Daffodil M Canson1, Troy Dumenil2, Michael T Parsons3, Tracy A O'Mara3, Aimee L Davidson1, Satomi Okano4, Bethany Signal5, Tim R Mercer6, Dylan M Glubb3, Amanda B Spurdle7. 1. Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia. 2. Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. 3. Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. 4. Statistics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. 5. Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. 6. Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia. 7. Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia. Electronic address: Amanda.Spurdle@qimrberghofer.edu.au.
Abstract
PURPOSE: Branchpoint elements are required for intron removal, and variants at these elements can result in aberrant splicing. We aimed to assess the value of branchpoint annotations generated from recent large-scale studies to select branchpoint-abrogating variants, using hereditary cancer genes as model. METHODS: We identified branchpoint elements in 119 genes associated with hereditary cancer from 3 genome-wide experimentally-inferred and 2 predicted branchpoint data sets. We then identified variants that occur within branchpoint elements from public databases. We compared conservation, unique variant observations, and population frequencies at different nucleotides within branchpoint motifs. Finally, selected minigene assays were performed to assess the splicing effect of variants at branchpoint elements within mismatch repair genes. RESULTS: There was poor overlap between predicted and experimentally-inferred branchpoints. Our analysis of cancer genes suggested that variants at -2 nucleotide, -1 nucleotide, and branchpoint positions in experimentally-inferred canonical motifs are more likely to be clinically relevant. Minigene assay data showed the -2 nucleotide to be more important to branchpoint motif integrity but also showed fluidity in branchpoint usage. CONCLUSION: Data from cancer gene analysis suggest that there are few high-risk alleles that severely impact function via branchpoint abrogation. Results of this study inform a general scheme to prioritize branchpoint motif variants for further study.
PURPOSE: Branchpoint elements are required for intron removal, and variants at these elements can result in aberrant splicing. We aimed to assess the value of branchpoint annotations generated from recent large-scale studies to select branchpoint-abrogating variants, using hereditary cancer genes as model. METHODS: We identified branchpoint elements in 119 genes associated with hereditary cancer from 3 genome-wide experimentally-inferred and 2 predicted branchpoint data sets. We then identified variants that occur within branchpoint elements from public databases. We compared conservation, unique variant observations, and population frequencies at different nucleotides within branchpoint motifs. Finally, selected minigene assays were performed to assess the splicing effect of variants at branchpoint elements within mismatch repair genes. RESULTS: There was poor overlap between predicted and experimentally-inferred branchpoints. Our analysis of cancer genes suggested that variants at -2 nucleotide, -1 nucleotide, and branchpoint positions in experimentally-inferred canonical motifs are more likely to be clinically relevant. Minigene assay data showed the -2 nucleotide to be more important to branchpoint motif integrity but also showed fluidity in branchpoint usage. CONCLUSION: Data from cancer gene analysis suggest that there are few high-risk alleles that severely impact function via branchpoint abrogation. Results of this study inform a general scheme to prioritize branchpoint motif variants for further study.
Authors: Diana Baralle; Jenny Lord; Alexander J M Blakes; Htoo A Wai; Ian Davies; Hassan E Moledina; April Ruiz; Tessy Thomas; David Bunyan; N Simon Thomas; Christine P Burren; Lynn Greenhalgh; Melissa Lees; Amanda Pichini; Sarah F Smithson; Ana Lisa Taylor Tavares; Peter O'Donovan; Andrew G L Douglas; Nicola Whiffin Journal: Genome Med Date: 2022-07-26 Impact factor: 15.266