Helix Insight

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