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regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions
2012
Computer applications in the biosciences : CABIOS
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Results: We present regSNPs, an informatics strategy that integrates several established bioinformatics tools, for prioritizing regulatory SNPs, i.e. the SNPs in the promoter regions that potentially affect ...
Despite the technical advances, informatics methodologies need to be developed to prioritize thousands of variants for potential causative effects. ...
ACKNOWLEDGEMENTS The authors thank the valuable discussion from Dr Lang Li in the Center for Computational Biology and Bioinformatics at Indiana University School of Medicine. ...
doi:10.1093/bioinformatics/bts275
pmid:22611130
pmcid:PMC3389767
fatcat:bikoa7y35jfcvilnytnhutrqpy
RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants
2019
Genome Biology
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Single nucleotide variants (SNVs) in intronic regions have yet to be systematically investigated for their disease-causing potential. ...
Together, RegSNPs-intron and ASSET-seq enable effective prioritization of iSNVs for disease pathogenesis. ...
Further, a single nucleotide barcode was introduced to indicate whether the transcript came from the wild-type or variant construct. ...
doi:10.1186/s13059-019-1847-4
pmid:31779641
pmcid:PMC6883696
fatcat:gertixfnara6tn7b3bexixj6gu
RegSNPs-Intron: A Computational Framework For Prioritizing Intronic Single Nucleotide Variants in Human Genetic Disease
[article]
2019
bioRxiv
pre-print
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A large number of single nucleotide variants (SNVs) in the human genome are known to be responsible for inherited disease. ...
Together, regSNPs-intron and ASSET-seq enable effective prioritization of iSNVs for disease pathogenesis. regSNPs-intron is available at https://regsnps-intron.ccbb.iupui.edu. ...
Further, a single nucleotide barcode was introduced to indicate whether the transcript came from the wild-type or variant construct. ...
doi:10.1101/515171
fatcat:hcrh6tibm5awjnhin2i4dgr4cq
Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives
2019
Frontiers in Genetics
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Interestingly, despite the fact that every person has as many synonymous (sSNV) as non-synonymous single nucleotide variants, our ability to predict their effects is limited. ...
., we expect the generated set to be enriched for deleterious variants. ...
INTRODUCTION The vast majority of human genomic variation is accounted for by Single Nucleotide Variants (SNVs) (Bromberg et al., 2013) . ...
doi:10.3389/fgene.2019.00914
pmid:31649718
pmcid:PMC6791167
fatcat:sn2zwjsnhfaxvjkgkaczkogaz4
Innovative strategies for annotating the "relationSNP" between variants and molecular phenotypes
2019
BioData Mining
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Our understanding of how a single nucleotide polymorphism (SNP) leads to a pathogenic phenotype on a genome-wide scale is a fruitful endeavor for anyone interested in developing diagnostic tests, therapeutics ...
This review will discuss the history behind SNP annotation, commonly used tools, and newer strategies for SNP annotation. ...
Acknowledgments We thank Ritchie lab members for comments during the preparation of this review. Funding Support for this work was provided by NHGRI T32HG009495-01 and NIGMS P50 GM115318. ...
doi:10.1186/s13040-019-0197-9
pmid:31114635
pmcid:PMC6518798
fatcat:so36jmt2wfazrdcojn3c42mjpa
EMBnet.journal 18 Suppl. B
2012
EMBnet journal
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Carlo Bernasconi and the Collegio Ghislieri in Pavia for their active support. ...
The second level adds a list of single-nucleotide polymorphisms (SNP) present in TFBSs in the regulatory regions of each gene (i.e. building a Disease-gene-SNP hierarchy), prioritized by the expected level ...
Only heterozygous single nucleotide polymorphisms (SNPs) were selected for the following analysis, defined as SNPs with a coverage of at least 10 reads for each allele. ...
doi:10.14806/ej.18.b.592
fatcat:wlwsmbdlfzbjtk7vyhiabdov6q
Computational modeling of splicing regulation
[article]
2017
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Yunlong Liu, you have been a tremendous mentor for me. I would like to thank you for encouraging my research and for allowing me to grow as a research ...
Chapter 4 regSNP-intron: A Tool for Prioritizing Intronic Single Nucleotide Substitution ......................................................................................................... 4.1 Introduction ...
Second, we developed a machine learning algorithm to prioritize the disease-causing probability of intronic single-nucleotide variants (iSNVs) by evaluating their cisacting impact on both alternative splicing ...
doi:10.7912/c29h0d
fatcat:325245cu5zg6rf4vrs5uggmhse
Characterization of environmental and genetic factors in multiple-case lymphoid cancer families
2020
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allergies, autoimmune conditions and some lymphoid cancers, provides a framework for understanding these risk factors. ...
Susceptibility genes involved in immune function and DNA repair have been identified; however, there remains a large gap in our knowledge of genetic and environmental factors for familial lymphoid cancers ...
nucleotide polymorphism
SNV
Single nucleotide variant
SS
Sjögren syndrome
SVS
SNP and Variation Suite
THRLBCL
T-cell/histiocyte rich diffuse large B-cell lymphoma
TOPMed
Trans-Omics for ...
doi:10.14288/1.0390430
fatcat:5bxsgq4djrd45otyfv5icfs3iu