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SNiPA: an interactive, genetic variant-centered annotation browser

Matthias Arnold, Johannes Raffler, Arne Pfeufer, Karsten Suhre, Gabi Kastenmüller
2014 Computer applications in the biosciences : CABIOS  
Motivation: Linking genes and functional information to genetic variants identified by association studies remains difficult.  ...  Resources containing extensive genomic annotations are available but often not fully utilized due to heterogeneous data formats.  ...  SNiPA combines a comprehensive set of genomic annotations with a genetic variant-based genome browser to simplify the task of variant annotation.  ... 
doi:10.1093/bioinformatics/btu779 pmid:25431330 pmcid:PMC4393511 fatcat:ls4fxg2z2nbixlodftc7txhdz4

Broadening our understanding of the genetics of Juvenile Idiopathic Arthritis (JIA): Interrogation of three dimensional chromatin structures and genetic regulatory elements within JIA-associated risk loci

Kaiyu Jiang, Haeja Kessler, Yungki Park, Marc Sudman, Susan D. Thompson, James N. Jarvis, Arnar Palsson
2020 PLoS ONE  
We also used in vitro reporter assays to establish as proof-of-concept the idea that genetic variants in linkage disequilibrium with GWAS-identified tag SNPs alter enhancer function.  ...  Similarly, we identified a 1,669 bp sequence in an intergenic region of the IL6R locus where SNPs identified in children with JIA increase enhancer function in reporter assays.  ...  (G>T) were common genetic variants annotated in the 1000 Genomes Project data.  ... 
doi:10.1371/journal.pone.0235857 pmid:32730263 fatcat:nnjfhyr2kbdphekad3i2n3gy7y

Novel Thrombotic Function of a Human SNP in STXBP5 Revealed by CRISPR/Cas9 Gene Editing in MiceHighlights

Qiuyu Martin Zhu, Kyung Ae Ko, Sara Ture, Michael A. Mastrangelo, Ming-Huei Chen, Andrew D. Johnson, Christopher J. O'Donnell, Craig N. Morrell, Joseph M. Miano, Charles J. Lowenstein
2016 Arteriosclerosis, Thrombosis and Vascular Biology  
Taken together, these data suggest that the genetic variant Stxbp5(N437S) decreases thrombosis.  ...  in high resolution. 25 Using the well-annotated chromatin interaction analysis with paired-end tag sequencing data sets on human K562 cells, distal chromatin interactions were found associated with insulator  ... 
doi:10.1161/atvbaha.116.308614 pmid:28062498 pmcid:PMC5269475 fatcat:wtjls456x5epdadl52zsradqkq

Germline Genetic Variants in the Wnt/ -Catenin Pathway as Predictors of Colorectal Cancer Risk

M. A. T. Hildebrandt, M. E. Reyes, M. Lin, Y. He, S. V. Nguyen, E. T. Hawk, X. Wu
2016 Cancer Epidemiology, Biomarkers and Prevention  
Rare highpenetrance genetic mutations in components of this pathway result in familial colorectal cancer, yet the impact of common, germline variants remains unknown.  ...  In silico informatic tools were used to predict functional effects of variants.  ...  Additional support provided by the Center for Translational and Public Health Genomics of the Duncan Family Institute and by the NIH through MD Anderson's Cancer Center Support Grant CA016672.  ... 
doi:10.1158/1055-9965.epi-15-0834 pmid:26809274 pmcid:PMC4779688 fatcat:ml3hglp42zcjpgwmhvpb7y3vqq

Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development

Jeremy W. Prokop, Caleb P. Bupp, Austin Frisch, Stephanie M. Bilinovich, Daniel B. Campbell, Daniel Vogt, Chad R. Schultz, Katie L. Uhl, Elizabeth VanSickle, Surender Rajasekaran, André S. Bachmann
2021 Genes  
An analysis of variants from ClinVar, Geno2MP, TOPMed, gnomAD, and COSMIC revealed an intellectual disability and seizure connected loss-of-function variant, ODC G84R (rs138359527, NC_000002.12:g.10444500C  ...  Expression quantitative trait loci (eQTLs) reveal multiple functionally annotated, non-coding variants regulating ODC1 that associate with psychiatric/neurological phenotypes.  ...  Using the SNP coordinates and the USCS genome browser, GeneHancer [51] , Switchgear TSS, ENCODE TF binding, and conserved transcription factor binding annotations were extracted.  ... 
doi:10.3390/genes12040470 pmid:33806076 fatcat:2jv4h2yiezftnmxe5rl54mabsq

A childhood acute lymphoblastic leukemia genome-wide association study identifies novel sex-specific risk variants

Sandeep K. Singh, Philip J. Lupo, Michael E. Scheurer, Anshul Saxena, Amy E. Kennedy, Boubakari Ibrahimou, Manuel Alejandro Barbieri, Ken I. Mills, Jacob L. McCauley, Mehmet Fatih Okcu, Mehmet Tevfik Dorak
2016 Medicine  
.; Okcu, Mehmet Fatih; and Dorak, Mehmet Tevfik, "A childhood acute lymphoblastic leukemia genome-wide association study identifies novel sex-specific risk variants" (2016). All Faculty. 172.  ...  , SNP = single nucleotide polymorphism, TFBS = transcription factor binding sites, TXCCC = Texas Children's Cancer Center, US = United States.  ...  Complementary annotations were performed using CADD, [29] RegulomeDB, [30] HaploReg v4, [31] SNiPA, [32] and rVarBase.  ... 
doi:10.1097/md.0000000000005300 pmid:27861356 pmcid:PMC5120913 fatcat:gwvtkildivhzbnhjg4ncdjhzp4

Polymorphisms in genes related to epithelial–mesenchymal transition and risk of non-small cell lung cancer

Kunlin Xie, Yuanqing Ye, Yong Zeng, Jian Gu, Hushan Yang, Xifeng Wu
2017 Carcinogenesis  
In this study, we examined whether genetic variants in EMT-related genes are associated with risk of non-small cell lung cancer (NSCLC).  ...  Our results suggest that EMT-related gene variants may be involved in susceptibility to NSCLC; if confirmed, they might help identify higher-risk individuals.  ...  .), and The University of Texas MD Anderson Cancer Center institutional support for the Center for Translational and Public Health Genomics. Conflict of Interest Statement: None declared.  ... 
doi:10.1093/carcin/bgx079 pmid:28968839 fatcat:m7ma2txlnvcllhnjzuv3uf373q

Tissue-specific multiOMICs analysis of atrial fibrillation [article]

Ines Assum, Julia Krause, Markus O Scheinhardt, Elke Hammer, Christian Mueller, Christin S Boerschel, Uwe Voelker, Lenard Conradi, Bastiaan Geelhoed, Tanja Zeller, Renate Schnabel, Matthias Heinig
2020 bioRxiv   pre-print
We identified widespread effects of genetic variants on transcript (cis eQTL) and protein (cis pQTL) abundance of nearby genes with an overrepresentation of GWAS variants for AF.  ...  CONCLUSIONS: We established an integrative multiOMICs approach for the identification of AF core gene candidates and applied this technique to uncover trans-acting genetic networks in AF.  ...  Annotations Genome annotations Ensembl BioMart [45] GRCh37.p13 hg19 annotations were used as genome annotations ( Acknowledgement  ... 
doi:10.1101/2020.04.06.021527 fatcat:crnnpstyfrfnfo3n5oyjgzhekm

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes

Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro, Ilya Ioshikhes
2021 PLoS Computational Biology  
We develop a pipeline using B-lymphocyte multi-dimensional epigenome and connectome data and deploy BMDC to assess genetic variants in the context of Type 1 Diabetes (T1D).  ...  Others are included in the well-established T1D GRS2 genetic risk scoring method.  ...  This forms an output trio composed of an associated regulatory element-genetic variant-gene.  ... 
doi:10.1371/journal.pcbi.1009382 pmid:34543288 pmcid:PMC8483327 fatcat:76h55gtz3jghlnfn5lx6j4vj2i

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual

Diana L. Cousminer, Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, Matthew C. Pahl, Shana E. McCormack, Alessandra Chesi, Jonathan A. Mitchell, Joseph M. Kindler, Denis Baird, April Hartley (+18 others)
2021 Genome Biology  
Conclusions Using a new longitudinal approach, we expand the number of genetic loci putatively associated with pediatric bone gain.  ...  Background Bone accrual impacts lifelong skeletal health, but genetic discovery has been primarily limited to cross-sectional study designs and hampered by uncertainty about target effector genes.  ...  variant), rs2301718, which showed a cis interaction with TET2 and falls in a binding site for RBPj, a primary nuclear mediator of Notch and an osteogenic driver [38] (Additional file 2: Fig.  ... 
doi:10.1186/s13059-020-02207-9 pmid:33397451 pmcid:PMC7780623 fatcat:xvqmwagxrrb2jcpj2fvkukvsp4

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping [article]

Diana L Cousminer, Yadav Wagley, James Pippin, Ahmed Elhakeem, Gregory Way, Shana McCormack, Alessandra Chesi, Jonathan Mitchell, Joeseph Kindler, Denis Baird, April Hartley, Laura D Howe (+17 others)
2020 medRxiv   pre-print
Bone accrual impacts lifelong skeletal health, but genetic discovery has been hampered by cross-sectional study designs and uncertainty about target effector genes.  ...  Variant-to-gene mapping identified contacts between GWAS loci and nearby gene promoters, and siRNA knockdown of gene expression clarified the putative effector gene at three specific loci in two osteoblast  ...  The top panel of each browser image shows open chromatin peaks assessed by ATAC-seq, with cis interaction loops shown below.  ... 
doi:10.1101/2020.02.17.20024133 fatcat:mlnndzltrver5lacdhgcgdm7yy

regSNPs-ASB: A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data

Siwen Xu, Weixing Feng, Zixiao Lu, Christina Y. Yu, Wei Shao, Harikrishna Nakshatri, Jill L. Reiter, Hongyu Gao, Xiaona Chu, Yue Wang, Yunlong Liu
2020 Frontiers in Bioengineering and Biotechnology  
Expression quantitative trait loci (eQTL) analysis is useful for identifying genetic variants correlated with gene expression, however, it cannot distinguish between causal and nearby non-functional variants  ...  This new computational tool will enable efficient prioritization of genetic variants identified as eQTL for further studies to validate their causal regulatory function.  ...  The linkage disequilibrium results were plotted by the genetic variantcentered annotation browser, SNiPA (Arnold et al., 2015) .  ... 
doi:10.3389/fbioe.2020.00886 pmid:32850739 pmcid:PMC7405637 fatcat:dam2fuaeifaajftzv7v3akgnty

A recall-by-genotype study on polymorphisms in the TMPRSS6 gene and oral iron absorption: a study protocol

Momodou W. Jallow, Susana Campino, Andrew M. Prentice, Carla Cerami
2019 F1000Research  
Discussion: This study will increase understanding of the role of genetic variations in TMPRSS6 on oral iron absorption in subjects of West African origin.  ...  The effects of a single variant allele at one SNP and the additive effect of two or three variant alleles from either two or all three SNPs will be investigated.  ...  Arnold M, Raffler J, Pfeufer A, Suhre K, Kastenmüller G: SNiPA: an interactive, genetic variant-centered annotation browser.  ... 
doi:10.12688/f1000research.19080.1 fatcat:muctqo7s4feyxiljkbvdywiyna

Multi-omics Data Integration for Identifying Osteoporosis Biomarkers and Their Biological Interaction and Causal Mechanisms

Chuan Qiu, Fangtang Yu, Kuanjui Su, Qi Zhao, Lan Zhang, Chao Xu, Wenxing Hu, Zun Wang, Lanjuan Zhao, Qing Tian, Yuping Wang, Hongwen Deng (+1 others)
2020 iScience  
By linking genetic data, we identified 199 targeted BMD-associated expression/methylation/metabolite quantitative trait loci (eQTLs/meQTLs/metaQTLs).  ...  Our study provided an innovative framework and insights into the pathogenesis of osteoporosis.  ...  Genome Browser.  ... 
doi:10.1016/j.isci.2020.100847 pmid:32058959 pmcid:PMC6997862 fatcat:3hen3e7qlfc4nll4v4n6ljhguy

Identification of 22 susceptibility loci associated with testicular germ cell tumors

John Pluta, Louise C. Pyle, Kevin T. Nead, Rona Wilf, Mingyao Li, Nandita Mitra, Benita Weathers, Kurt D'Andrea, Kristian Almstrup, Lynn Anson-Cartwright, Javier Benitez, Christopher D. Brown (+46 others)
2021 Nature Communications  
the interconnected nature of two known pathways that promote TGCT susceptibility: male germ cell development within its somatic niche and regulation of chromosomal division and structure, and implicate an  ...  We would like to thank Emily Carver and David Ruggieri of IMS for conducting data harmonization, the Center for Applied Genomics at CHOP for technical assistance, specifically Renata Pellagrino, PhD, Laboratory  ...  Logistic regression was used to determine associations between TGCT status and genotype, assuming an additive genetic model.  ... 
doi:10.1038/s41467-021-24334-y pmid:34301922 pmcid:PMC8302763 fatcat:7gjoxfakhrg6tf4aweafpszfzy
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