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Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes.
Hsu JS, Kwan JS, Pan Z, Garcia-Barcelo MM, Sham PC, Li M. Hsu JS, et al. Bioinformatics. 2016 Oct 15;32(20):3065-3071. doi: 10.1093/bioinformatics/btw381. Epub 2016 Jun 26. Bioinformatics. 2016. PMID: 27354691
This inheritance mode-specific framework achieved higher accuracy (area under curve = 0.84) in XL mode. CONCLUSION: The inheritance-mode specific pathogenicity prioritization (ISPP) outperformed other well-known metho …
This inheritance mode-specific framework achieved higher accuracy (area under curve = 0.84) in XL mode. CONCLUSI …
Mapping the human genetic architecture of COVID-19.
COVID-19 Host Genetics Initiative. COVID-19 Host Genetics Initiative. Nature. 2021 Dec;600(7889):472-477. doi: 10.1038/s41586-021-03767-x. Epub 2021 Jul 8. Nature. 2021. PMID: 34237774 Free PMC article.
Although environmental, clinical and social factors have a role in the chance of exposure to SARS-CoV-2 and the severity of COVID-19(1,2), host genetics may also be important. Identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevan …
Although environmental, clinical and social factors have a role in the chance of exposure to SARS-CoV-2 and the severity of COVID-19(1,2), h …
MutationDistiller: user-driven identification of pathogenic DNA variants.
Hombach D, Schuelke M, Knierim E, Ehmke N, Schwarz JM, Fischer-Zirnsak B, Seelow D. Hombach D, et al. Nucleic Acids Res. 2019 Jul 2;47(W1):W114-W120. doi: 10.1093/nar/gkz330. Nucleic Acids Res. 2019. PMID: 31106342 Free PMC article.
It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combines MutationTaster's pathogenicity predictions with a phenotype-based approach. Phenotypic information is not limited to sympto …
It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combin …
Therapeutic Prospects of Exon Skipping for Epidermolysis Bullosa.
Vermeer FC, Bremer J, Sietsma RJ, Sandilands A, Hickerson RP, Bolling MC, Pasmooij AMG, Lemmink HH, Swertz MA, Knoers NVAM, van der Velde KJ, van den Akker PC. Vermeer FC, et al. Int J Mol Sci. 2021 Nov 12;22(22):12222. doi: 10.3390/ijms222212222. Int J Mol Sci. 2021. PMID: 34830104 Free PMC article. Review.
The subtype and severity of EB is linked to the gene involved and the specific variants in that gene, which also determine its mode of inheritance. ...Antisense-oligonucleotide (ASO)-mediated exon skipping aims to counteract pathogenic sequence variant …
The subtype and severity of EB is linked to the gene involved and the specific variants in that gene, which also determine its mod …
Prioritization of Variants Detected by Next Generation Sequencing According to the Mutation Tolerance and Mutational Architecture of the Corresponding Genes.
Roca I, Fernández-Marmiesse A, Gouveia S, Segovia M, Couce ML. Roca I, et al. Int J Mol Sci. 2018 May 27;19(6):1584. doi: 10.3390/ijms19061584. Int J Mol Sci. 2018. PMID: 29861492 Free PMC article. Review.
This describes the type and location of mutations previously identified in the gene, and their association with different phenotypes or degrees of severity. The third is the mode of inheritance (inherited vs. de novo) of the variants detected. Here, we discuss the i …
This describes the type and location of mutations previously identified in the gene, and their association with different phenotypes or degr …
Improving the clinical interpretation of missense variants in X linked genes using structural analysis.
Sallah SR, Ellingford JM, Sergouniotis PI, Ramsden SC, Lench N, Lovell SC, Black GC. Sallah SR, et al. J Med Genet. 2022 Apr;59(4):385-392. doi: 10.1136/jmedgenet-2020-107404. Epub 2021 Mar 25. J Med Genet. 2022. PMID: 33766936 Free PMC article.
We also determined gene-specific pathogenicity thresholds that improved the performance of VEST4, REVEL and ClinPred, the three best-performing tools out of the seven that were evaluated; this was the case in 11, 11 and 12 different genes, respectively. ...In additi …
We also determined gene-specific pathogenicity thresholds that improved the performance of VEST4, REVEL and ClinPred, the thre …
Gene-based association analysis identifies 190 genes affecting neuroticism.
Belonogova NM, Zorkoltseva IV, Tsepilov YA, Axenovich TI. Belonogova NM, et al. Sci Rep. 2021 Jan 28;11(1):2484. doi: 10.1038/s41598-021-82123-5. Sci Rep. 2021. PMID: 33510330 Free PMC article.
Within all genes identified, we distinguished two slightly overlapping groups obtained from using protein-coding and non-coding variants. Many genes in the former group included potentially pathogenic variants. For some genes in the latter group, we found evidence of pleio …
Within all genes identified, we distinguished two slightly overlapping groups obtained from using protein-coding and non-coding variants. Ma …
A population-based approach for gene prioritization in understanding complex traits.
Mezzavilla M, Cocca M, Guidolin F, Gasparini P. Mezzavilla M, et al. Hum Genet. 2020 May;139(5):647-655. doi: 10.1007/s00439-020-02152-4. Epub 2020 Mar 30. Hum Genet. 2020. PMID: 32232557
Gene prioritization is the process of determining which variants and genes identified in genetic analyses are likely to cause a disease or a variation in a phenotype. ...In contrast, some genes showed a high negative score only in specific populations, e.g., MYT1L i …
Gene prioritization is the process of determining which variants and genes identified in genetic analyses are likely to cause a disea …
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.
Huang YF, Siepel A. Huang YF, et al. Genome Res. 2019 Aug;29(8):1310-1321. doi: 10.1101/gr.245522.118. Epub 2019 Jun 27. Genome Res. 2019. PMID: 31249063 Free PMC article.
We applied LASSIE to 51 high-coverage genome sequences annotated with 33 genomic features and constructed a map of allele-specific selection coefficients across all protein-coding sequences in the human genome. ...In addition, the estimated selection coefficients are highl …
We applied LASSIE to 51 high-coverage genome sequences annotated with 33 genomic features and constructed a map of allele-specific se …
A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease.
Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. Oliver GR, et al. PLoS One. 2019 Oct 2;14(10):e0223337. doi: 10.1371/journal.pone.0223337. eCollection 2019. PLoS One. 2019. PMID: 31577830 Free PMC article.
METHODS: We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering st …
METHODS: We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspect …
17 results