ライフサイエンスコーパス: allele-specific

1 let of the cytoplasmic membrane and were not allele specific.

2 SEP3 and subcellular localization were SHELL allele-specific.

3 Finally, we found epigenetic, allele-specific activation of the testis-specific gene n

4 ing genomic imprinting, the contributions of allele-specific active histone modifications to imprinti

5 associated variants demonstrated significant allele-specific activity in reporter assays.

6 The locus shows allele-specific activity that is concomitantly modulated

7 rs604723 that exhibits strong SMC-selective, allele-specific activity.

8 ial Splicing Events), a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq

9 s208308, rs208309, and rs373655596) promotes allele-specific alternative splicing, increasing mRNA le

10 nt a framework for statistical estimation of allele-specific amplification imbalance at any given pos

11 , we show that BaalChIP effectively corrects allele-specific analysis for copy-number variation and i

12 of genes, the majority of which were mutant allele specific and were not observed upon estrogen trea

13 plotype phasing revealed numerous regions of allele-specific and allele-independent asynchronous repl

14 R-DLGAP2 was found to be genotype-dependent, allele-specific and associated with reward processing in

15 We found allele-specific and lineage-specific de novo methylation

16 cell death and early nodule senescence in an allele-specific and rhizobial strain-specific manner, an

17 It supports both region-based and allele-specific annotations and introduces advanced func

18 pockets of these four molecules to identify allele specific as well as common features of peptide bi

19 h quantitative trait locus (QTL) mapping and allele-specific (AS) analyses.

20 addition to traditional QTLs by association, allele-specific (AS) QTLs are a powerful measure of cis-

21 We developed an allele-specific assay for transposase-accessible chromat

22 These robust allele-specific assays could prove valuable for monitori

23 The case-control cohort was genotyped with allele-specific assays.

24 r previous assay based on the combination of allele-specific, asymmetric rapid PCR, and melting analy

25 he functional effect of these variants using allele-specific behaviour.

26 tational approach, called BEAPR, to identify allele-specific binding (ASB) events in eCLIP-Seq data.

27 f genomic features, peak identification, and allele-specific binding detection.

28 oic acid receptor 6), apparently mediated by allele-specific binding of the transcription factor THRb

29 d paper assessed the feasibility of applying allele-specific binding to filter potential regulatory s

30 seq) data, AlleleHMM identified thousands of allele specific blocks of transcription in both coding a

31 ere, we propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical v

32 diploid organism and the characterization of allele-specific bursting.

33 P, located 280 bp upstream which provides an allele-specific C-methylation site.

34 Mismatched HLA class II allele-specific CD4(+) T cells recognized primary leukem

35 ferential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA proces

36 ta for inhibitor-protein complexes to design allele-specific chemical probes.

37 orous framework for investigating fine-scale allele-specific chromatin conformations.

38 le binding of Yin Yang 1 (YY1), confirmed by allele-specific chromatin immunoprecipitation in primary

39 IA-PET2 can use phased genotype data to call allele-specific chromatin interactions.

40 , a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genom

41 NP-derived PAM was found to confer stringent allele-specific cleavage, while a guide-specific approac

42 These allele-specific CNAs affect genomic regions containing w

43 he reconstruction of tumor evolution, timing allele-specific CNAs before and after WGDs, identifying

44 The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and

45 analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to in

46 d efficient strategy for deriving global and allele-specific copy number alternations (CNA) from canc

47 Allele-specific copy number analysis of tumors (ASCAT) a

48 Allele-specific copy number and serial sampling analyses

49 HHLA), a computational tool to determine HLA allele-specific copy number from sequencing data.

50 We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ens

51 We identified extensive allele-specific copy-number aberrations (CNAs) in these

52 Analysis of SNVs in relation to allele-specific copy-number changes pinpoints the common

53 Now, with the success of allele-specific covalent inhibitors against the most fre

54 g K562 haplotype information, we produced an allele-specific CRISPR targeting map.

55 ression and DNA methylation and assembled an allele-specific CRISPR/Cas9 targeting map.

56 We identified multiple allele-specific deletions and duplications within the tu

57 Using sensitive allele-specific detection methods, we demonstrate that M

58 onal methods have been developed to discover allele specific differences in functional genomic data.

59 locks of neighboring SNPs that share similar allele specific differences in mark abundance.

60 ene annotations, preventing the discovery of allele specific differences in unexpected genomic region

61 In normal colon tissue, small allele-specific differences exist only in MLH1 promoter

62 In contrast, allele-specific differences in both MLH1 methylation and

63 and identified those with the potential for allele-specific differences in the formation of non-Wats

64 th widespread lineage-, position- and mutant allele-specific differences, many of which are likely fu

65 Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS

66 e trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a

67 xpression phenomenon primarily controlled by allele-specific DNA methylation at the imprinting contro

68 Dynamic allele-specific DNA methylation at the two SEs was also

69 a mouse model with nonrandom XCI to examine allele-specific DNA methylation in frontal cortex.

70 CpGenie produces allele-specific DNA methylation prediction with single-n

71 cing data for allele-specific expression and allele-specific DNA methylation.

72 Here we profile parental allele-specific DNase I hypersensitive sites in mouse zy

73 y sequencing identify 76 genes with paternal allele-specific DNase I hypersensitive sites that are de

74 largely conserved across individuals with no allele-specific effect within an IgH variable gene famil

75 0 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding.

76 ree transcriptional regulatory elements with allele-specific effects and a scaffold/matrix attachment

77 actions, and genome editing in vitro to show allele-specific effects on ARHGAP29 expression and cell

78 ISPR-based genome editing that confirmed its allele-specific effects on FAM13A expression and on cell

79 e introduce MPRAscore, a novel tool to infer allele-specific effects on transcription from MPRA data.

80 rt and enables robust statistical calling of allele-specific effects.

81 ional depletion of transcription factors and allele-specific enhancer analysis reveal an essential ro

82 f expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primar

83 ucture after fertilization coincides with an allele-specific enrichment of methylation of histone H3

84 expressed non-coding RNAs exhibited the same allele-specific epigenetic features as endo-MEGs, indica

85 Genomic imprinting is often associated with allele-specific epigenetic modifications.

86 ic X-chromosome inactivation (XCI) confounds allele-specific epigenomic profiling.

87 cting (allele-specific) vs trans-acting (non-allele-specific) eQTLs.

88 ure precise repair of excision junctions and allele-specific excision, with important implications fo

89 C showed that the associated variant induces allele-specific exon inclusion (P = 0.0024).

90 riven megakaryocyte enhancer is confirmed in allele-specific experiments.

91 nctional predictions implicated ABLIM1 as an allele-specific expressed gene in neuronal tissue.

92 tory elements in diploid organisms may cause allele specific expression (ASE) - unequal expression of

93 Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from

94 We employ RNAseq analyses to assess allele-specific expression (ASE) and biallelic loss-of-e

95 Allele-specific expression (ASE) at single-cell resoluti

96 le Bayesian statistical approach to quantify allele-specific expression (ASE) in complex RNA-seq data

97 The study of allele-specific expression (ASE) in interspecific hybrid

98 Allele-specific expression (ASE) is a fundamental proble

99 Specifically, existing methods do not test allele-specific expression (ASE) of a gene as a whole an

100 xpression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals.

101 d mechanism of gene regulation in disease is allele-specific expression (ASE), the preferential expre

102 subjects with AUD and 30 controls to analyze allele-specific expression (ASE).

103 pression quantitative trait loci (eQTLs) and allele-specific expression (ASE).

104 n cis-regulatory variation using analyses of allele-specific expression (ASE).

105 aberrantly cis-activated genes that exhibit allele-specific expression accompanied by an elevated ou

106 We discovered widespread, dynamic allele-specific expression across the genome, where the

107 The analysis of allele-specific expression allowed classification of cis

108 This included IL2RA, where allele-specific expression analyses were consistent with

109 Allele-specific expression analysis in the C. maxima x C

110 CETALDEHYDE SYNTHASE gene RhPAAS An in-depth allele-specific expression analysis in the progeny demon

111 An allele-specific expression analysis showed overwhelmingl

112 We also employed allele-specific expression analysis to find potential re

113 By extending classic allele-specific expression analysis to the allopolyploid

114 Using allele-specific expression analysis, expressed fs-indels

115 d whole-genome bisulfite sequencing data for allele-specific expression and allele-specific DNA methy

116 ng a causal variant and causal mechanism for allele-specific expression and disease association at th

117 We re-analyzed published HepG2 datasets for allele-specific expression and DNA methylation and assem

118 nslated regions of HLA genes are involved in allele-specific expression and may therefore underlie so

119 formatics pipeline to assay parent-of-origin allele-specific expression and report more than 300 loci

120 RNA transcription, splicing, and allele-specific expression are each important determinan

121 In addition, we discovered that total and allele-specific expression are positively correlated wit

122 introduces the observation that differential allele-specific expression can link genetic variants fro

123 esults show that gene isoform expression and allele-specific expression cooperate to provide high div

124 , we analyzed for the first time genome-wide allele-specific expression data from diploid and triploi

125 ion between cis promoter DNA methylation and allele-specific expression imbalance (P = 2.0 x 10-10).

126 number of studies have measured genome-wide allele-specific expression in hybrids and observed that

127 ies, correlation with growth-related traits, allele-specific expression in interspecific hybrids, and

128 al effects of multiple causal variants using allele-specific expression in sorted CD4(+) T cells from

129 Allele-specific expression is traditionally studied by b

130 Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids.

131 like deficits in fear memory and hippocampal allele-specific expression of Igf2, which were reversed

132 aternal deletion did not affect the parental allele-specific expression of imprinted genes, indicatin

133 of allelic bursting and track changes in the allele-specific expression patterns of cells sampled ove

134 These analyses coupled with allele-specific expression show that iPSCs retain a dono

135 Allele-specific expression was also higher in these pati

136 rategy that allows candidate gene testing by allele-specific expression without prior knowledge of th

137 abnormalities by analyzing gene expression, allele-specific expression, and alternative splicing fro

138 ntal stages unravel ~19% of genes displaying allele-specific expression, including many associated wi

139 rigins, have been used to assess genome-wide allele-specific expression.

140 ulation of transcription, isoform usage, and allele-specific expression.

141 ciations between environmental variables and allele-specific expression.

142 antification of relative gene expression and allele-specific expression.

143 priate for analyzing genomic data to examine allele-specific expression.

144 ajor drivers of variations in total gene and allele-specific expression.

145 so enable transcripts to be phased to detect allele-specific expression.

146 an epigenetic phenomenon leading to parental allele-specific expression.

147 rent genes depending on expression level and allele-specific expression.

148 may be expressed in a cell type-specific and allele-specific fashion.

149 ze germline selection in Drosophila using an allele-specific fluorescent in situ-hybridization approa

150 n), which uses the same technology to reveal allele-specific function of these variants at the DNA-pr

151 In >50% of these cases, allele-specific GATA2 expression was observed, either by

152 Allele-specific gene disruption induced by non-homologou

153 Placentas retained monoallelic allele-specific gene expression of IGF2, but 32.4% of co

154 E), an epigenetic mechanism characterized by allele-specific gene expression that varies between clon

155 ryo and how these structures might relate to allele-specific gene regulation remain open.

156 is a highly dynamic epigenomic correlate of allele-specific gene regulation.

157 ne 27 (H3K27me3) mediates autosomal maternal allele-specific gene silencing and has an important role

158 prove valuable for monitoring the impact of allele-specific gene silencing strategies currently bein

159 higher RNA transcript levels but identifies allele-specific gene transcripts showing haplotype-speci

160 the potential for each to be targeted using allele-specific gene-editing, RNAi, or small-molecule ap

161 tially be treated effectively by suppressing allele-specific genes using small interfering RNA (siRNA

162 Studies have linked allele-specific genetic changes to gene expression, DNA

163 ghlight how combining between-individual and allele-specific genetic signals improves the functional

164 These results demonstrate that allele-specific genome editing with AsCas12a can correct

165 ed in GenHap can be extended to the study of allele-specific genomic features, such as expression, me

166 void of DNA methylation but harbour maternal allele-specific H3K27me3.

167 rt the identification of 337 high-stringency allele-specific H3K4me3 and H3K36me3 peaks in maize endo

168 ain-specific adult foraging behavior through allele-specific histone methylation of a for promoter (p

169 the molecular level, we have developed novel allele-specific HTT mRNA and protein quantification meth

170 ad allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin.

171 us matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specifi

172 e Xist gene is essential to achieve paternal allele-specific imprinted X-chromosome inactivation (XCI

173 We investigated allele-specific imputation challenges in regard to geogr

174 We further show that allele-specific inactivation of either of two essential

175 in the different endemic sites, ranging from allele-specific inhibition to allele-independent inhibit

176 tly, direct inhibition of mutant RAS through allele-specific inhibitors provides the best therapeutic

177 PRL-1 mutants exhibit allele-specific interactions with the light- and clock-r

178 Allele-specific KIR expression is maintained by DNA meth

179 demonstrate the feasibility of AAV9-mediated allele-specific knockdown and provide proof of concept f

180 res ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin in

181 spora delbrueckii FBA1 efficiently and in an allele-specific manner, leading to DNA repair by gene co

182 HLA-C varies widely across individuals in an allele-specific manner.

183 tory element repressed TERT expression in an allele-specific manner.

184 s) and enhancers within imprinted loci in an allele-specific manner.

185 sustaining inflammation in beta-cells in an allele-specific manner.

186 ith increased production of chemokines in an allele-specific manner.

187 endocrine pancreas development varies in an allele-specific manner.

188 We introduce PLASMA (Population Allele-Specific Mapping), a fine-mapping method that int

189 Finally, we found extensive allele-specific mCH and mCG at autosomal imprinted regio

190 In heterozygous genomes, allele-specific measurements can reveal biologically sig

191 Allele-specific measurements of transcription factor bin

192 Our findings reveal allele-specific mechanisms by which variant SHELL allele

193 igh differentiation-induced variability, our allele-specific method detected thousands of quantitativ

194 es to perform genotype-dependent analyses of allele-specific methylation (ASM) and non-allelic methyl

195 l physics and develop a method for detecting allele-specific methylation (ASM) events within segments

196 the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in

197 ic expression are positively correlated with allele-specific methylation in a subset of the different

198 f bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous i

199 pe heterogeneity, cellular contamination and allele-specific methylation.

200 emergence of real-time PCR assays utilizing allele-specific molecular detection technology that is h

201 w for single-cell RNA-seq data that computes allele-specific molecule counts of the HLA genes based o

202 nts can be derived from such data, important allele-specific mutations-such as copy-neutral loss of h

203 urrent mutational hotspot associated with an allele-specific neurodevelopmental phenotype in NACC1.

204 or the repressor Broad, driving differential allele-specific nutcracker expression.

205 romatin Immunoprecipitation and Quantitative Allele-Specific Occupation), which uses the same technol

206 and quantified by 4-color flow cytometry or allele-specific oligonucleotide real-time quantitative p

207 BCR-ABL1(T315I) was tested by allele-specific oligonucleotide reverse transcription-qu

208 ied thousands of genetic variants exhibiting allele-specific open chromatin (ASoC).

209 Notably, we find frequent allele-specific overexpression of variants in tumor-supp

210 to this QTL were used to develop Kompetitive allele specific PCR (KASP) markers, and the validated KA

211 A multiplex allele-specific PCR targeting outbreak-specific single n

212 TaqMan real-time PCR technology and combines allele-specific PCR with a blocking reagent (minor groov

213 otyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create sca

214 s microfluidic compartmentalization, in situ allele-specific PCR, and fluorescence microscopy.

215 Those SNPs were converted into Kompetitive Allele-Specific Polymerase assays (KASP) and analyzed in

216 ing and sequencing, and highly sensitive and allele-specific polymerase chain reaction (AS-PCR) assay

217 Allele-specific polymerase chain reaction (PCR) (amplifi

218 were genotyped with the LRRK2 'Kompetitive' allele-specific polymerase chain reaction assay and/or e

219 In this study, BRAF(V600E) allele-specific polymerase chain reaction was used to ma

220 the level of the nascent transcriptome using allele-specific Precision nuclear Run-On sequencing (PRO

221 Allele-specific primers were designed and optimized to d

222 This approach could be used to design allele-specific probes for studying cellular functions o

223 an epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromati

224 al changes in transcription and chromatin by allele-specific profiling.

225 98 using HepG2 cell line demonstrated strong allele-specific promoter and enhancer activity and diffe

226 Allele-specific protein-RNA binding is an essential aspe

227 We developed a computational method ASPRIN (Allele-Specific Protein-RNA Interaction) that uses a joi

228 ariants that affect alternative splicing via allele-specific protein-RNA interactions.

229 alanced DNA pulldown-Western blot) to detect allele-specific protein:fSNP binding.

230 r other cis-haplotype variations, we applied allele-specific quantification assays to a panel of HD l

231 t currently available methods do not perform allele-specific quantification at the molecule level.

232 le is not clear due to the lack of sensitive allele-specific quantification methods and the presence

233 ed with in silico analyses and validated via allele-specific quantification of antibody-precipitated

234 hat included a serum tryptase determination, allele-specific quantitative PCR (ASqPCR) for the KIT D8

235 Allele-specific quantitative PCR showed that the vast ma

236 ificial population using microsatellites and allele-specific quantitative PCR.

237 is differentially expressed in glomeruli of allele-specific rat models during onset of albuminuria.

238 processing, joint segmentation of total- and allele-specific read counts, and integer copy number cal

239 Allele-specific read mapping identified variants that al

240 relapse trial using sequencing and sensitive allele-specific real-time polymerase chain reaction.

241 ase I plasma pilot incorporated quantitative allele-specific real-time target and signal amplificatio

242 AlleleHMM is a powerful tool for discovering allele specific regions in functional genomic datasets.

243 d their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates ge

244 zed mutations identified in probands possess allele-specific regulatory activity, and we highlight a

245 013701, a putative COPD-causing variant with allele-specific regulatory activity.

246 approach, we identified 24 variant REs with allele-specific regulatory activity.

247 chromatin accessible region while displaying allele-specific reporter activity.

248 Using CRISPR interference (CRISPRi), allele-specific reporter assays, and chromatin conformat

249 We used allele-specific reporters at the endogenous Sox2 and Mir

250 e potentially in place to modulate cell- and allele-specific responses.

251 (LOI) is an epigenetic event that relaxes an allele-specific restriction on gene expression.

252 an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis.

253 atin-associated, and we discover hundreds of allele-specific RNA-chromatin interactions.

254 Here we show the efficacy of allele-specific RNAi as a potential therapy for Charcot-

255 Using in vivo single-cell approaches (allele-specific RNAseq, nascent RNA-fluorescent in situ

256 We show that allele-specific SbMATE transactivation occurs and is cau

257 33 genomic features and constructed a map of allele-specific selection coefficients across all protei

258 ic and machine-learning model, called Linear Allele-Specific Selection InferencE (LASSIE), for estima

259 ver alterations that arise from context- and allele-specific selective pressures that are dependent i

260 organisms incorporated exogenous DNA and/or allele specific sequence that allow for genotyping strat

261 s showed a clear association with the HLA-DP allele-specific sequences of the binding groove.

262 We investigated the efficacy of allele-specific silencing by RNA interference to prevent

263 ection of hair structural phenotypes through allele-specific silencing of mutant keratin genes.

264 gy mediated by mirtrons as an alternative to allele-specific silencing using spinocerebellar ataxia 7

265 The study demonstrates that allele-specific silencing with miRYR2-U10 prevents life-

266 ata that we simulate using MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolutio

267 rograming to study human Xi reactivation and allele-specific single nucleotide polymorphisms (SNPs) t

268 Using allele-specific single-cell RNA sequencing, we here esti

269 oison recipient cells that lack the cognate, allele-specific SitI immunity protein.

270 We hypothesized that a mutant allele-specific small interfering RNA could rescue the c

271 pt and model system for the potential use of allele-specific small interfering RNA in treating KID sy

272 In vitro treatment with allele-specific small interfering RNA led to robust inhi

273 Notably, allele-specific small interfering RNA treatment caused o

274 Herein, we describe an allele-specific strategy toward an engineered protein-pr

275 of seed dormancy by asDOG1 in cis results in allele-specific suppression of DOG1 expression and promo

276 ease to assess the use of CRISPR/Cas9 in two allele-specific systems, comparing cleavage using a SNP-

277 a robust, highly selective, and broad-range allele-specific TaqMan real-time PCR platform consisting

278 Allele-specific targeting of enCRISPRa to oncogenic TAL1

279 We encounter allele-specific TE methylation and demethylation of aber

280 is associated with CRC, which identifies 731 allele-specific TF binding at 116 CRC risk loci.

281 types associated with MPZ, supporting future allele-specific therapeutic silencing strategies.

282 4-PBA treatment as a promising strategy for allele-specific therapy of ABCC6-associated calcificatio

283 ated to each allele might be exploitable for allele-specific therapy.

284 By evaluating allele-specific transcript abundance in the F1 hybrids,

285 Finally, using allele-specific transcription data, we present evidence

286 Identification of allele-specific transcription factor (TF) binding is of

287 in, rs679482 is predicted to bind DMRT2, and allele-specific transcription factor binding analysis in

288 scores are assay-specific, are predictive of allele-specific transcription factor binding and are enr

289 Allele-specific transcription factor binding from ChIP-s

290 Here we measure allele-specific transcription factor binding occupancy o

291 Putative allele-specific transcription factors were identified wi

292 Allele-specific transcription revealed that two of seven

293 Many genes exhibit evidence for allele-specific transcriptional activation by PrCa maste

294 r(2) = 0.947 with rs3219090), as displaying allele-specific transcriptional activity.

295 We introduce HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity), an alg

296 to the deletion breakpoints, with subsequent allele-specific upregulation of FLT3 expression, expecte

297 e summarize recent observations on cell- and allele-specific variability of genome architecture, disc

298 These data demonstrate HLA-A allele-specific variation in PAS usage, which modulates

299 TL) mapping and the detection of cis-acting (allele-specific) vs trans-acting (non-allele-specific) e

300 Recognition is shown to be traA allele-specific, where polymorphisms within TraA dictate