Fuchs Endothelial Corneal Dystrophy associated risk variant, rs3768617 in LAMC1 shows allele specific binding of GFI1B

Gene ◽  
2022 ◽  
pp. 146179
Author(s):  
Maynak Chakraborty ◽  
Rajesh Kumar Das ◽  
Sujata Samal ◽  
Sujata Das ◽  
Debasmita Pankaj Alone
Keyword(s):  
Specific Binding ◽  
Corneal Dystrophy ◽  
Risk Variant ◽  
Allele Specific

scholarly journals Allele-Specific siRNA Silencing for the Common Keratin 12 Founder Mutation in Meesmann Epithelial Corneal Dystrophy

2013 ◽  
Vol 54 (1) ◽  
pp. 494 ◽  
Author(s):  
Edwin H. A. Allen ◽  
Sarah D. Atkinson ◽  
Haihui Liao ◽  
Jonathan E. Moore ◽  
Deena M. Leslie Pedrioli ◽  
...  
Keyword(s):  
Founder Mutation ◽  
Corneal Dystrophy ◽  
Allele Specific ◽  
The Common ◽  
Sirna Silencing ◽  
Keratin 12

scholarly journals Best Paper Selection

2017 ◽  
Vol 26 (01) ◽  
pp. 191-192
Keyword(s):  
Gene Fusion ◽  
Specific Binding ◽  
Integrative Genomics ◽  
Transcriptome Data ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Regulatory Circuits ◽  
Cancer Subtype ◽  
Network Modules ◽  
Allele Specific

Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. Nat Commun 2016 Apr 18;7:11101 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837449/ Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, Bergmann S. Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. Nat Methods 2016 Apr;13(4):366-70 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967716/ Zhang D, Chen P, Zheng CH, Xia J. Identification of ovarian cancer subtype-specific network modules and candidate drivers through an integrative genomics approach. Oncotarget 2016 Jan 26;7(4):4298-309 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4826206/ Zhang, J, White, NM, Schmidt, HK, Fulton, RS, Tomlinson, C, Warren, WC, Wilson, RK, Maher, CA. INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res 2016;26(1):108-18

scholarly journals iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding

2012 ◽  
Vol 13 (S18) ◽  
Author(s):  
Yingying Wei ◽  
Xia Li ◽  
Qianfei Wang ◽  
Hongkai Ji
Keyword(s):  
Specific Binding ◽  
Allele Specific

scholarly journals The c-Myc Oncogene Directly Induces the H19 Noncoding RNA by Allele-Specific Binding to Potentiate Tumorigenesis

2006 ◽  
Vol 66 (10) ◽  
pp. 5330-5337 ◽  
Author(s):  
Dalia Barsyte-Lovejoy ◽  
Suzanne K. Lau ◽  
Paul C. Boutros ◽  
Fereshteh Khosravi ◽  
Igor Jurisica ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Specific Binding ◽  
Myc Oncogene ◽  
Allele Specific

scholarly journals A Common Promoter Variant of TBX21 is Associated with Allele Specific Binding to Yin-Yang 1 and Reduced Gene Expression

2011 ◽  
Vol 73 (5) ◽  
pp. 449-458 ◽  
Author(s):  
J.-R. Li ◽  
J.-G. Li ◽  
G.-H. Deng ◽  
W.-L. Zhao ◽  
Y.-J. Dan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Specific Binding ◽  
Yin Yang 1 ◽  
Yin Yang ◽  
Allele Specific

scholarly journals Which genetic variants in DNase I sensitive regions are functional?

2014 ◽  
Author(s):  
Gregory A Moyerbrailean ◽  
Chris T Harvey ◽  
Cynthia A Kalita ◽  
Xiaoquan Wen ◽  
Francesca Luca ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Complex Traits ◽  
Computational Models ◽  
Specific Binding ◽  
Dnase I ◽  
Regulatory Sequences ◽  
Dnase I Footprinting ◽  
Show Evidence ◽  
Allele Specific ◽  
The Impact

Ongoing large experimental characterization is crucial to determine all regulatory sequences, yet we do not know which genetic variants in those regions are non-silent. Here, we present a novel analysis integrating sequence and DNase I footprinting data for 653 samples to predict the impact of a sequence change on transcription factor binding for a panel of 1,372 motifs. Most genetic variants in footprints (5,810,227) do not show evidence of allele-specific binding (ASB). In contrast, functional genetic variants predicted by our computational models are highly enriched for ASB (3,217 SNPs at 20% FDR). Comparing silent to functional non-coding genetic variants, the latter are 1.22-fold enriched for GWAS traits, have lower allele frequencies, and affect footprints more distal to promoters or active in fewer tissues. Finally, integration of the annotations into 18 GWAS meta-studies improves identification of likely causal SNPs and transcription factors relevant for complex traits.

scholarly journals Fine-mapping identifies causal variants for RA and T1D in DNASE1L3, SIRPG, MEG3, TNFAIP3 and CD28/CTLA4 loci

2017 ◽  
Author(s):  
Harm-Jan Westra ◽  
Marta Martinez Bonet ◽  
Suna Onengut ◽  
Annette Lee ◽  
Yang Luo ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Functional Analysis ◽  
Type 1 Diabetes ◽  
Specific Binding ◽  
Common Variants ◽  
Enhancer Activity ◽  
Allele Specific ◽  
Causal Variants ◽  
Coding Variants

We fine-mapped 76 rheumatoid arthritis (RA) and type 1 diabetes (T1D) loci outside of the MHC. After sequencing 799 1kb regulatory (H3K4me3) regions within these loci in 568 individuals, we observed accurate imputation for 89% of common variants. We fine-mapped1,2 these loci in RA (11,475 cases, 15,870 controls)3, T1D (9,334 cases and 11,111 controls) 4 and combined datasets. We reduced the number of potential causal variants to ≤5 in 8 RA and 11 T1D loci. We identified causal missense variants in five loci (DNASE1L3, SIRPG, PTPN22, SH2B3 and TYK2) and likely causal non-coding variants in six loci (MEG3, TNFAIP3, CD28/CTLA4, ANKRD55, IL2RA, REL/PUS10). Functional analysis confirmed allele specific binding and differential enhancer activity for three variants: the CD28/CTLA4 rs117701653 SNP, the TNFAIP3 rs35926684 indel, and the MEG3 rs34552516 indel. This study demonstrates the potential for dense genotyping and imputation to pinpoint missense and non-coding causal alleles.

scholarly journals A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Jieming Chen ◽  
Joel Rozowsky ◽  
Timur R. Galeev ◽  
Arif Harmanci ◽  
Robert Kitchen ◽  
...  
Keyword(s):  
Specific Binding ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Allele Specific
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