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 Then, we describe effective allele-specific absolute normalization and quantificatio

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

4 After testing candidate SNPs for allele-specific activity in a luciferase-based enhancer

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

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

7 p.F508del (delF508_CTT) were genotyped using allele-specific amplification polymerase chain reaction.

8 Allele-specific analyses of gene regulation can further

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

10 tomizable pipeline of command line tools for allele-specific analysis of next-generation sequencing d

11 We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical l

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

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

14 Our results serve as an allele-specific annotation for the 1000 Genomes variant

15 ing for HD could be extended to personalized allele-specific approaches in essentially all HD individ

16 Both allele- and non-allele-specific approaches to gene suppression have made

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

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

19 romatin interaction detection techniques and allele specific assays in T and B cell lines, we provide

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

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

22 e specificity involving three components: an allele-specific avirulence effector, a resistance gene a

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

24 prioritize 64 candidate variants and perform allele-specific binding and expression analyses at seven

25 We annotate variants associated with allele-specific binding and expression in 382 individual

26 luation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the pow

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

28 accuracy, peak resolution, and most notably, allele-specific binding detection.

29 Parental-origin allele-specific binding is methylation-dependent and map

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

31 gle-nucleotide polymorphisms associated with allele-specific binding.

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

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

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 putative DMRT1 promoter was associated with allele-specific changes in transcription factor binding

37 This allele-specific characteristic of Wig1 is likely to be e

38 Here using assays of chromatin conformation, allele-specific chromatin immunoprecipitation and genome

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

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

41 By profiling human DNA replication in an allele-specific, chromosomally phased manner, we determi

42 Allele-specific cis-effects on ORMDL expression were ass

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

44 iC-Pro can use phased genotype data to build allele-specific contact maps.

45 rbid regulates this process in cis, enabling allele-specific control of Bcl2l11 transcription.

46 ed to both enhance CNV detection and produce allele-specific copy number (ASCN) calls.

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

48 Allele-specific copy number analysis (ASCN) from next ge

49 be a new method, falcon, for finding somatic allele-specific copy number changes by next generation s

50 The allele-specific copy number estimates obtained by falcon

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

52 imating cancerous cell purity, tumor ploidy, allele-specific copy number, and clonality and represent

53 Estimation of allele-specific copy number, which quantifies the number

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

55 chromosome haplotypes and corrects for local allele-specific coverage biases.

56 Other features of PrimerMapper include allele-specific design features for SNP genotyping, a re

57 a from electromobility shift assays, suggest allele-specific differences at rs7132434 for AP-1 transc

58 , SNPs highly correlated with rs7132434 show allele-specific differences in BHLHE41 expression (trend

59 Genes with significant allele-specific differences in mRNA decay rates have hig

60 We observed allele-specific differences in NEUROD1 binding in islet-

61 mino acid resolution will help elucidate the allele-specific differences in their function and could

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

63 (ICRs), cis-regulatory elements that exhibit allele-specific differential DNA methylation.

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

65 xpression at imprinted genes is regulated by allele-specific DNA methylation at imprinting control re

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

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

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

69 t reinforces PEAR1 enhancer activity through allele-specific DNA methylation.

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

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

72 vidence that a particular SNP in IBSP has an allele-specific effect on mRNA levels, which would, in t

73 These allele-specific effects are consistent with a computatio

74 ggest a previously unknown mechanism linking allele-specific effects of rs13102260 on HTT expression

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

76 indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest

77 a-associated polymorphisms were analyzed for allele-specific effects on transcription factor binding

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

79 he A risk allele, which increased global and allele-specific EGR2 expression.

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

81 ation of methylation levels and for study of allele-specific epigenetic events such as imprinting.

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

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

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

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

86 With allele-specific events filtered out or appropriately tak

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

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

89 Allele specific expression (ASE) has become an important

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

91 Recently, allele-specific expression (ASE) analysis emerged as a p

92 ve strategy combining association study with allele-specific expression (ASE) analysis in MCC gene.

93 firmed these results in silico by performing allele-specific expression (ASE) analysis, which demonst

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

95 Finally, we suggest a way of measuring allele-specific expression (ASE) by crossing the line of

96 Such allele-specific expression (ASE) has been extensively ex

97 Here, we examined allele-specific expression (ASE) in an F1 hybrid to stud

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

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

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

101 Allele-specific expression (ASE) is a useful way to iden

102 In contrast, analysis of allele-specific expression (ASE) is becoming a popular a

103 is-acting regulatory variation by leveraging allele-specific expression (ASE) patterns in association

104 RNA sequencing enables allele-specific expression (ASE) studies that complement

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

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

107 of gene expression and allow measurement of allele-specific expression (ASE).

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

109 quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substan

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

111 An allele-specific expression analysis showed overwhelmingl

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

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

114 We examined embryo and endosperm allele-specific expression and DNA methylation genome-wi

115 nome is ideally suited for the comparison of allele-specific expression and functional genomic data o

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

117 In this study, we quantified allele-specific expression and methylation genome-wide i

118 se that enables single-cell visualization of allele-specific expression and prospective isolation of

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

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

121 al of Zea mays (maize) indicates significant allele-specific expression biases in at least one tissue

122 onstrate that a large fraction of stochastic allele-specific expression can be explained by technical

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

124 The possibility to study allele-specific expression in different contexts makes o

125 m. domesticus was characterized by studying allele-specific expression in fertile hybrid males using

126 lying our approach to investigate stochastic allele-specific expression in individual cells, we demon

127 n five cardiometabolic-relevant tissues, and allele-specific expression in RNA sequencing data for ad

128 e in situ hybridization method that measures allele-specific expression in single cells to address th

129 sting that these mutations lead to decreased allele-specific expression in vivo.

130 We postulate that this switch in allele-specific expression is related to the functional

131 Allele-specific expression is traditionally studied by b

132 Embryonic genotype controls allele-specific expression of 1594 genes and a highly ov

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

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

135 Furthermore, not only was there loss of allele-specific expression of imprinted genes in LOS, bu

136 Here, we determined allele-specific expression of imprinted genes previously

137 -specific aberrations in DNA methylation and allele-specific expression of imprinted genes.

138 Thus, parsing the relationship between allele-specific expression of these genes and disease is

139 ions likely to be implicated in RNA editing, allele-specific expression or loss, somatic mutagenesis

140 es: we predict that only 17.8% of stochastic allele-specific expression patterns are attributable to

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

142 ical problems that require quantification of allele-specific expression using RNA-seq, such as cis-re

143 with total expression variation (eQTLs) and allele-specific expression variation (aseQTLs) mapped wi

144 Allele-specific expression was also higher in these pati

145 Among this widespread allele-specific expression, we identify germline polymor

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

147 homozygosity and corresponding increases in allele-specific expression.

148 loci, which we validate through analysis of allele-specific expression.

149 kinetics of gene expression and patterns of allele-specific expression.

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

151 ciations between environmental variables and allele-specific expression.

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

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

154 , copy-neutral loss-of-heterozygosity (LOH), allele-specific gains/amplifications.

155 Allele-specific gene disruption induced by non-homologou

156 y an imprinting center that is necessary for allele-specific gene expression and to reprogram parent-

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

158 rowth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chrom

159 n epigenetic mechanism resulting in parental allele-specific gene expression.

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

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

162 for capturing heterozygosity in personalized allele-specific gene-silencing approaches.

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

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

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

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

167 Allele-specific haplotypes were constructed based on lin

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

169 did not distinguish the active and inactive alleles, specific histone modifications were differentia

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

171 oci and demonstrate significant evidence for allele-specific impact on expression levels.

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

173 of Cd22 but also that its expression became allele specific in tumors.

174 CRISPR/Cas9 sites, aiming at the mutant HTT allele-specific inactivation for a given diplotype.

175 n, unequivocally indicating permanent mutant allele-specific inactivation of the HD mutant allele.

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

177 SRK, like its trans-activation, is based on allele-specific interaction between receptor and ligand.

178 L.) Mildew resistance locus a (Mla) confers allele-specific interactions with natural variants of th

179 nt Cdk2 phenotype cell cycle arrest, whereas allele specific knockdown of mutant CDK2 with siSN resul

180 Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate h

181 (approximately 50% of alleles methylated and allele-specific loss of MLH1 expression) that was stable

182 notype on gene expression was measured using allele-specific luciferase reporter assays.

183 cancer metabolism in vitro and in vivo in an allele-specific manner by binding the Cleavage Factor I

184 GFR signaling pathway appears to occur in an allele-specific manner that may have important implicati

185 sequence-specific ZFP57 binding sites in an allele-specific manner using hybrid ES cell lines from r

186 ause intron retention or exon skipping in an allele-specific manner, with approximately 70% of the SN

187 iR-155 and miR-105 repressed NPPA mRNA in an allele-specific manner, with the minor allele of each re

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

189 with and phosphorylates SUB1A in a tolerant-allele-specific manner.

190 lling the binding and activity of AFF3 in an allele-specific manner.

191 esponse to innate and adaptive stimuli in an allele-specific manner.

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

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

194 A multiplex allele-specific (MAS) assay has been developed for the d

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

196 Allele-specific measurements demonstrate that the presen

197 Allele-specific measurements of transcription factor bin

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

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

200 rns are important as they may originate from allele-specific methylation (ASM) or cell-specific methy

201 ns, BSPAT can automatically detect potential allele-specific methylation (ASM) patterns, which can gr

202 ver <2% of the genome and cannot account for allele-specific methylation (ASM).

203 Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease

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

205 ylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the u

206 ation co-occurrence patterns and a potential allele-specific methylation case.

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

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

209 Measurement of allele-specific mRNA levels in human pancreatic islet sa

210 ediated gene targeting approach to introduce allele-specific mutations plus an allele-selective siRNA

211 nce of germline polymorphisms in determining allele-specific mutations, and we identify somatic genet

212 self-enhanced transport regulation based on allele-specific nature of lncRNAs and their temporal dyn

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

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

215 ed immunoglobulin and T-cell receptor genes (allele-specific oligonucleotide [ASO]-PCR) are claimed t

216 of multiparametric flow cytometry (MFC) and allele-specific oligonucleotide polymerase chain reactio

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

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

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

220 Three competitive allele-specific PCR (KASP) markers were developed based

221 The application of pyrosequencing and allele-specific PCR techniques established that mutation

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

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

224 Variations of PCR, including primer walking, allele-specific PCR, and nested PCR provide specialized

225 were shown to bear common PIK3CA variants by allele-specific PCR.

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

227 asured using 454 deep sequencing and a novel allele-specific polymerase chain reaction (AS-PCR) diagn

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

229 98 using HepG2 cell line demonstrated strong allele-specific promoter and enhancer activity and diffe

230 that SNPs detected by eQTeL are enriched for allele-specific protein binding and histone modification

231 3 Finally, repressor regulatory activity and allele-specific protein binding by transcription factors

232 ility shift assays on the shortlist detected allele-specific protein binding to the lead SNP rs488837

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

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

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

236 We present RASQUAL (Robust Allele-Specific Quantitation and Quality Control), a new

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

238 -exome sequence (WES) data, information from allele-specific read counts has not yet been adequately

239 ethod, called AS-GENSENG, which incorporates allele-specific read counts in CNV detection and estimat

240 y to exploit information from both total and allele-specific read counts while accounting for various

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

242 Allele-specific read evidence was found for 76% of the d

243 d correctly phased 86% of the deletions with allele-specific read evidence.

244 describe WASP, a suite of tools for unbiased allele-specific read mapping and discovery of molecular

245 It is conceivable that allele-specific reads from high-throughput sequencing da

246 Genotyping was performed using allele-specific real-time polymerase chain reaction assa

247 Luciferase reporter assays revealed an allele-specific regulation of genes hosting the variants

248 ical significance of glucocorticoid-mediated allele-specific regulation of the hAGT gene.

249 Luciferase assays demonstrate allele-specific regulatory activity and, together with d

250 Our study reveals N-glycosylation as an allele-specific regulatory mechanism important for regul

251 These findings uncover a complex, allele-specific regulatory mechanism of cancer metabolis

252 S determinants regulate allele-specific rejection of "self" pollen by the pistil

253 V(D)J recombination-generated junctional and allele-specific residues for achieving high affinity of

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

255 We used allele-specific ribosome profiling in interspecies hybri

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

257 ly measured biased expression, compiled from allele-specific RNA-seq and genotyping array data.

258 Allele-specific RNA-seq of neural progenitor cells gener

259 the inactive X chromosome by high-resolution allele-specific RNA-seq.

260 argeted gene-replacement and introduction of allele-specific RNAi sensitivity mutations in the CDK2 a

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

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

263 Allele-specific sequencing reads provide a powerful sign

264 variant nucleotide and exon-intron boundary, allele-specific sequencing was used.

265 quencing depth alone for SCNA inference, the allele specific signals are undervalued.

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

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

268 Allele-specific silencing of mutant keratins through RNA

269 Extension of allele-specific silencing strategies to the few remainin

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

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

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

273 In this study, we developed allele-specific small interfering RNAs capable of select

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

275 e that mutations in TTLL5 delineate a novel, allele-specific syndrome causing defects in two as yet p

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

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

278 These genetic data have implications for allele-specific therapy currently being developed for PX

279 S1121W, Q1347H, and R1314W), suggesting that allele-specific therapy may be useful for selected patie

280 4-PBA treatment as a promising strategy for allele-specific therapy of ABCC6-associated calcificatio

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

282 Here we argue that the existence of risk alleles specific to a single diagnostic category is unli

283 eotide polymorphisms can be used to generate allele-specific tracks.

284 n self-incompatible Brassicaceae is based on allele-specific trans-activation of the highly polymorph

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

286 llele, consistent with a difference in liver allele-specific transcript abundance.

287 two alleles were similar, we could show that allele-specific transcript levels were significantly hig

288 ion were negatively correlated, demonstrated allele-specific transcription bias, and, along with CXCL

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

290 ociates with DNase I hypersensitivity sites, allele-specific transcription factor (TF) binding, and e

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

292 Putative allele-specific transcription factors were identified wi

293 Allele-specific transcription revealed that two of seven

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

295 Here we define maternal and paternal allele-specific Ube3a protein expression throughout post

296 indole core present in IBA and 4OGlcI3F, and allele-specific uncoupling of a subset of PEN3 functions

297 f age, there was no evidence of differential allele-specific vaccine efficacy.

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