ライフサイエンスコーパス: indel

1 fer in one 18-nucleotide insertion/deletion (indel).

2 ic insertions, deletions or other mutations (indels).

3 n SNPs and 1.5 million insertions-deletions (indels).

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

5 variants and small insertions and deletions (InDels).

6 T2D-risk variants, including the rs140130268 indel.

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

8 for identifying and representing equivalent indels.

9 n has a distinct pattern in genes with small indels.

10 y in proteins with transcription-related NFS indels.

11 ingle nucleotide polymorphisms (SNPs) and 82 indels.

12 catalog that has 26% more SNVs and 45% more indels.

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

14 lational 'correction' of problem or 'savior' indels.

15 lead variants of five significant loci were indels.

16 le nucleotide polymorphisms (SNPs) and 8.8 M indels.

17 e genome has increased to 71 M SNPs and 12 M indels.

18 y realistic models of sequence evolution via indels.

19 g tens of thousands of heterozygous SNPs and indels.

20 coverage of uncommon variants, and includes indels.

21 strongly or disagreed strongly with reported INDELs.

22 ides through short mutational paths based on indels.

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

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

25 d for reference assemblies, SNP datasets and indels.

26 , particularly novel large insertions, small indels (10-50 bp), and short tandem repeat expansions an

27 yndromic RP (19%): 29 missense mutations, 10 indels, 14 nonsense mutations, 9 frameshift mutations, a

28 s and Technology for both SNVs (>99.99%) and indels (99.92%) and add a validated truth catalog that h

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

30 Insertions and deletions (indels) account for more nucleotide differences between

31 Insertions and deletions (indels) account for more nucleotide differences between

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

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

34 We compared the proportion and number of indels across the cohort, with a subset of results repli

35 mber variation and insertions and deletions (indels) across fourteen BCG strains.

36 The data reported suggest that the indel affects the miR168-guided regulation of NbAGO1 mRN

37 y modified loci, causing unwanted mutations (indels) alongside intended changes.

38 ates its clear superiority in finding common indels among call sets.

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

40 Our whole-genome indel analysis was concordant with the SNP phylogeny, an

41 rst genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error r

42 or disagreement between the aligners' called INDEL and the reported INDEL is merely a result of the a

43 lly intensive local realignment around known INDELs and base quality score recalibration (BQSR).

44 bution of eSTRs from that of linked SNPs and indels and found that eSTRs contribute 10-15% of the cis

45 Indels and fragment deletion were both stably inherited

46 nlike adult bnAbs targeting this site, lacks indels and has low SHM.

47 Selected cases of both indels and HPTs are described.

48 s, calling structural variants, medium-sized indels and large insertions on standard compute hardware

49 including single nucleotide variants, small indels and large structural variants.

50 -validation and independent tests on both FS indels and NS variants.

51 s of 129 and C57BL/6J mouse strains revealed indels and single nucleotide polymorphisms resulting in

52 this study, as in previous studies, is that indels and SNPs in repetitive regions were not assessed

53 ants defined as missense plus LoFs, in frame indels and stop-loss variants (n = 13 014, OR = 0.97, P

54 utation rates and characteristics of de novo indels and SVs in the general population have remained l

55 Using the operator representation of indels and the technique of time-dependent perturbation

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

57 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present

58 e polymorphism, small insert/deletion (DEL) (indel) and structural variation (SV).

59 sequences with insertions and/or deletions (indels) and improves the efficiency for large datasets p

60 Small insertions and deletions (indels) and large structural variations (SVs) are major

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

62 ery high levels of insertions and deletions (indels) and substitutions is enriched in regions of open

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

64 ret retrieves genotype data for 1KG SNPs and indels, and computes allelic frequencies for 1KG populat

65 pipeline was used to detect point mutations, indels, and copy number alterations.

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

67 nt classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mo

68 iants, including single-nucleotide variants, indels, and structural variants, revealed biallelic BRCA

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

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

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

72 In-frame complex indels are enriched in PIK3R1 and EGFR, whereas frameshi

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

74 These data reveal that indels are exceptionally abundant, being more common tha

75 Approximately 27.4 M unique SNPs and 5 M indels are identified across these strains compared to t

76 ach sequence at alignment positions in which indels are invoked in other sequences.

77 Complex insertions and deletions (indels) are formed by simultaneously deleting and insert

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

79 97.6% of unconfirmed genome-wide significant indel associations.

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

81 g data of 24 MSI colorectal cancers revealed indels at 54 million mononucleotide microsatellites of t

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

83 While most indels at non-coding regions were a single base pair, 3

84 bundance of random insertions and deletions (indels) at the target locus resulting from the cellular

85 at exhibit high cleavage activity (up to 60% indels) at their targets within the CCR5 and HBB genes a

86 ATHMM-indel is available via a web server at indels.biocompute.org.uk.

87 Associations between indel burden and treatment response were assessed across

88 UPS-indel to state-of-the-art approaches for indel call set comparison demonstrates its clear superio

89 BQSR had virtually negligible effect on INDEL calling and generally reduced sensitivity for SNP

90 g, but increased sensitivity was observed in INDEL calling for the Stampy + GATK UnifiedGenotyper pip

91 ow to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequenci

92 The existence of bias in INDEL calling might have a serious influence in downstre

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

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

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

96 FATHMM-indel can accurately predict the functional impact and p

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

98 Indels can be deleterious and contribute to disease susc

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

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

101 sing this method is more challenging because indels caused by a single cut in non-coding regions are

102 The indels characterized here have either 1 more or less A,

103 equencing reliably identifies substitutions, indels, CNAs, and gene fusions, with similar accuracy to

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

105 VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the d

106 transducer theories, both of which give the indel component of the probability of a given sequence a

107 ncludes substitutions, insertions/deletions (indels), copy number alterations (CNAs), and a wide rang

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

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

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

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

112 lpel is an open-source software for reliable indel detection based on the microassembly technique.

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

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

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

116 Major indel differences were detected between Brachypodium pla

117 Using a standard server, indel discovery and characterization in the exonic regio

118 the critical importance of improving complex indel discovery and interpretation in medical research.

119 Furthermore, complex indels display strong tissue specificity (such as VHL in

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

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

122 and vicinities of UTRs are more enriched of indel eQTLs and 3.6 (single-tissue)-9.2%(multi-tissue) o

123 s and disease GWAS loci affected by SNPs and indels eQTLs showing tissue-consistent or tissue-specifi

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

125 ed; and (iii) exon-exon splice junctions and indels (features) in columnar formats that juxtapose cov

126 We found that the density of SNPs/indels flanking the breakpoints of deletions (in-phase v

127 cellular DNA with minimal (typically </=1%) indel formation.

128 InDels formed by CRISPR/Cas9 were detected by sequence a

129 These results suggest that frequency of InDels found in KI mice generated by the CRISPR/Cas tech

130 and a manual investigation of all gene-sized indels found in the strains.

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

132 ucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 1

133 ion of single nucleotide variants (SNVs) and indels from cfDNA is constrained by several factors such

134 a method to discover structural variants and indels from next generation sequencing data.

135 se results suggest that the annotated coding indels from the 1000 Genomes Project, while contributing

136 Their fidelity, including indel generation, is significant for their use as reagen

137 mers and show how rapid and accurate SNP and indel genotyping can be carried out across the genomes i

138 Indel Group in Genomes (IGG) markers are primer pairs th

139 The majority of indels harbor putative de novo MYB, ETS1, or RUNX1 conse

140 introduce a median of 15 amino acids, while InDels have a more extensive impact with a median of 66

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

142 the human genome, insertions and deletions (indels) have been linked to many diseases, but the disco

143 of the phenotypic variance on average, with indels having larger effects than SNPs.

144 the total contribution from all parsimonious indel histories and that from all next-parsimonious hist

145 the equivalence relations between different indel histories, we find a "sufficient and nearly necess

146 as a summation over all alignment-consistent indel histories.

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

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

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

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

151 unction, and the baseline characteristics of indels in 2504 individuals of 26 populations from the 10

152 198 missense/nonsense mutations and 76 small indels in 76.4% of patients.

153 hanges and flanking primers for all SNPs and Indels in a user-defined gene or region of the zebrafish

154 or high-quality base substitutions and short indels in both small and large datasets is excellent, wi

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

156 We discovered 285 complex indels in cancer-associated genes (such as PIK3R1, TP53,

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

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

159 We found three InDels in four KI mice but not in a control mouse.

160 we find that the likelihood of occurrence of indels in homopolymeric stretches is strongly related to

161 ariants of 16.3 million SNVs and 2.3 million InDels in mapped regions.

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

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

164 c approach based on the analysis of SNPs and indels in phased human genomes, we observe that replicat

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

166 ent a systematic analysis of somatic complex indels in the coding sequences of samples from over 8,00

167 the high prevalence of annotated homozygous indels in the general population.

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

169 quencing projects revealed a large number of indels in various cancer types.

170 -gain, stop-loss, nonsynonymous variants, or indels) in CLCN6 were associated with lower diastolic BP

171 arry nucleotide insertions and/or deletions (InDels) in other genes, which could have unintentionally

172 ta can lead to insertion or deletion errors (indels) in the consensus genome sequence, which in turn

173 Imputation of indels increased 9.9% power and identifies indel-specifi

174 editing schemes in mouse embryos, including indel (insertion/deletion) mutations, point mutations, l

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

176 ique single nucleotide polymorphisms (SNPs), indels (insertions or deletions), or amino acid changes

177 Most indels involve A or T nucleotides and occur preferential

178 rains (the original highly virulent PC22A, S indel Iowa106, and S 197del PC177), and two representati

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

180 FATHMM-indel is available via a web server at indels.biocompute

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

182 the aligners' called INDEL and the reported INDEL is merely a result of the arbitrary selection of o

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

184 The reliable detection of indels is still a challenging problem, especially for va

185 riants (CNVs) and insertion/deletion events (indels) is significantly elevated in offspring of expose

186 ified single-nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromos

187 tures, such as overlapping indels, power-law indel-length distributions, and indel rate variation acr

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

189 Indels localized to the CRISPR/Cas9 cleavage site were m

190 eads containing alternative alleles at those INDEL locations.

191 genome-wide rates of formation and repair of indels made during replication of yeast nuclear DNA.

192 t of each SNP as well as the large number of Indel markers provides a foundation for locating candida

193 We use the high density of SNP and indel markers to analyze patterns of meiotic recombinati

194 r downstream analysis; for example, a single indel may shift the reading frame and incorrectly trunca

195 The former category includes the "long indel" model (a space-homogeneous SID model) and the mod

196 In contrast, MMR defects hugely increase indel mutagenesis in long repetitive sequences.

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

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

199 statistical model for the somatic background indel mutation rate of microsatellites to assess mutatio

200 also uncover an extremely high rate of small indel mutation relative to other species, primarily asso

201 th CRISPR/Cas9-mediated HDR gene editing and indel mutation, the gene-edited F0 embryos are uniformly

202 the highest proportion (0.12) and number of indel mutations across the pan-cancer cohort (p<2.2 x 10

203 generate precise gene insertions as well as indel mutations at the target site in the rice genome.

204 DMY-TALENs resulted in indel mutations at the targeted loci (46.8%).

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

206 ), more than double the median proportion of indel mutations in all other cancer types examined.

207 We found that CRISPR/Cas9 introduced InDel mutations into exon 2 of the ICP0 gene profoundly

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

209 CR assay that quickly quantitates a range of indel mutations with detection as low as 0.02% mutant in

210 tion of specific nucleotide substitutions or indel mutations, respectively.

211 nvestigated whether the frameshift nature of indel mutations, which create novel open reading frames

212 highest pan-cancer proportion and number of indel mutations.

213 Rates for insertion/deletion (indel) mutations have been found to vary widely when exa

214 to RT mutations, insertion and/or deletion (indel) mutations were common.

215 Indel normalization, visualization and annotation of the

216 The frequencies of indels observed in the target loci of golden (gol), kctd

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

218 In vitro digestion assay suggested that each InDel occurred as a de novo mutation, was carried-over f

219 f de novo SVs, nucleotide substitutions, and indels occurred as a single event.

220 inked to many diseases, but the discovery of indels of more than a few bases in size from short-read

221 oach to identify the precise breakpoints for indels of size less than a user specified threshold, and

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

223 fidence single nucleotide variants and short indels, of which 12.5% are novel.

224 These indels often occurred in both alleles.

225 fects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial ge

226 tigated the possible effects of small coding indels on protein structure and function, and the baseli

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

228 nation, it generates virtually no detectable indels or other stochastic DNA modification products.

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

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

231 d approximate posterior distributions of the indel parameters.

232 llows simulating sequences with the inferred indel parameters.

233 sequence simulations under randomly sampled indel parameters.

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

235 le amino acid polymorphism (SAP) peptides, 2 INDEL peptides, 49 splice junction peptides, and 75 nove

236 ng >99% of the genome, with an average of 10 indels per gene.

237 olymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number

238 ed to date segregate for insertion-deletion (indel) polymorphisms where susceptible alleles are compl

239 ally realistic features, such as overlapping indels, power-law indel-length distributions, and indel

240 isting of all SNPs and insertions/deletions (indels) present in SPRET/Ei from the Mouse Genomes Proje

241 efficient and can be corrupted by additional indels, preventing its widespread use for modelling gene

242 Examination of the accuracy of another indel probabilistic model in the light of our formulatio

243 Recently, indel probabilistic models are mostly based on either hi

244 Thus, our formulation will provide other indel probabilistic models with a sound reference point.

245 robability of the sequence evolution through indel processes.

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

247 s, power-law indel-length distributions, and indel rate variation across regions.

248 logy, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc

249 Insertions and deletions (indels) represent the second most common type of genetic

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

251 ependently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genet

252 e genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal

253 carrying resistant and susceptible alleles, indels reveal costs that may be masked when susceptible

254 The analysis of indels revealed a total of 66 loci of non-core genes tha

255 Structural analysis of NFS indels revealed that they predominantly adopt coil or di

256 onal validation identified a common intronic indel, rs144361550 (-/GGGCCC; r(2) = 0.947 with rs321909

257 When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of

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

259 f indels increased 9.9% power and identifies indel-specific eQTLs for 325 genes.

260 mous gene variants were identified including indels, stop-gain/loss, splice variants, and recurrent g

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

262 divided into groups whose alignments yielded INDELs that agreed strongly or disagreed strongly with r

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

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

265 d that this reference contained thousands of INDELs that were constructed in a biased manner.

266 us single-nucleotide variants and frameshift indels (that is, extreme mutations, P<4.5 x 10(-5)).

267 on small (1-50 bp) insertions and deletions (indels) that are consistent with the pattern of inherita

268 For both SNVs and indels, the distributions of coverage depth, genotype qu

269 For indels, the proportions of false-positive variants were

270 ily to detect single-nucleotide variants and indels, they can also be used to identify a subset of ge

271 t the functional impact and prioritise small indels throughout the whole non-coding genome.

272 Moreover, comparing UPS-indel to state-of-the-art approaches for indel call set

273 r prevalence, the contribution of somatic MS indels to cancer has been largely unexplored, owing to d

274 can rapidly identify V- and J-segments with indels to high accuracy for mutated sequences when the m

275 ely detects small-scale variation, including indels, to clinical standards.

276 (typically at least 99.9%) and low rates of indels (typically no more than 0.1%).

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

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

279 on, we have identified a putative functional indel variant at chr13q22.1 that associates with decreas

280 P-value revealed a 30 bp insertion/deletion (indel) variant that was significantly associated with pa

281 ariants (SNVs) and short insertion/deletion (indel) variants from deep whole-genome sequencing (WGS).

282 f single nucleotides and insertion/deletion (INDEL) variants of the human population.

283 These indels varied in length, position, and number per indivi

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

285 This indel was the most significant cis-eQTL variant in a set

286 A mean of 105 coding HQ SNVs and 32 indels was identified exclusively by WES whereas 692 HQ

287 A high frequency of indels was observed at both target sites and one off-tar

288 gle-nucleotide polymorphisms and 1.2 million indels were examined.

289 clusively by WES whereas 692 HQ SNVs and 105 indels were identified exclusively by WGS.

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

291 regions were a single base pair, 3 base pair indels were observed when a coding region of HIV-1 was t

292 es analyzed; nearly all instances of complex indels were overlooked (81.1%) or misannotated (17.6%) i

293 orphisms (SNPs) and 25 insertions/deletions (indels) were detected in HvP5CS1 among 287 barley (Horde

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

295 ochastic evolution of an entire sequence via indels with quite general rate parameters.

296 t with the concomitance of the in-phase SNPs/indels with the deletion events.

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

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

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

300 enalties that favor insertions or deletions (indels) within each sequence at alignment positions in w