Documentation / References
References
Scientific publications and standards cited throughout the Helix Insight documentation.
ACMG Classification
Richards S, Aziz N, Bale S, 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):405-424. PMID: 25741868
Tavtigian SV, Greenblatt MS, Harrison SM, et al. "Modeling the ACMG/AMP variant classification guidelines as a Bayesian classification framework." Genet Med. 2018;20(9):1054-1060. PMID: 29300386
Tavtigian SV, Harrison SM, Boucher KM, Biesecker LG. "Fitting a naturally scaled point system to the ACMG/AMP variant classification guidelines." Hum Mutat. 2020;41(11):1734-1737. PMID: 32720330
Computational Predictors
Pejaver V, Byrne AB, Feng BJ, et al. "Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria." Am J Hum Genet. 2022;109(12):2163-2177. PMID: 36413997
Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, et al. "Predicting splicing from primary sequence with deep learning." Cell. 2019;176(3):535-548. PMID: 30661751
Walker LC, Hoya M, Wiggins GAR, et al. "Using the ClinGen/ACMG/AMP framework to assess splicing impact of sequence variants." Hum Mutat. 2023;44:1-12. PMID: 36864581
Cheng J, Novati G, Pan J, et al. "Accurate proteome-wide missense variant effect prediction with AlphaMissense." Science. 2023;381(6664):eadg7492. PMID: 37733863
Quang D, Chen Y, Xie X. "DANN: a deep learning approach for annotating the pathogenicity of genetic variants." Bioinformatics. 2015;31(5):761-763. PMID: 25338716
Population Databases
Chen S, Francioli LC, Goodrich JK, et al. "A genomic mutational constraint map using variation in 76,156 human genomes." Nature. 2024;625:92-100. PMID: 38057664
Karczewski KJ, Francioli LC, Tiao G, et al. "The mutational constraint spectrum quantified from variation in 141,456 humans." Nature. 2020;581:434-443. PMID: 32461654
Landrum MJ, Lee JM, Benson M, et al. "ClinVar: improving access to variant interpretations and supporting evidence." Nucleic Acids Res. 2018;46(D1):D1062-D1067. PMID: 29165669
Annotation Tools
McLaren W, Gil L, Hunt SE, et al. "The Ensembl Variant Effect Predictor." Genome Biol. 2016;17:122. PMID: 27268795
Liu X, Li C, Mou C, et al. "dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs." Genome Med. 2020;12:103. PMID: 33261662
Phenotype Ontology
Kohler S, Gargano M, Matentzoglu N, et al. "The Human Phenotype Ontology in 2024: phenotypes around the world." Nucleic Acids Res. 2024;52(D1):D1333-D1346. PMID: 37953324
Lin D. "An information-theoretic definition of similarity." Proc 15th Int Conf Machine Learning. 1998;pp. 296-304.
Clinical Genetics Resources
Rehm HL, Berg JS, Brooks LD, et al. "ClinGen -- the Clinical Genome Resource." N Engl J Med. 2015;372:2235-2242. PMID: 26014595
Stenton SL, Kremer LS, Gusic M, et al. "Systematic application of computational variant interpretation tools for germline variant classification." Am J Hum Genet. 2024;111:1-15. PMID: 38552641