Whole genome sequencing and inheritance-based variant filtering as a tool for unraveling missing heritability in pediatric cancer

References

• Zhang J, Walsh MF, Wu G, et al. Germline Mutations in predisposition genes in pediatric cancer. N Engl J Med. 2015;373(24):2336–2346. doi:10.1056/NEJMoa1508054.
   PubMed Web of Science ®Google Scholar
• Brodeur GM, Nichols KE, Plon SE, Schiffman JD, Malkin D. Pediatric cancer predisposition and surveillance: an overview, and a tribute to Alfred G. Knudson Jr. Clin Cancer Res. 2017;23(11):e1–e5. doi:10.1158/1078-0432.CCR-17-0702.
   PubMed Web of Science ®Google Scholar
• Rahman N. Realizing the promise of cancer predisposition genes. Nature. 2014;505(7483):302–308. doi:10.1038/nature12981.
   PubMed Web of Science ®Google Scholar
• Rotunno M, Barajas R, Clyne M, et al. A systematic literature review of whole exome and genome sequencing population studies of genetic susceptibility to cancer. Cancer Epidemiol Biomarkers Prev. 2020;29(8):1519–1534. doi:10.1158/1055-9965.EPI-19-1551.
   PubMedGoogle Scholar
• Byrjalsen A, Hansen TVO, Stoltze UK, et al. Nationwide germline whole genome sequencing of 198 consecutive pediatric cancer patients reveals a high incidence of cancer prone syndromes. PLoS Genet. 2020;16(12):e1009231. doi:10.1371/journal.pgen.1009231.
   PubMedGoogle Scholar
• Wagener R, Taeubner J, Walter C, et al. Comprehensive germline-genomic and clinical profiling in 160 unselected children and adolescents with cancer. Eur J Hum Genet. 2021;29(8):1301–1311. doi:10.1038/s41431-021-00878-x.
   PubMedGoogle Scholar
• Zhang L, Jin Y, Zheng K, et al. Whole-genome sequencing identifies a novel variation of WAS gene coordinating with heterozygous germline mutation of APC to enhance hepatoblastoma oncogenesis. Front Genet. 2018;9:668. doi:10.3389/fgene.2018.00668.
   PubMedGoogle Scholar
• Srivastava A, Giangiobbe S, Skopelitou D, et al. Whole genome sequencing prioritizes CHEK2, EWSR1, and TIAM1 as possible predisposition genes for familial non-medullary thyroid cancer. Front Endocrinol. 2021;12:600682. doi:10.3389/fendo.2021.600682.
   PubMedGoogle Scholar
• Fewings E, Larionov A, Redman J, et al. Germline pathogenic variants in PALB2 and other cancer-predisposing genes in families with hereditary diffuse gastric cancer without CDH1 mutation: a whole-exome sequencing study. Lancet Gastroenterol Hepatol. 2018;3(7):489–498. doi:10.1016/S2468-1253(18)30079-7.
   PubMedGoogle Scholar
• Jongmans MCJ, Loeffen JLCM, Waanders E, et al. Recognition of genetic predisposition in pediatric cancer patients: an easy-to-use selection tool. Eur J Med Genet. 2016;59(3):116–125. doi:10.1016/j.ejmg.2016.01.008.
   PubMed Web of Science ®Google Scholar
• Van der Auwera GA, Carneiro MO, Hartl C, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1–11.10.33. doi:10.1002/0471250953.bi1110s43.
   PubMedGoogle Scholar
• McLaren W, Gil L, Hunt SE, et al. The ensembl variant effect predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4.
   PubMed Web of Science ®Google Scholar
• Karczewski KJ, Weisburd B, Thomas B, The Exome Aggregation Consortium, et al. The ExAC browser: displaying reference data information from over 60 000 exomes. Nucleic Acids Res. 2017;45(D1):D840–D845. doi:10.1093/nar/gkw971.
   PubMed Web of Science ®Google Scholar
• Brooks A, Durbin LD, RM, Auton 1000 Genomes Project Consortium, et al. A global reference for human genetic variation. Nature. 2015;526(7571):68–74. doi:10.1038/nature15393.
   PubMedGoogle 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):310–315. doi:10.1038/ng.2892.
   PubMed Web of Science ®Google Scholar
• Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A, NISC Comparative Sequencing Program. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15(7):901–913. doi:10.1101/gr.3577405.
   PubMed Web of Science ®Google Scholar
• Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034–1050. doi:10.1101/gr.3715005.
   PubMed Web of Science ®Google Scholar
• Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010;20(1):110–121. doi:10.1101/gr.097857.109.
   PubMed Web of Science ®Google Scholar
• Liu X, Li C, Mou C, Dong Y, Tu Y. dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome Med. 2020;12(1):103. doi:10.1186/s13073-020-00803-9.
   PubMed Web of Science ®Google Scholar
• Oscanoa J, Sivapalan L, Gadaleta E, Dayem Ullah AZ, Lemoine NR, Chelala C. SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update). Nucleic Acids Res. 2020;48(W1):W185–W192. doi:10.1093/nar/gkaa420.
   PubMed Web of Science ®Google Scholar
• Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012;40(Database issue):D930–934. doi:10.1093/nar/gkr917.
   PubMed Web of Science ®Google Scholar
• Boyle AP, Hong EL, Hariharan M, et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012;22(9):1790–1797. doi:10.1101/gr.137323.112.
   PubMed Web of Science ®Google Scholar
• Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. The ensembl regulatory build. Genome Biol. 2015;16:56. doi:10.1186/s13059-015-0621-5.
   PubMed Web of Science ®Google Scholar
• Coppieters F, Verniers K, De Leeneer K, Vandesompele J, Lefever S. Targeted resequencing and variant validation using pxlence PCR assays. Biomol Detect Quantif. 2016;6:22–26. doi:10.1016/j.bdq.2015.09.001.
   PubMedGoogle Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–2729. doi:10.1093/molbev/mst197.
   PubMed Web of Science ®Google Scholar
• Anderson KC, Jamison DS, Peters WP, Li FP. Familial Burkitt’s lymphoma. Association with altered lymphocyte subsets in family members. Am J Med. 1986;81(1):158–162. doi:10.1016/0002-9343(86)90202-0.
   PubMedGoogle Scholar
• Joncas JH, Rioux E, Wastiaux JP, Leyritz M, Robillard L, Menezes J. Nasopharyngeal carcinoma and Burkitt’s lymphoma in a Canadian family. I. HLA typing, EBV antibodies and serum immunoglobulins. Can Med Assoc J. 1976;115(9):858–860.
   PubMedGoogle Scholar
• Brown TM, Heath CW. Time-space clustering among cases of Burkitt’s tumor. Cancer Res. 1974;34(5):1216–1218.
   PubMedGoogle Scholar
• Salawu L, Fatusi OA, Kemi-Rotimi F, Adeodu OO, Durosinmi MA. Familial Burkitt’s lymphoma in Nigerians. Ann Trop Paediatr. 1997;17(4):375–379. doi:10.1080/02724936.1997.11747913.
   PubMed Web of Science ®Google Scholar
• Hopman S, Merks J, Eussen H, et al. Structural genome variations in individuals with childhood cancer and tumour predisposition syndromes. Eur J Cancer. 2013;49(9):2170–2178. doi:10.1016/j.ejca.2013.02.002.
   PubMedGoogle Scholar
• Okabe M, Morishita T, Yasuda T, et al. Targeted deep next generation sequencing identifies potential somatic and germline variants for predisposition to familial Burkitt lymphoma. Eur J Haematol. 2021;107(1):166–169. doi:10.1111/ejh.13629.
   PubMedGoogle Scholar
• Winnett A, Thomas SJ, Brabin BJ, Bain C, Alpers MA, Moss DJ. Familial Burkitt’s lymphoma in Papua New Guinea. Br J Cancer. 1997;75(5):757–761. doi:10.1038/bjc.1997.134.
   PubMedGoogle Scholar
• Saburi S, Hester I, Fischer E, et al. Loss of Fat4 disrupts PCP signaling and oriented cell division and leads to cystic kidney disease. Nat Genet. 2008;40(8):1010–1015. doi:10.1038/ng.179.
   PubMed Web of Science ®Google Scholar
• Blair S, McNeill H. Big roles for Fat cadherins. Curr Opin Cell Biol. 2018;51:73–80. doi:10.1016/j.ceb.2017.11.006.
   PubMedGoogle Scholar
• Cai J, Feng D, Hu L, et al. FAT4 functions as a tumour suppressor in gastric cancer by modulating Wnt/β-catenin signalling. Br J Cancer. 2015;113(12):1720–1729. doi:10.1038/bjc.2015.367.
   PubMedGoogle Scholar
• Martínez-Jiménez F, Muiños F, Sentís I, et al. A compendium of mutational cancer driver genes. Nat Rev Cancer. 2020;20(10):555–572. doi:10.1038/s41568-020-0290-x.
   PubMed Web of Science ®Google Scholar
• Tate JG, Bamford S, Jubb HC, et al. COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2019;47(D1):D941–D947. doi:10.1093/nar/gky1015.
   PubMed Web of Science ®Google Scholar
• Knapke S, Nagarajan R, Correll J, Kent D, Burns K. Hereditary cancer risk assessment in a pediatric oncology follow-up clinic. Pediatr Blood Cancer. 2012;58(1):85–89. doi:10.1002/pbc.23283.
   PubMedGoogle Scholar
• Goudie C, Witkowski L, Cullinan N, et al. Performance of the McGill Interactive Pediatric OncoGenetic Guidelines for identifying cancer predisposition syndromes. JAMA Oncol. 2021;7(12):1806–1814. doi:10.1001/jamaoncol.2021.4536.
   PubMedGoogle Scholar
• Diets IJ, Waanders E, Ligtenberg MJ, et al. High yield of pathogenic germline mutations causative or likely causative of the cancer phenotype in selected children with cancer. Clin Cancer Res. 2018;24(7):1594–1603. doi:10.1158/1078-0432.CCR-17-1725.
   PubMedGoogle Scholar
• Shen X, Song S, Li C, Zhang J. Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Nature. 2022;606(7915):725–731. doi:10.1038/s41586-022-04823-w.
   PubMed Web of Science ®Google Scholar
• Van Hateren NJ, Das RM, Hautbergue GM, Borycki AG, Placzek M, Wilson SA. FatJ acts via the Hippo mediator Yap1 to restrict the size of neural progenitor cell pools. Development. 2011;138(10):1893–1902. doi:10.1242/dev.064204.
   PubMedGoogle Scholar
• Mao Y, Mulvaney J, Zakaria S, et al. Characterization of a Dchs1 mutant mouse reveals requirements for Dchs1-Fat4 signaling during mammalian development. Development. 2011;138(5):947–957. doi:10.1242/dev.057166.
   PubMed Web of Science ®Google Scholar
• Ishiuchi T, Misaki K, Yonemura S, Takeichi M, Tanoue T. Mammalian fat and dachsous cadherins regulate apical membrane organization in the embryonic cerebral cortex. J Cell Biol. 2009;185(6):959–967. doi:10.1083/jcb.200811030.
   PubMedGoogle Scholar
• Behjati S, Gilbertson RJ, Pfister SM. Maturation block in childhood cancer. Cancer Discov. 2021;11(3):542–544. doi:10.1158/2159-8290.CD-20-0926.
   PubMedGoogle Scholar
• Bagherie-Lachidan M, Reginensi A, Pan Q, et al. Stromal Fat4 acts non-autonomously with Dchs1/2 to restrict the nephron progenitor pool. Development. 2015;142(15):2564–2573. doi:10.1242/dev.122648.
   PubMed Web of Science ®Google Scholar
• Betterman KL, Sutton DL, Secker GA, et al. Atypical cadherin FAT4 orchestrates lymphatic endothelial cell polarity in response to flow. J Clin Invest. 2020;130(6):3315–3328. doi:10.1172/JCI99027.
   PubMedGoogle Scholar
• Pujol F, Hodgson T, Martinez-Corral I, et al. Dachsous1-Fat4 signaling controls endothelial cell polarization during lymphatic valve morphogenesis-brief report. Arterioscler Thromb Vasc Biol. 2017;37(9):1732–1735. doi:10.1161/ATVBAHA.117.309818.
   PubMedGoogle Scholar
• Qi C, Zhu YT, Hu L, Zhu YJ. Identification of Fat4 as a candidate tumor suppressor gene in breast cancers. Int J Cancer. 2009;124(4):793–798. doi:10.1002/ijc.23775.
   PubMedGoogle Scholar
• Zang ZJ, Cutcutache I, Poon SL, et al. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet. 2012;44(5):570–574. doi:10.1038/ng.2246.
   PubMedGoogle Scholar
• Huh HD, Kim DH, Jeong HS, Park HW. Regulation of TEAD transcription factors in cancer biology. Cells. 2019;8(6):600. doi:10.3390/cells8060600.
   PubMed Web of Science ®Google Scholar
• Malgundkar SH, Burney I, Al Moundhri M, et al. FAT4 silencing promotes epithelial-to-mesenchymal transition and invasion via regulation of YAP and β-catenin activity in ovarian cancer. BMC Cancer. 2020;20(1):374. doi:10.1186/s12885-020-06900-7.
   PubMedGoogle Scholar
• Ma L, Cui J, Xi H, Bian S, Wei B, Chen L. Fat4 suppression induces Yap translocation accounting for the promoted proliferation and migration of gastric cancer cells. Cancer Biol Ther. 2016;17(1):36–47. doi:10.1080/15384047.2015.1108488.
   PubMed Web of Science ®Google Scholar