMed Central Google Scholar
Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, et al. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018;173(2):355-70.e14.
Article CAS PubMed PubMed Central Google Scholar
Kamps R, Brandão RD, van den Bosch BJ, Paulussen ADC, Xanthoulea S, Blok MJ, et al. Next-generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int J Mol Sci. 2017;18(2):308.
Article PubMed PubMed Central Google Scholar
Guo X, Shi J, Cai Q, Shu XO, He J, Wen W, et al. Use of deep whole-genome sequencing data to identify structure risk variants in breast cancer susceptibility genes. Hum Mol Genet. 2018;27(5):853–9.
Article CAS PubMed PubMed Central Google Scholar
Suzuki T, Tsurusaki Y, Nakashima M, Miyake N, Saitsu H, Takeda S, et al. Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing. J Hum Genet. 2014;59(12):649–54.
Article CAS PubMed Google Scholar
Tan NB, Stapleton R, Stark Z, Delatycki MB, Yeung A, Hunter MF, et al. Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review. Mol Genet Genomic Med. 2020;8(11):e1508.
Article PubMed PubMed Central Google Scholar
Robertson AJ, Tan NB, Spurdle AB, Metke-Jimenez A, Sullivan C, Waddell N. Re-analysis of genomic data: an overview of the mechanisms and complexities of clinical adoption. Genet Med. 2022;24(4):798–810.
Article CAS PubMed Google Scholar
Mitchell G, Campbell I, Dawkins H, Fox S, Hiller J, James P, et al. An Introduction to ICCon - Inherited Cancer Connect Partnership [Poster Abstract]. Asia Pac J Clin Oncol. 2013;9(S3):100–59.
Harris PA, Taylor R, Thielke R, Payne J, Gonzalez N, Conde JG. Research electronic data capture (REDCap)–a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform. 2009;42(2):377–81.
Harris PA, Taylor R, Minor BL, Elliott V, Fernandez M, O’Neal L, et al. The REDCap consortium: building an international community of software platform partners. J Biomed Inform. 2019;95:103208.
Article PubMed PubMed Central Google Scholar
Tudini E, Davidson AL, Dressel U, Andrews L, Antill Y, Crook A, et al. Implementing gene curation for hereditary cancer susceptibility in Australia: achieving consensus on genes with clinical utility. J Med Genet. 2021;58(12):853–8.
Article CAS PubMed Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):3.
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv: 1303.3997v2. 2013.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article PubMed PubMed Central Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Article CAS PubMed PubMed Central Google Scholar
Kassahn KS, Holmes O, Nones K, Patch AM, Miller DK, Christ AN, et al. Somatic point mutation calling in low cellularity tumors. PLoS One. 2013;8(11):e74380.
Article CAS PubMed PubMed Central Google Scholar
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. The ensembl variant effect predictor. Genome Biol. 2016;17(1):122.
Article PubMed PubMed Central Google Scholar
Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018;46(D1):D1062–7.
Article CAS PubMed Google Scholar
Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581(7809):434–43.
Article CAS PubMed PubMed Central Google Scholar
Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28(18):i333–9.
Article CAS PubMed PubMed Central Google Scholar
Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011;21(6):974–84.
Article CAS PubMed PubMed Central Google Scholar
Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R, et al. Fast computation and applications of genome mappability. PLoS ONE. 2012;7(1): e30377.
Article CAS PubMed PubMed Central Google Scholar
Trost B, Walker S, Wang Z, Thiruvahindrapuram B, MacDonald JR, Sung WWL, et al. A comprehensive workflow for read depth-based identification of copy-number variation from whole-genome sequence data. Am J Hum Genet. 2018;102(1):142–55.
Article CAS PubMed PubMed Central Google Scholar
Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, et al. A structural variation reference for medical and population genetics. Nature. 2020;581(7809):444–51.
Article CAS PubMed PubMed Central Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–92.
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.
Article PubMed PubMed Central Google Scholar
Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am J Hum Genet. 2016;99(4):877–85.
Article CAS PubMed PubMed Central Google Scholar
Choi Y, Chan AP. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics. 2015;31(16):2745–7.
Article CAS PubMed PubMed Central Google Scholar
Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46(3):310–5.
Article CAS PubMed PubMed Central Google Scholar
Eratne D, Schneider A, Lynch E, Martyn M, Velakoulis D, Fahey M, et al. The clinical utility of exome sequencing and extended bioinformatic analyses in adolescents and adults with a broad range of neurological phenotypes: an Australian perspective. J Neurol Sci. 2021;420:117260.
Article CAS PubMed Google Scholar
Gordon LG, White NM, Elliott TM, Nones K, Beckhouse AG, Rodriguez-Acevedo AJ, et al. Estimating the costs of genomic sequencing in cancer control. BMC Health Serv Res. 2020;20(1):492.
Article PubMed PubMed Central Google Scholar
eviQ Cancer Treatments Online 2017: Cancer Institute NSW; Available from: https://www.eviq.org.au/.
Kundu S, Brinkmeyer MK, Livingston AL, David SS. Adenine removal activity and bacterial complementation with the human MutY homologue (MUTYH) and Y165C, G382D, P391L and Q324R variants associated with colorectal cancer. DNA Repair. 2009;8(12):1400–10.
Article CAS PubMed PubMed Central Google Scholar
Southey MC, Teo ZL, Dowty JG, Odefrey FA, Park DJ, Tischkowitz M, et al. A PALB2 mutation associated with high risk of breast cancer. Breast Cancer Res. 2010;12(6):R109.
Article CAS PubMed PubMed Central Google Scholar
Thompson ER, Gorringe KL, Rowley SM, Wong-Brown MW, McInerny S, Li N, et al. Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls. Breast Cancer Res. 2015;17(1):111.
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