Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer …

D Canson, D Glubb, AB Spurdle - Human Mutation, 2020 - Wiley Online Library
It is possible to estimate the prior probability of pathogenicity for germline disease gene
variants based on bioinformatic prediction of variant effect/s. However, routinely used …

Synonymous variants: necessary nuance in our understanding of cancer drivers and treatment outcomes

NM Kaissarian, D Meyer… - Journal Of The National …, 2022 - academic.oup.com
Once called “silent mutations” and assumed to have no effect on protein structure and
function, synonymous variants are now recognized to be drivers for some cancers. There …

Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes

T Landrith, B Li, AA Cass, BR Conner, H LaDuca… - NPJ precision …, 2020 - nature.com
Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and
predisposition to cancer. However, identification of variants that impact splicing remains a …

Diagnostic capabilities of nanopore long‐read sequencing in muscular dystrophy

CC Bruels, HR Littel, AL Daugherty… - Annals of clinical …, 2022 - Wiley Online Library
Many individuals with muscular dystrophies remain genetically undiagnosed despite clinical
diagnostic testing, including exome sequencing. Some may harbor previously undetected …

Pathogenicity and selective constraint on variation near splice sites

J Lord, G Gallone, PJ Short, JF McRae… - Genome …, 2019 - genome.cshlp.org
Mutations that perturb normal pre-mRNA splicing are significant contributors to human
disease. We used exome sequencing data from 7833 probands with developmental …

Teenage-onset colorectal cancers in a digenic cancer predisposition syndrome provide clues for the interaction between mismatch repair and polymerase δ …

E Schamschula, M Kinzel, A Wernstedt, K Oberhuber… - Biomolecules, 2022 - mdpi.com
Simple Summary Colorectal cancer (CRC) in adolescents and young adults (AYA) is rare.
Genetic causes include autosomal recessive and dominant monogenic disorders due to …

Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants

L Sanoguera-Miralles, A Valenzuela-Palomo… - Clinical …, 2024 - academic.oup.com
Background Disrupted pre-mRNA splicing is a frequent deleterious mechanism in hereditary
cancer. We aimed to functionally analyze candidate spliceogenic variants of the breast …

Functional classification of DNA variants by hybrid minigenes: Identification of 30 spliceogenic variants of BRCA2 exons 17 and 18

E Fraile-Bethencourt, B Díez-Gómez… - PLoS …, 2017 - journals.plos.org
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction
of variants of uncertain clinical significance (VUS) whose functional and clinical …

Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome

HM van der Klift, AR Mensenkamp, M Drost… - Human …, 2016 - Wiley Online Library
Monoallelic PMS2 germline mutations cause 5%–15% of Lynch syndrome, a midlife cancer
predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional …

Benchmarking splice variant prediction algorithms using massively parallel splicing assays

C Smith, JO Kitzman - Genome Biology, 2023 - Springer
Background Variants that disrupt mRNA splicing account for a sizable fraction of the
pathogenic burden in many genetic disorders, but identifying splice-disruptive variants …