Genome-wide functional annotation of variants: a systematic review of state-of-the-art tools, techniques and resources

Authors: Eleftherios Pilalis, Dimitrios Zisis, Christina Andrinopoulou, Theodora Karamanidou, Maria Antonara, Thanos G. Stavropoulos, Aristotelis Chatziioannou

Source: Frontiers in Pharmacology, Vol 16 (2025)

Subject Terms: genome-wide, variant annotation, genomic variation, whole-genome sequencing, intergenic, GWAS, Therapeutics. Pharmacology, RM1-950

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Relation: https://www.frontiersin.org/articles/10.3389/fphar.2025.1474026/full; https://doaj.org/toc/1663-9812

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A comprehensive and bias-free evaluation of genomic variant clinical interpretation tools

Authors: Minh Trang, Nguyen, Anh Vu, Mai Nguyen, Hoang Anh, Tran, Nguyet Minh, Do, Thanh Nguyen, Nguyen

Source: 2021 13th International Conference on Knowledge and Systems Engineering (KSE) Knowledge and Systems Engineering (KSE), 2021 13th International Conference on. :1-5 Nov, 2021

Relation: 2021 13th International Conference on Knowledge and Systems Engineering (KSE)

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection

Authors: Negi, Shloka ¹, Stenton, Sarah L. ^{2, 3}, Berger, Seth I. ⁴, Canigiula, Paolo ⁴, McNulty, Brandy ¹, Violich, Ivo ¹, Gardner, Joshua ¹, Hillaker, Todd ¹, O’Rourke, Sara M. ¹, O’Leary, Melanie C. ², Carbonell, Elizabeth ², Austin-Tse, Christina ^{2, 5}, Lemire, Gabrielle ^{2, 3}, Serrano, Jillian ^{2, 3}, Mangilog, Brian ², VanNoy, Grace ², Kolmogorov, Mikhail ⁶, Vilain, Eric ⁷, O’Donnell-Luria, Anne ^{2, 3, 5, 9}, Délot, Emmanuèle ^{7, 9}, Miga, Karen H. ^{1, 9}, Monlong, Jean ^{8, 9, ∗}, Paten, Benedict ^{1, 9, ∗∗}

Source: In The American Journal of Human Genetics 6 February 2025 112(2):428-449

Zazz: Variant Annotation and Exploration of Next Generation Sequencing Variants

Authors: Astrinaki, Maria, Kanterakis, Alexandros, Latsoudis, Helen, Potamias, George, Kafetzopoulos, Dimitris

Source: 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Bioinformatics and Bioengineering (BIBE), 2019 IEEE 19th International Conference on. :856-860 Oct, 2019

Relation: 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)

Prevalence of the cancer-associated germline variants in Russian adults and long-living individuals: using the ACMG recommendations and computational interpreters for pathogenicity assessment

Authors: Mariia Gusakova, Irina Dzhumaniiazova, Elena Zelenova, Daria Kashtanova, Mikhail Ivanov, Aleksandra Mamchur, Antonina Rumyantseva, Mikhail Terekhov, Sergey Mitrofanov, Liliya Golubnikova, Aleksandra Akinshina, Konstantin Grammatikati, Irina Kalashnikova, Vladimir Yudin, Valentin Makarov, Anton Keskinov, Sergey Yudin

Source: Frontiers in Oncology, Vol 14 (2024)

Subject Terms: cancer, automated variant annotation, ACMG, germline variants, cancer genetic, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

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Relation: https://www.frontiersin.org/articles/10.3389/fonc.2024.1420176/full; https://doaj.org/toc/2234-943X

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DVA: predicting the functional impact of single nucleotide missense variants

Authors: Dong Wang, Jie Li, Edwin Wang, Yadong Wang

Source: BMC Bioinformatics, Vol 25, Iss S1, Pp 1-16 (2024)

Subject Terms: Missense variants, Functional impact, Variant annotation, Disease-related, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

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Relation: https://doaj.org/toc/1471-2105

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Comparing Classifications from Multiple Variant Annotation Software Solutions Using Real-World Next Generation Sequencing Data from Oncology Testing

Authors: Roy Khalife, Tara M. Love, Lara Sucheston-Campbell, Michael J. Clark, Helle Sorensen, Shuba Krishna, Anthony Magliocco

Source: Journal of Molecular Pathology, Vol 5, Iss 1, Pp 81-95 (2024)

Subject Terms: next generation sequencing (NGS), genomic analysis, variant annotation, bioinformatics, tier classification, tertiary analysis software, Pathology, RB1-214

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Relation: https://www.mdpi.com/2673-5261/5/1/6; https://doaj.org/toc/2673-5261

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COSAP: Comparative Sequencing Analysis Platform

Authors: Mehmet Arif Ergun, Omer Cinal, Berkant Bakışlı, Abdullah Asım Emül, Mehmet Baysan

Source: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-15 (2024)

Subject Terms: NGS Analysis, Variant classification, Variant annotation, Copy number variation, Microsatellite instability, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

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Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/e4920c7c08214fa6b988e50cd4930490

Plant Genomics 2019

Contributors: You, Frank M.

Subject Terms: Aristolochia, chloroplast genome, molecular evolution, compare analysis, phylogeny, brassinosteroid-signaling kinase, gene family, expression profile, alternative splicing, intron retention, genome-wide analysis, drought tolerance, foxtail millet, LIM genes, transgenic rice, protein phosphatase (PP2C), cotton, syntenic relationships, expression patterns, evolutionary analysis, Populus trichocarpa, multiple organellar RNA editing factor, drought stress, RNA editing, genome, β-glucosidase, Brassica rapa, BrBGLU10, pollen development, co-expression analysis, VQ genes family, Eucalyptus grandis, expression pattern, plant hormones, abiotic stress, calcium-dependent protein kinases, CDPK-related kinases, cucurbitaceae, hst1, Na+ accumulation, SNP, rapid generation advance, salt tolerant, variant annotation, whole-genome sequencing, expression, genome-wide, identification of peroxidase genes, duplication pattern, stress, cassava, ABCDE model, cereals, evolutionary relationships, flower organ identity, floral speciation, MADS-box genes, maize, ZmTCP, natural variation, subgroup IId, CsWRKY7, flowering, Arabidopsis, Camellia sinensis, pomegranate, sequence diversity, site-specific selection, tomato, MADS-box, floral organ, fruit development, polygalacturonase (PGs), pectin methylesterase (PMEs), collinearity analysis, gene duplications, expression profiling, grapevine, Rehmannia glutinosa L., replant disease, rhizosphere microbes, NB-LRR, plant hormone, apple, aquaporin, functional analysis, stress tolerance, Salicaceae, phylogenetic relationship, plastid genome, comparative genomics, repeat sequences, stress marker genes, sesame, gene co-expression, abiotic stress tolerance, hub genes, meta-analysis, agrobacterium, transient expression, virus-induced gene silencing (VIGS), tobacco rattle virus (TRV), cassava (Manihot esculenta), chalcone synthase, chromatin accessibility, epigenetic inheritance, genetic engineering, methylation, ODNs, CRISPR/Cas9, genome editing, plant breeding, multiplex genome editing, crop improvement, TALEN, ZFN, biotic stress, avocado, carotenoid biosynthesis, mesocarp, seed, de novo assembly from short read sequencing, full-length transcript sequencing, differentially expressed genes, gene dosage, pigment, turnip, gene expression, antioxidant, nutritional quality, B3 superfamily, transcription factor, ovule abortion, Vitis vinifera, expression analysis, cold response, Pittosporum tobira, leaf variegation, linoleic acid, ROS scavenging enzyme, heat shock protein, invasive weed, Rhizoctonia solani, phytohormone signaling, systemic signal, plant defense, calcium signaling, ABA, drought, salinity, citrulline, genome-wide association study, haplotype, watermelon, acetolactate synthase, ferrochelatase, rice, large grain gene, large grain-isogenic Koshihikari, fine mapping, NGS, GW2, co-integration, gene recombination, semidwarf gene, d60, linkage, chromosome 2, Brachypodium, comparative chromosome barcoding, dysploidy, karyotype structure and evolution, model grass genus, molecular cytogenetics, polyploidy, plant genome, artificial microRNA, gene silencing, Lagerstroemia indica, ornamental value, anthocyanins, leaf coloration, directional improvement, YABBY, pineapple, subcellular localization, oak species identification, Quercus, mutation hotspots, Centranthera grandiflora Benth, transcriptome, catalpol biosynthesis, acteoside biosynthesis, azafrin biosynthesis, wheat, Dasypyrum villosum, alien substitution line, GISH, molecular marker, marker-assisted selection, regulation, RNA-seq, biosynthesis pathway, chalcones, stilbenes, common bean, Fusarium oxysproum, plant–pathogen interaction, metabolome, evolution, genome fractionation, ABC transporters, transcription factors, transposable elements, whole-genome duplication, RNA-sequencing, ChIP-sequencing, transcriptional regulatory mechanism, data integration, karyopherin, solanum tuberosum, chemical fungicide, disease control, Neoscytalidium dimidiatum, royal poinciana, stem canker, UAE, bioinformatics, VvGAST, GASR, Cis-elements, wheat genome, kernel hardness, Puroindoline, Puroindoline b-2 variants, genotype-to-phenotype association, synteny, phylogenetic analysis, genomic selection, missing data, minor allele frequency, GDSL lipase, GPAT6, cutin, habaneros, Capsicum chinense, fruit, RNA-Seq, flax, genome-wide association study (GWAS), single nucleotide polymorphism (SNP), prediction accuracy, quantitative trait loci (QTL), quantitative trait nucleotides (QTNs), Fabaceae, Lupinus, glutamine synthetase (GS), phosphoenolpyruvate carboxylase (PEPC), gene families, duplication/triplication, structural genomics, genome organization, genome evolution, microRNA, miRNA156, seed development, fatty acid synthesis, linseed flax, anthocyanin biosynthetic genes, cis-regulatory motifs, DEGs, network analysis, qRT-PCR, reddish purple Chinese cabbage, abscisic acid, flavonolignans, metabolite profiling, Silybum marianum, silymarin, aquaporins, bright yellow-2 suspension cells, Nicotiana tabacum, substrate specificity, TaCKX1, TaCKX expression, grain yield, cytokinins, phytohormones, RNAi, wheat spikes, genome-wide identification, 2OGD family, hormone biosynthetic and metabolism genes, tomato fruit ripening, DNA methylation, phenomics, Philosophy

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Access URL: https://directory.doabooks.org/handle/20.500.12854/101421
https://mdpi.com/books/pdfview/book/7518

Rare variant association studies: Significance, methods, and applications in chronic pain studies

Authors: Esfahani, Sahel Jahangiri ^{#, 1}, Ao, Xiang ^{†, 1}, Oveisi, Anahita ^‡, Diatchenko, Luda ^{†, ⁎}

Source: In Osteoarthritis and Cartilage December 2024

SVAT: Secure outsourcing of variant annotation and genotype aggregation

Authors: Miran Kim, Su Wang, Xiaoqian Jiang, Arif Harmanci

Source: BMC Bioinformatics, Vol 23, Iss 1, Pp 1-39 (2022)

Subject Terms: Variant annotation, Genomic privacy, Allele frequency, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

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Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/1a1ee615b58b47c59f3fa9c03752042a

OpenVar: functional annotation of variants in non-canonical open reading frames

Authors: Marie A. Brunet, Sébastien Leblanc, Xavier Roucou

Source: Cell & Bioscience, Vol 12, Iss 1, Pp 1-7 (2022)

Subject Terms: Small ORF, Alternative ORF, Variant annotation, NGS, Genome, SNP, Biotechnology, TP248.13-248.65, Biology (General), QH301-705.5, Biochemistry, QD415-436

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Relation: https://doaj.org/toc/2045-3701

Access URL: https://doaj.org/article/9e1dd63cff7c499e851c87f91e7a2b6e

Spectrum of genetic disorders and gene variants in the United Arab Emirates national population: insights from the CTGA database

Authors: Sami Bizzari, Pratibha Nair, Sayeeda Hana, Asha Deepthi, Mahmoud Taleb Al-Ali, Lihadh Al-Gazali, Stephany El-Hayek

Source: Frontiers in Genetics, Vol 14 (2023)

Subject Terms: variant, Emirati, database, variant annotation, rare disease, Genetics, QH426-470

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Relation: https://www.frontiersin.org/articles/10.3389/fgene.2023.1177204/full; https://doaj.org/toc/1664-8021

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Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants

Authors: Qingmei Han, Ying Yang, Shengyang Wu, Yingchun Liao, Shuang Zhang, Hongbin Liang, David S. Cram, Yu Zhang

Source: BMC Genomics, Vol 22, Iss 1, Pp 1-9 (2021)

Subject Terms: Cruxome, Next Generation Sequencing, Mendelian disorders, Variant annotation, Variant interpretation, Whole Exome Sequencing, Biotechnology, TP248.13-248.65, Genetics, QH426-470

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Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/1f753f65cabe47a4a00794e8fd248284

Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants

Authors: Ching-Yu Shih, Amrita Chattopadhyay, Chien-Hui Wu, Yu-Wen Tien, Tzu-Pin Lu

Source: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-12 (2021)

Subject Terms: Transcript annotation, Variant annotation, R package, TransAT, Allele frequency, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

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Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/37aaa645f3904e41bdf57855d23f317a

SNPAAMapper-Python: A highly efficient genome-wide SNP variant analysis pipeline for Next-Generation Sequencing data

Authors: Chang Li, Kevin Ma, Nicole Xu, Chenjian Fu, Andrew He, Xiaoming Liu, Yongsheng Bai

Source: Frontiers in Artificial Intelligence, Vol 5 (2022)

Subject Terms: Next-Generation Sequencing, SNP, python, mutation, variant annotation, pipeline, Electronic computers. Computer science, QA75.5-76.95

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Relation: https://www.frontiersin.org/articles/10.3389/frai.2022.991733/full; https://doaj.org/toc/2624-8212

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A performance evaluation study: Variant annotation tools - the enigma of clinical next generation sequencing (NGS) based genetic testing

Authors: Sachleen Tuteja, Sabah Kadri, Kai Lee Yap

Source: Journal of Pathology Informatics, Vol 13, Iss , Pp 100130- (2022)

Subject Terms: Variant annotation, Genetic testing, Alamut®, VEP, ANNOVAR, Gene panel, Computer applications to medicine. Medical informatics, R858-859.7, Pathology, RB1-214

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Relation: http://www.sciencedirect.com/science/article/pii/S2153353922007246; https://doaj.org/toc/2153-3539

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Bioinformatics pipeline to guide late‐onset Alzheimer's disease (LOAD) post‐GWAS studies: Prioritizing transcription regulatory variants within LOAD‐associated regions

Authors: Michael W. Lutz, Ornit Chiba‐Falek

Source: Alzheimer’s & Dementia: Translational Research & Clinical Interventions, Vol 8, Iss 1, Pp n/a-n/a (2022)

Subject Terms: Alzheimer's disease genetics, expression analysis, genetic variant annotation and prioritization, transcription factor binding analysis, Neurology. Diseases of the nervous system, RC346-429, Geriatrics, RC952-954.6

File Description: electronic resource

Relation: https://doaj.org/toc/2352-8737

Access URL: https://doaj.org/article/b7bb4b8b56164a25a5c68881f5114f63

Editorial: Deciphering Non-Coding Regulatory Variants: Computational and Functional Validation

Authors: Li Chen, Mulin Jun Li

Source: Frontiers in Bioengineering and Biotechnology, Vol 9 (2021)

Subject Terms: non-coding variants, regulatory variants, variant annotation, functional prediction, functional validation, non-coding variants, functional validation, Biotechnology, TP248.13-248.65

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Relation: https://www.frontiersin.org/articles/10.3389/fbioe.2021.769614/full; https://doaj.org/toc/2296-4185

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AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting

Authors: Christian Wünsch, Henrik Banck, Carsten Müller-Tidow, Martin Dugas

Source: BMC Medical Genomics, Vol 13, Iss 1, Pp 1-17 (2020)

Subject Terms: Genomics, NGS sequencing, Variant calling, Variant annotation, Variant filtering, Variant interpretation, Internal medicine, RC31-1245, Genetics, QH426-470

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Relation: https://doaj.org/toc/1755-8794

Access URL: https://doaj.org/article/463aa481642a440c82ab5dbc9f503a48