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regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions

Mingxiang Teng, Shoji Ichikawa, Leah R. Padgett, Yadong Wang, Matthew Mort, David N. Cooper, Daniel L. Koller, Tatiana Foroud, Howard J. Edenberg, Michael J. Econs, Yunlong Liu
2012 Computer applications in the biosciences : CABIOS  
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

Hai Lin, Katherine A. Hargreaves, Rudong Li, Jill L. Reiter, Yue Wang, Matthew Mort, David N. Cooper, Yaoqi Zhou, Chi Zhang, Michael T. Eadon, M. Eileen Dolan, Joseph Ipe (+2 others)
2019 Genome Biology  
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]

Hai Lin, Katherine A Hargreaves, Rudong Li, Jill L Reiter, Matthew Mort, David N Cooper, Yaoqi Zhou, Michael T Eadon, M. Eileen Dolan, Joseph Ipe, Todd Skaar, Yunlong Liu
2019 bioRxiv   pre-print
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

Zishuo Zeng, Yana Bromberg
2019 Frontiers in Genetics  
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

Jason E. Miller, Yogasudha Veturi, Marylyn D. Ritchie
2019 BioData Mining  
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

EMBnet Journal
2012 EMBnet journal  
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]

Hai Lin
2017
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

Samantha Jean Jones
2020
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