ライフサイエンスコーパス: indel

1 Ps and 4.0 million insertions and deletions (indels).

2 nes resulting from insertions and deletions (indels).

3 e numbers of small insertions and deletions (indels).

4 variants and small insertions and deletions (InDels).

5 wa, especially for insertions and deletions (indels).

6 de variants (SNVs) and insertions/deletions (indels).

7 ) and 16 for small insertions and deletions (Indels).

8 t of antibodies by insertions and deletions (InDels).

9 fting indel is followed by a frame-restoring indel.

10 he BCL11A erythroid enhancer at +58 with few indels.

11 kase (RDN) that mediate HDR while minimizing indels.

12 e ability of Cas9 to generate high levels of indels.

13 variants 22 missense variants and 2 in-frame indels.

14 t efficiency and a low ratio of HDR products:indels.

15 eoepitopes derived from small to large-sized indels.

16 lower sensitivity than vg, particularly for indels.

17 el and others displaying numerous infrequent indels.

18 for identifying and representing equivalent indels.

19 le nucleotide polymorphisms (SNPs) and 1.9 M indels.

20 ides through short mutational paths based on indels.

21 Vs have larger effect sizes than do SNVs and indels.

22 ASXL1), including 196 point mutations and 20 indels.

23 d for reference assemblies, SNP datasets and indels.

24 ent by USVL531-PMR by comparing the SNPs and InDels.

25 ed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in th

26 This paper describes Genesis-indel, a computational pipeline that explores the unmapp

27 This paper describes UPS-indel, a utility tool that creates a universal positioni

28 ence is characterized by insertion/deletion (indels) accumulating as fast as single nucleotide varian

29 detect mosaic single-nucleotide variants and indels, achieving a multifold increase in specificity co

30 a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers

31 s) of somatic single nucleotide variants and indels across 5095 clinical samples profiled using a cus

32 enerate large libraries with random in-frame InDels across the entire single-chain variable fragment

33 The indels affect short homopolymer tracts of A/T and increa

34 We present FATHMM-indel, an integrative approach to predict the functional

35 tein, and high efficiency generation of both indel and knock-in allele can be achieved by electropora

36 29% efficiency and with minimal formation of indel and off-target mutations, despite the absence of t

37 th some targets showing one highly preferred indel and others displaying numerous infrequent indels.

38 Indel and SNV formation are associated with both copy-nu

39 However, indel and structural variation events are enriched at th

40 We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitoch

41 mark single nucleotide variations, 176% more indels and 12% larger benchmark regions than previously

42 served evolutionary patterns in which excess indels and early transcription were favoured in originat

43 Indels and fragment deletion were both stably inherited

44 etecting the presence of mutations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer,

45 the repeat region, with the risk of creating indels and genomic instability.

46 easures of genomic rearrangements, including indels and inversions, which is a similar result to what

47 modified gRNAs and demonstrate induction of indels and large genomic deletions in combination with r

48 llows the recovery of new peaks enriched for indels and SNVs.

49 However a reliable benchmark for large indels and structural variants (SVs) is more challenging

50 ing fully phased single-nucleotide variants, indels and structural variants.

51 -to help GIAB curators manually review large indels and SVs within the human genome, and report their

52 ally, we explore two user cases that involve indels and the disruption of enhancers associated with a

53 joining a GFP protein coding region produced indels and viral-based GFP overexpression.

54 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants.

55 vo single-nucleotide variants/indels (dnSNVs/indels) and de novo copy number variants (dnCNVs).

56 both smaller-scale insertions and deletions (indels) and of single-nucleotide variant (SNV) mutations

57 de variants, short insertions and deletions (indels), and novel DNA motifs.

58 cluding miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the sam

59 le-nucleotide polymorphisms (SNPs), in-frame indels, and deletions; 2) single/multigene deletion; and

60 able genomic analysis tools to call SNPs and INDELs, and generate lists of the most likely causal mut

61 MuTect, for accurate detection of somatic MS indels, and MSMutSig, for identification of genes contai

62 aries of random variants with short in-frame InDels, and screen TRIAD libraries to evolve a promiscuo

63 mutations, splice site variants, frameshift indels, and stop gain/lost.

64 theoretically proven to find all equivalent indels, and thus exhaustive.

65 icity prediction scores generated by MutPred-Indel are shown to differentiate highly recurrent from n

66 Most HT-induced indels are 1-2 bp in size and particularly affect homopo

67 Evidence suggests indels are a highly immunogenic mutational class, which

68 Although fs-indels are degraded through the nonsense-mediated decay

69 e-specific expression analysis, expressed fs-indels are enriched in genomic positions predicted to es

70 Frameshift (FS) indels are enriched in olfactory receptor activity while

71 receptor activity while non-frameshift (NFS) indels are enriched in transcription-related proteins.

72 tional annotation further reveals that these indels are strongly correlated with pathways of cancer a

73 Insertions and deletions (indels) are a common source of variation and can frequen

74 Short insertions and deletions (InDels) are a common type of mutation found in nature an

75 Frameshift insertion/deletions (fs-indels) are an infrequent but highly immunogenic mutatio

76 Insertions and deletions (InDels) are frequently observed in natural protein evolu

77 Storing biologically equivalent indels as distinct entries in databases causes data redu

78 iations and 89.8% of unconfirmed genome-wide indel associations.

79 ets increases variability, leading to either indels at 1-2 target sites or inter-target deletions.

80 g, for identification of genes containing MS indels at a higher frequency than expected by chance.

81 tolerates mutations in the unedited allele, indels at the integration site, and the addition of resi

82 m wild-type versus mutant alleles with small indels based on size is beyond the resolution capacity o

83 manipulating gene expression outcomes using INDEL-based mutagenesis and strategies useful in mitigat

84 results in chromosomal losses and hemizygous indels because of cleavage of both alleles.

85 s that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed

86 mosome segments at high-resolution, SNVs and indels (both corrected for CN in aneuploid regions), los

87 Associations between indel burden and treatment response were assessed across

88 The dnSNV/indel burden did not differ between AED-exposed children

89 ls of somatic point mutations and also small indels, but surprisingly limited impact on organismal lo

90 The introduction of insertion-deletions (INDELs) by non-homologous end-joining (NHEJ) pathway und

91 fied system is also desirable to compare the indel calling results produced by different tools.

92 which also can be used to compare different indel calling results.

93 mbers of false positive and negative SNV and INDEL calls that were shown to be enriched among discord

94 emonstrate that the number and pattern of MS indels can accurately distinguish microsatellite-stable

95 tioning system for indels so that equivalent indels can be uniquely determined by their coordinates i

96 lymorphisms (SNPs) and insertions/deletions (indels) can result in altered on-target sites and novel

97 ant patients to identify somatic SNVs, small indels, CNVs and gene fusions in 508 tumor-related genes

98 ver, much less is known about the effects of InDels compared to point mutations and amino acid substi

99 s (SNVs) and small insertions and deletions (indels) compared to adult cancers.

100 This variation includes multi-kilobase indels containing entire genes, and orthologs for which

101 sualization of upstream TF binding motifs in InDel-containing enhancers.

102 ants (SNVs), small insertions and deletions (indels), copy-number variations (CNVs), loss of heterozy

103 osomal segments at high resolution, SNVs and Indels (corrected for aneuploidy), regions with loss of

104 used for the biological data where SNVs and indels could be detected with very high sensitivity were

105 inhibitor response data revealed frameshift indel count to be significantly associated with checkpoi

106 over 91 million single nucleotide and small indels, creating a large catalog of genomic variation fo

107 )/Cas9 editing (including regional deletion, indel, CRISPR interference, and single-base editing), we

108 MIC coding, and 553 more in COSMIC noncoding indel dataset in addition to the ones reported jointly b

109 vaccine studies shows direct evidence of fs-indel derived neoantigens eliciting immune response, par

110 The focus of indel-derived neoantigen identification has been on leve

111 aic single-nucleotide variants and 60-80% of indels detected in human brain whole-genome sequencing d

112 s the sensitivity and specificity of SNV and indel detection at very low variant allele frequencies.

113 First, Indel Detection by Amplicon Analysis (IDAA) determines t

114 sults demonstrate substantial improvement in indel detection for a variety of data types, including t

115 sed ReAlignment are used for small and large indel detection, and results are presented in a comprehe

116 While in indel detection, BGISEQ showed slightly higher sensitivi

117 ssy compression of quality scores on SNP and INDEL detection.

118 of cases harboring likely deleterious dnSNVs/indels did not differ significantly between AED-unexpose

119 epository Kipoi, apply to variants including indels directly from VCF files.

120 ne single nucleotide polymorphisms and seven indels distinguish C57BL/6J from DBA/2J within Hnrnph1,

121 gated for de novo single-nucleotide variants/indels (dnSNVs/indels) and de novo copy number variants

122 Finally, we identified seven MS indel driver hotspots: four in known cancer genes (ACVR2

123 SpartaABC we demonstrate the differences in indel dynamics among three protein-coding genes across m

124 i development and the first to interrogate U-indel editing in EMF and MCF life cycle stages.

125 uire extensive uridine insertion/deletion (U-indel) editing for their maturation.

126 cessfully generalize to long reads with high indel error rates.

127 produces many fewer mis-assemblies and large indel errors.

128 reverse transcriptase base substitution and indel 'errors' in the run of A's in the product.

129 y (NMD) pathway, we hypothesise that some fs-indels escape degradation and elicit anti-tumor immune r

130 InDel events have important consequences in protein evol

131 We found 30 CRMs with enriched SNVs and indels (FDR < 0.05).

132 -lactamases to be the somewhat predictive of InDel fitness effects.

133 report that short insertions and deletions (indels), followed by single nucleotide variants (SNVs),

134 and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models con

135 The evolved variants mediated indel formation and base editing in human cells and enab

136 nome editing, and alters the balance between indel formation and homology-directed repair.

137 tracrRNA can improve reporter knockdown and indel formation at several targets within the long termi

138 P with a sequence modified tracrRNA enhanced indel formation at the CCR5 target site in primary CD4+

139 tranded DNA breaks (which causes substantial indel formation) and homology-directed repair (which typ

140 ines, which correlated with higher levels of indel formation.

141 d through a bioinformatic pipeline to detect indels, frameshifts, or hypermutations that would render

142 UNG domain to yield miniCGBE1, which reduced indel frequencies but only modestly decreased editing ef

143 l rearrangements in yeast and displayed high indel frequency in human genomes.

144 ediated gene editing led to a markedly lower indel frequency than that by the DSB-mediated approach.

145 growth causes an ~19- to 23-fold increase in indel frequency, resulting in a disproportionate increas

146 e substantial effort has gone into detecting indels from DNA, there is still opportunity for improvem

147 Further, detection of indels from RNA-Seq data has largely been an afterthough

148 or predicting somatic, germline and artifact indels from tumor RNA-Seq data.

149 imple, fast and inexpensive and can identify indels >2 bp.

150 Small insertions and deletions (indels) have a significant influence in human disease an

151 Insertion and deletion (indels) have been recognized as an important source gene

152 rther emphasizing the importance of rescuing indels hidden in the unmapped reads in cancer and diseas

153 atic mutational hotspots near VMP1/MIR21 and indel hotspots in surfactant protein genes (SFTPA1, SFTP

154 ted highly recurrent and tumor-type-specific indel hotspots targeting the noncoding regions of highly

155 Genes adjacent to indel hotspots were functionally related to G-protein co

156 UPS-indel identifies 15% redundant indels in dbSNP, 29% in C

157 Genesis-indel identifies 72,997 novel high-quality indels previo

158 NGS-based HLA, single-nucleotide-variant and indel imputation of large-scale genome-wide-association-

159 ns identified and confirmed a one-nucleotide indel in an intergenic region that significantly alters

160 In silico analysis indicated that the indel in GPRC6A generates a loss of the C-terminal tail

161 and gain of a MYB interaction with an 18-bp indel in the TAL1 superenhancer.

162 identified >1,000 previously undescribed MS indels in cancer genes.

163 UPS-indel identifies 15% redundant indels in dbSNP, 29% in COSMIC coding, and 13% in COSMIC

164 l is able to identify 456,352 more redundant indels in dbSNP; 2,118 more in COSMIC coding, and 553 mo

165 short palindromic repeats)/Cas9 to introduce indels in exon 3 of FMR1, we generated an isogenic human

166 NAIndel robustly predicts 88-100% of somatic indels in five diverse test datasets of pediatric and ad

167 racrRNA duplex that can effectively generate indels in four genetic loci (two active and two inactive

168 Indels in microsatellites of coding genes can result in

169 functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome.

170 vestigate the potential pathogenic impact of indels in non-coding regions of the human genome.

171 solates also had nonsense mutations or small indels in rocA RocA and CovS mutants had similar levels

172 CRISPR gene editing creates indels in targeted genes that are detected by genotyping

173 of the fitness effects of single amino acid InDels in TEM-1 beta-lactamase.

174 single-nucleotide variants (SNVs) and small indels in the same samples.

175 using a single TRBO construct, resulting in indels in three genes.

176 alytical challenges for discovery of somatic indels in tumor transcriptome.

177 Our approach can identify indels in up to four targets from a single reaction, whi

178 Surprisingly, indel (insertions and deletions) percentages averaged ne

179 Most indels involve A or T nucleotides and occur preferential

180 GATK LeftAlignAndTrimVariants shows that UPS-indel is able to identify 456,352 more redundant indels

181 Genesis-indel is applied to the unmapped reads of 30 breast canc

182 ter the same codon, or when a frame-shifting indel is followed by a frame-restoring indel.

183 UPS-indel is theoretically proven to find all equivalent ind

184 n of expressed somatic insertions/deletions (indels) is an unmet need due to artifacts generated in P

185 or indel), zygosity, alternative allele and indel length from aligned reads.

186 tribution of small insertions and deletions (indels) less well characterised.

187 hile editing of replicating genomes produced indels, linear molecules, and large genomic sequence los

188 As a group, the phenotypic means of the indel lines consistently differed from control nonindel

189 overall wider phenotypic distribution of the indel lines for the phenology-related traits.

190 to ~5% of neoepitopes arising from SNVs and indels may require variant phasing for their accurate as

191 Ryr1TM/Indel mice become progressively inactive from that point

192 In summary, Ryr1TM/Indel mice exhibit a post-natal lethal recessive form of

193 Ryr1TM/Indel mice exhibit an overt phenotype beginning at 14 da

194 Thus, Ryr1TM/Indel mice represent a powerful model for both establish

195 ering subclonal (VAF range 0.01-0.15) driver indels missed by targeted deep-sequencing, outperforming

196 The signal sequence of TEM-1 tolerated InDels more than the mature protein.

197 ariants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and comple

198 f an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutat

199 roach, and suggests that the results of this InDel mutagenesis and conventional exploration of point

200 into the contribution of DNA repair towards indel mutagenesis in human cells.

201 We found 1 novel TGM1 indel mutation (Ile469_Cys471delinsMetLeu) and 8 TGM1 mi

202 with minimal off-target mutagenesis and with indel mutation frequencies of 40-50% and homology-direct

203 ype, clonal Igh gene rearrangement, and Bcor indel mutation, whereas control recipients did not.

204 copy of a targeted locus harbors an induced indel mutation.

205 ates and particularly accelerate the rate of indel mutation.

206 with the accumulation of insertion-deletion (indel) mutational load.

207 overlap with the genes that do not have any indel mutations called from the originally mapped reads

208 ecific neoantigens showed that enrichment of indel mutations for high-affinity binders was three time

209 ing) severe atopy, heterozygous missense and indel mutations in CARD11 presented with immunologic phe

210 Inherited frameshift indel mutations of human erythroid-specific isozyme ALAS

211 oding multiple epitopes that originated from indel mutations shared among patients with MSI-H endomet

212 Furthermore, neoantigens derived from indel mutations were nine times enriched for mutant spec

213 e accumulation of multiple nonsynonymous and indel mutations.

214 rating a high frequency (50-80%) of targeted indel mutations.

215 d levels of unwanted C-to-W (W = A or T) and indel mutations.

216 Finally, we demonstrated that indel neoantigens predicted from RNA-seq were associated

217 , DeepMS could discover 37 SBS, 5 DBS, and 9 Indel new signatures, many of which represent associatio

218 -unexposed unaffected children (median dnSNV/indel number/child [range] = 3 [0-7] vs 3 [1-5], p = 0.5

219 e provide examples of the different types of indels obtained by Cas9-mediated cleavage of the GFP gen

220 survivors due to primary-site deletions and indels occur at a 5.8 x 10(-6) frequency, while survival

221 HT-induced indels occur disproportionately in nucleosome-free regio

222 ctivity but showed a reduction in off-target indels of up to 3,000-fold.

223 enome 10-fold with deletions and insertions (indels) of known sizes and positions.

224 tion in the form of insertions or deletions (indels) of the repeated motif.

225 These RNP bionanoparticles generated Indels on different targets in different cells with effi

226 e and three missense changes) and two coding indels, one of them found in two unrelated patients.

227 lusively induces C:G>T:A transitions with no indels or mtDNA depletion.

228 of recombination in cagY, but we also found indels or nonsynonymous changes in 13 other essential ca

229 lacking a syntenic homolog because of local indels or scrambled synteny.

230 ead to mixtures of insertions and deletions (indels) or other rearrangements at the cleavage site.

231 ogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) indivi

232 Here, we introduce a method to evaluate indels, orientating them relative to gene transcription.

233 Additionally, some of the indels overlap with the genes that do not have any indel

234 R1158H, p.E1163K, p.D1165H, and the in-frame indel p.VYEEDM1161V) identified in Sezary Syndrome, the

235 ian-computation rejection algorithm to infer indel parameters from sequence data.

236 sequence simulations under randomly sampled indel parameters.

237 eans to decide which insertion and deletion (indel) parameters to choose, so that the resulting seque

238 ore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs.

239 stematic analyses of insertion and deletion (indel) polymorphisms of NSP2 divided PRRSVs into 25 patt

240 This mouse (Ryr1TM/Indel) possesses a patient-relevant point mutation (T470

241 ned to the locus and manifesting as SNVs and indels predominantly within genes.

242 ur method corrects nearly all mismatches and indels present in a publically available human PacBio Is

243 s-indel identifies 72,997 novel high-quality indels previously not found, among which 16,141 have not

244 Indel profiles are robust, but they can be influenced by

245 Here, we examined indel profiles at over 1,000 genomic sites in human cell

246 as genetic perturbation, through analysis of indel rate and transcriptional activation.

247 satellite instable (MSI) samples have a high indel rate within active enhancers.

248 RDN variants generally result in higher HDR:indel ratios and lower off-target activity than Cas9 nuc

249 NMD-escape fs-indels represent an attractive target for biomarker opti

250 non-frameshifting insertions and deletions (indels) represent an understudied group with widespread

251 We detected 72,741 SNPs and 2,500 Indels, representing about six-fold more diversity than

252 A concordance analysis of SNPs and INDELs requiring homozygosity unique to all unilateral a

253 these indels shows significant enrichment of indels residing in oncogenes and tumour suppressor genes

254 d novel association with MHC class II region indel rs145954018, and independent association with the

255 21893 in KRT25 (c.800G>A) and the frameshift indels rs37146475 in GPRC6A (c.2323-2324insT) and c.1366

256 RNAIndel leverages features derived from indel sequence context and biological effect in a machin

257 Enhancers with indels show evidence of positive selection, increased ta

258 Statistical analysis of these indels shows significant enrichment of indels residing i

259 e-substitution signatures and eight produced indel signatures.

260 t creates a universal positioning system for indels so that equivalent indels can be uniquely determi

261 as hindered by the complex mosacism and wide indel spectrum revealed by NGS and fragment analysis.

262 fied proteins, gene somatic changes of short indels, splice site, nonsense, or missense mutations wer

263 e substitutions, small insertions/deletions (InDels), structural variants, and/or ploidy variations.

264 n look for single nucleotide variants, small indels, structural variants, repeat expansions and viral

265 on effects associated with the p.VYEEDM1161V indel suggest that the C2 domain may have a role in regu

266 The sequence contexts of indels targeting lineage-defining genes were significant

267 ation codon (PTC) from a frameshift-inducing INDEL that elicits nonsense-mediated decay (NMD) of the

268 velop time-dependent evolutionary models for indels that are as tractable as the analogous models for

269 to track the progress of point mutations and indels that are associated with resistance to cancer the

270 xplores the unmapped reads to identify novel indels that are initially missed in the original procedu

271 otein products stem from the introduction of INDELs that promote internal ribosomal entry, convert ps

272 e present a machine learning method, MutPred-Indel, that predicts pathogenicity and identifies types

273 While we found InDels to be largely deleterious, partially overlapping

274 We also observed that the ability of such indels to suppress morpholino phenotypes does depend on

275 We examined the relationship between InDel tolerance and a variety of measures to help unders

276 ioinformatic algorithms to identify SNPs and INDELs use base quality score information; here, we eval

277 Functional analysis of an indel variant (c.3607+3_6del) in LRP6 suggested that the

278 We report VCPA, our SNP/Indel Variant Calling Pipeline and data management tool

279 We identify 818,054 indel variants (<50 bp) and 27,622 SVs (>=50 bp) per gen

280 -nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants

281 otide variants, small insertion or deletion (indel) variants and structural variants.

282 lowing detection of variation, in particular indel variation, that was previously missed.

283 DNA editing (i.e., recurrence of a specific indel) varies considerably among sites, with some target

284 Transposon-based introduction of InDels via the method TRIAD (transposition-based random

285 unintended nucleotide insertions/deletions (indels) via mutagenic nonhomologous end joining.

286 resulting in a disproportionate increase in indels (vs.

287 utational classes (e.g., insertion/deletion [indel] vs. single nucleotide variant [SNV]) are unknown.

288 mparative sequence analysis, 216 SNPs and 30 InDels were detected at the OsPLDalpha1 locus.

289 Likely deleterious dnSNVs/indels were detected in 9 of 67 (13%) children, none of

290 In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by

291 FP-sgRNA fusion transcript, it also produced indels when delivered with Cas9.

292 Editing of latent genomes caused short indels while editing of replicating genomes produced ind

293 Comparing the performance of UPS-indel with existing variant normalization tools vt norma

294 IV reverse transcriptase generates -1 and +1 indels with their ratio being sensitive to the relative

295 al data, SiNVICT was able to detect SNVs and indels with variant allele percentages as low as 0.5%.

296 We speculated that indels within 5' untranslated regions would be unlikely

297 ealing 132 NMP-linked SNPs and 59 NMP-linked indels within a single 1.1-Mb nonrecombining region on c

298 We found that indels within the Morpholino binding site are indeed abl

299 e.g. single nucleotide polymorphism (SNP) or indel) within a broader set of variants (e.g. all varian

300 rk model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length fr