Helena

Documentation / References

References

Scientific publications and standards cited throughout the Helena 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