ライフサイエンスコーパス: STR

1 STR genotyping with short-read sequence data is confound

2 STR in IGF1 promoter has been extensively studied for it

3 STR occurred only in neutropenic patients transfused wit

4 STR profiling just fulfills the purpose of authenticatio

5 STR-selective primers enable massively parallel, targete

6 STR-Seq employs in vitro CRISPR-Cas9-targeted fragmentat

7 STRs also accept short-chain aliphatic aldehydes to give

8 STRs are abundant throughout the human genome, and speci

9 STRs are especially valuable in conservation and ecologi

10 We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of

11 quencing technology that analyses over 2,000 STRs in parallel, and provides the accurate genotyping o

12 ression Project to identify more than 28,000 STRs for which repeat number is associated with expressi

13 to determine germline STR genotypes for 102 STR loci with high accuracy across diverse populations o

14 fied 138 individuals with risk alleles at 15 STR disease loci.

15 wide range of species and report a set of 15 STR markers for use in future bison studies that yielded

16 Dungans, and Karakalpaks using 35 SNP and 17 STR markers.

17 n and probability of exclusion of all the 21 STR loci were 0.99999999999999999993814 and 0.999998184,

18 In summary, these 21 STR loci showed a high level of genetic polymorphisms fo

19 While 15 to 23 STR loci normally give definitive results in simple kins

20 y increases to 99-100% when approximately 30 STRs are used.

21 ted by active surveillance and resulted in 5 STRs occurring 9 to 24 hours posttransfusion; none of th

22 oyed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus

23 n-specific repeat expansions and identify 52 STRs/VNTRs with at least 40 uninterrupted pure tracts as

24 We define a set of 1,584 STRs/VNTRs expanded specifically in humans, including la

25 RepeatHMM to infer normal ranges of 432,604 STRs using 21 long-read sequencing datasets on human gen

26 a GTR and delays <4 weeks in patients with a STR/biopsy resulted in worse survival.

27 mmends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencin

28 mprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR seque

29 esis through 20,000 sequences comprising all STR permutations in different lengths.

30 e specificity and developmental timing of an STR expansion gene, we used rolling circle amplification

31 Software tools such as lobSTR and STR-FM have been developed to address these demands, whi

32 recorded from multiple electrodes in PFC and STR while monkeys acquired new categories.

33 n of functional circuits between the PFC and STR.

34 of LFPs between, but not within, the PFC and STR.

35 nchrony was also seen between PFC spikes and STR LFPs, but not the reverse, reflecting the direct mon

36 chers investigating disease-related STRs and STR evolution.

37 cover and genotype a wide spectrum of SV and STR variants using five algorithms.

38 identify genomic features of SV classes and STRs that are associated with gene expression and comple

39 Because SVs and STRs range in size and type, it is necessary to apply mu

40 plete and well characterized maps of SVs and STRs to date.

41 eate a framework for measuring constraint at STRs by comparing observed versus expected mutation rate

42 Our crude DNA lysis combined with LAMP-AuNP/STR present effective point-of-care detection and facili

43 orensic parameters of 21 non-CODIS autosomal STR loci in Chinese Guanzhong Han population.

44 na), multiplexes amelogenin and 22 autosomal STRs, 17 of which are non-CODIS STRs.

45 imates of the linkage disequilibrium between STRs and common SNPs.

46 ter model to examine the interaction between STRs and SNPs in IGF1 promoter.

47 f heterozygosity (CN-LOH) were identified by STR and SNP arrays.

48 plotype consisting of three promoter SNPs (C-STR-T-T).

49 conventional capillary electrophoresis (CE) STR fragment size analysis.

50 d short tandem repeats (STRs), Y-chromosomal STRs and the control region of the mitochondrial genome.

51 estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2-6 bp repeat units that are accessib

52 22 autosomal STRs, 17 of which are non-CODIS STRs.

53 and we found 100% concordance over 5 common STRs with the GlobalFiler kit.

54 P=0.03) than those with partial and complete STR, respectively.

55 be processed by the Sgs1-Top3-Rmi1 complex (STR).

56 error-prone DNA synthesis, which constrains STR expansion.

57 distinguish heterozygous alleles containing STRs with consecutive repeat numbers.

58 each STR in the human genome by correlating STR genotypes with local sequence heterozygosity.

59 iated with rs1611115, rs2519152, and the DBH-STR polymorphism.

60 Here, we demonstrate STR-Seq, a next-generation sequencing technology that an

61 is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto the co

62 s, failure of passive surveillance to detect STR, and lack of specificity of STR criteria.

63 appropriate statistical methods in detecting STR-phenotype associations.

64 Here, we developed STR-FM, short tandem repeat profiling using flank-based

65 Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequen

66 ed with nanogold probe (AuNP) or styryl dye (STR).

67 ork to estimate mutation parameters for each STR in the human genome by correlating STR genotypes wit

68 enriched alkaloid products with up to 99% ee STRs are thus valuable asymmetric organocatalysts for ap

69 ously been leveraged for scalable, efficient STR recovery.

70 ression of nearby genes (known as expression STR, eSTR).

71 rvey identified 2,060 significant expression STRs (eSTRs).

72 With these new features, STR-Seq can identify a 0.1% minor genome fraction in a D

73 genome's representation of STR alleles, find STR loci with common loss-of-function alleles, and obtai

74 ) because of limited microarray coverage for STR-conferring mutations, and specificity was 99.2% (129

75 The 1-year risk for mortality for STR compared with biopsy was reduced significantly (RR,

76 enables the estimation of repeat counts for STRs.

77 rates and built a model to predict rates for STRs across the genome.

78 applications-we find that 90-98% of forensic STR records can be connected to corresponding SNP record

79 ested that the polysynaptic connections from STR to the PFC exerted a stronger overall influence.

80 We show that putatively functional STRs may be identified by deviation from predicted STR v

81 warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding

82 ate the need for targeted assays to genotype STRs accurately, and call for more appropriate statistic

83 wever, it has proven problematic to genotype STRs from high-throughput sequencing data.

84 ted an error correction model for genotyping STRs that can distinguish heterozygous alleles containin

85 riments, we use MIPSTR to determine germline STR genotypes for 102 STR loci with high accuracy across

86 rozen vials from the same ATCC lot, however, STR markers did not differ from ATCC reference for any s

87 e report the largest-scale analysis of human STR variation to date.

88 In STR groups, the animals were subjected to restraint stre

89 A benefit in STR at 60 min (RR: 1.25; 95% CI: 1.06 to 1.47; p = 0.007

90 rial contamination of platelets resulting in STR in neutropenic patients, failure of passive surveill

91 ion of PPC-STR neurons or their terminals in STR decreased history-dependent bias, while inactivation

92 However, we still struggle to incorporate STR variation into genotype-phenotype maps.

93 ve evidence of genetic studies on individual STRs suggests that STR variation profoundly affects phen

94 we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a

95 ss than half of other reports for integrated STR analysis and allows a compact, inexpensive microchip

96 ore, PPC biases action selection through its STR projection while controlling movements through PPC-p

97 LAMP-AuNP and LAMP-STR can detect as low as 9.7 fg (3.2 sea copies) and 7.2

98 The LAMP-STR quantitated sea in 10-1,000 CFU (7.2-720 copies).

99 calable solution for rapid recovery of large STR and SNP datasets in any species without needing a re

100 ively parallel, targeted sequencing of large STR sets.

101 her and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long

102 equencing data, it becomes practical to mine STR profiles in silico from genome sequences.

103 -32.7%) of these 284 reactions met 1 or more STR criteria, and sensitivity of STR criteria varied fro

104 lts showed that STRScan can profile 20% more STRs in the target set that are missed by lobSTR.

105 TRs, normal ranges of repeat counts for most STRs in human populations are not well known, preventing

106 little is known about the variation of most STRs in the human population.

107 to the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown.

108 ghlight the limitations of reported national STR data based on passive surveillance and the need to i

109 No STR locus was observed to deviate from the Hardy-Weinber

110 redictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, r

111 nome-wide analysis and validation of de novo STR mutations.

112 In the absence of STR, the fluorescence intensity is weak.

113 Upon addition of STR, the aptamer binds to its target, leading to release

114 lyses were based on the PCR amplification of STR loci followed by gel electrophoresis.

115 MIPSTR uses targeted capture of STR loci by single-molecule Molecular Inversion Probes (

116 ively characterize the various components of STR signal independent of a priori knowledge of the quan

117 r were successfully assessed by detection of STR in a spiked milk and blood serum without interferenc

118 our estimates, we identified determinants of STR mutation rates and built a model to predict rates fo

119 ize this call set to analyze determinants of STR variation, assess the human reference genome's repre

120 We also analysed the potential effect of STR and CNV variations, as well as the infection of the

121 p3 is required for the efficient function of STR.

122 ort tandem repeat PCR, and the generation of STR profiles for the isolated sperm cells.

123 R permutations and interrogate the impact of STR sequence and secondary structure on their genomic re

124 Investigation of STR-based clusters of haplotypes and their ages revealed

125 TREDPARSE extends the limit of STR size detection beyond the physical sequence read len

126 s information about the length and number of STR units amplified.

127 ately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NG

128 w-complexity reads; and (2) the high rate of STR amplification stutter.

129 e human reference genome's representation of STR alleles, find STR loci with common loss-of-function

130 t 1 or more STR criteria, and sensitivity of STR criteria varied from 5.1% to 45.5%.

131 Five sets of STR criteria were evaluated, including recent AABB crite

132 ce to detect STR, and lack of specificity of STR criteria.

133 ipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging

134 However, per-locus studies of STR mutations have been limited to highly ascertained pa

135 is scalable to genotyping many thousands of STR loci in thousands of individuals.

136 ient recovery of targeted loci-97.3-99.6% of STRs characterized with >/=10x non-redundant sequence co

137 to predict the complex genomic behaviour of STRs, including abundance and mutational constraints.

138 These results highlight the contribution of STRs to the genetic architecture of quantitative human t

139 wever, genome-wide studies of the effects of STRs on gene expression thus far have had limited power

140 ese results will guide future engineering of STRs and related enzymes for biocatalytic applications.

141 c effects of the pharmacologic inhibition of STRs in response to an oral glucose load in healthy lean

142 on the OGTT.The pharmacologic inhibition of STRs in the gastrointestinal tract alters insulin respon

143 ppm lactisole, a human-specific inhibitor of STRs.

144 rk to model the evolution and instability of STRs and VNTRs in apes.

145 well known, preventing the prioritization of STRs that may be associated with human diseases.

146 We review here the promise of STRs in contributing to complex trait heritability and h

147 t-generation sequencing approaches and other STR assays rely on a limited number of PCR amplicons, ty

148 We then tested our STR capture strategy on P. diadema fecal DNA, and report

149 Overall, STR-Seq has higher throughput, improved accuracy and pro

150 a valuable tool for prioritizing pathogenic STRs in medical genetics studies.

151 rticular, accurate detection of pathological STR expansion is limited by the sequence read length dur

152 This study suggests that the micro-patterned STR-functionalized SiNWs platform provides additional ad

153 probiotic (PROB), periodontal disease (PD), STR-PROB, STR-PD, STR-PROB-PD, and PROB-PD groups.

154 periodontal disease (PD), STR-PROB, STR-PD, STR-PROB-PD, and PROB-PD groups.

155 -plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have l

156 After learning, different pairs of PFC-STR electrodes showed stronger synchrony for one or the

157 d method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a geno

158 The 9-plex STR profiles of single cells from both pure and mixed po

159 mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulti

160 ted the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-bas

161 Furthermore, optogenetic inactivation of PPC-STR neurons or their terminals in STR decreased history-

162 urons projecting to the dorsal striatum (PPC-STR) and the posterior secondary motor cortex (PPC-pM2).

163 pecific, retrograde labeling showed that PPC-STR and PPC-pM2 represent largely distinct subpopulation

164 during decision making revealed that the PPC-STR population encodes history-dependent choice bias mor

165 nt largely distinct subpopulations, with PPC-STR receiving stronger inputs from association areas and

166 ay be identified by deviation from predicted STR variation and by association with quantitative pheno

167 (PROB), periodontal disease (PD), STR-PROB, STR-PD, STR-PROB-PD, and PROB-PD groups.

168 Yet profiling STRs from short-read sequencing data is challenging beca

169 Septic transfusion reactions (STRs) resulting from transfusion of bacterially contamin

170 a natural ligand for sweet taste receptors (STRs) that are expressed on the tongue and in the gastro

171 d that the intestinal sweet taste receptors (STRs), T1R2 and T1R3, were expressed in distinct epithel

172 ned using support tensor machine regression (STR) and ridge tensor regression (RTR).

173 to researchers investigating disease-related STRs and STR evolution.

174 lly described as species-time relationships (STRs), in the face of global climate change is a central

175 ation and identification of disease-relevant STRs from whole-genome long-read sequencing data on pati

176 ception of a few well-known disease-relevant STRs, normal ranges of repeat counts for most STRs in hu

177 Although short tandem repeat (STR) analysis is available as a reliable method for the

178 tion for rapid forensic short tandem repeat (STR) forensic profiling in a single disposable plastic c

179 ped across 15 autosomal short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH0

180 tional Park, analyze 35 short tandem repeat (STR) loci for genotyping efficiency, and compare heteroz

181 tionally genotyped four short tandem repeat (STR) loci that flank the lactase enhancer region.

182 cell authentication by short tandem repeat (STR) markers.

183 Short tandem repeat (STR) profiling has been routinely used in kinship testin

184 A short tandem repeat (STR) typing method is developed for forensic identificat

185 Short tandem repeat (STR) variants are highly polymorphic markers that facili

186 Short tandem repeat (STR) variation has been proposed as a major explanatory

187 nd a highly polymorphic short tandem repeat (STR) within its breakpoints.

188 Short tandem repeat (STR), or "microsatellite", is a tract of DNA in which a

189 n, but only one method (short tandem repeat [STR] profiling) has been the subject of a comprehensive

190 Functional short tandem repeats (STR) are polymorphic in the population, and the number o

191 like homopolymers and short tandem repeats (STR).

192 Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are imp

193 Short tandem repeats (STRs) are found in many prokaryotic and eukaryotic genom

194 Short tandem repeats (STRs) are highly mutable genetic elements that often res

195 Short tandem repeats (STRs) are highly variable elements that play a pivotal r

196 Short tandem repeats (STRs) are hyper-mutable sequences in the human genome.

197 Short tandem repeats (STRs) are implicated in dozens of human genetic diseases

198 ral variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are

199 Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the

200 Short tandem repeats (STRs) are prone to expansion mutations that cause multip

201 ral variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants whi

202 We show that genetic short tandem repeats (STRs) contain sufficient entropy to generate strong encr

203 Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, d

204 Short tandem repeats (STRs) have been implicated in a variety of complex trait

205 and the other with 13 short tandem repeats (STRs) used in forensic applications-we find that 90-98%

206 llelic and composed of short tandem repeats (STRs) with individual motifs composed of mononucleotides

207 Short tandem repeats (STRs), also known as microsatellites, are among the larg

208 ng large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral scle

209 of the contribution of short tandem repeats (STRs), which constitute one of the most polymorphic and

210 lymorphisms (SNPs) and short tandem repeats (STRs), Y-chromosomal STRs and the control region of the

211 ymorphic loci known as Short Tandem Repeats (STRs).

212 Short terminal repeats (STRs) were performed simultaneously on DNA obtained from

213 Patients who underwent a subtotal resection (STR) had worsened survival with RT delay <=4 weeks and p

214 s total resection (GTR), subtotal resection (STR), and biopsy.

215 ynaptic pathways as shown for left and right STR, which do not share direct anatomical connections, b

216 Several STR loci that are entirely guanine or cytosines (G or C)

217 that MIPSTR can detect low-frequency somatic STR variants.

218 or due to amplification stutter from somatic STR mutations.

219 Lastly, we suggest that somatic STR variation within individuals may serve as a read-out

220 The unstable expansion of some STRs was associated with various genetic disorders (e.g.

221 ptures using a micro-patterned streptavidin (STR)-functionalized silicon nanowire (SiNW) platform, wh

222 For the second-line drug streptomycin (STR), overall concordance between the agar proportion me

223 ive and sensitive detection of streptomycin (STR) based on Exonuclease III (Exo III), SYBR Gold and a

224 four rats were divided into control, stress (STR), probiotic (PROB), periodontal disease (PD), STR-PR

225 en the prefrontal cortex (PFC) and striatum (STR) is thought critical for cognition and has been link

226 articular, we demonstrate that the striatum (STR) can be segregated according to differential rs-fMRI

227 Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions.

228 We used STR-FM to study STR error rates and patterns in publicly available human

229 for kinship applications as a supplementary STR kit following the minimum criteria for validation re

230 ddresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to research

231 We identify a set of high-impact SVs/STRs associated with the expression of three or more eGe

232 Strictosidine synthase (STR) catalyzes the Pictet-Spengler condensation of trypt

233 , and an approach for highly parallel target STR recovery.

234 rticularly useful for the NGS-based targeted STR profiling, e.g., in genetic and human identity testi

235 an that uses a greedy algorithm for targeted STR profiling in next-generation sequencing (NGS) data.

236 te recent advances in sequencing technology, STR variation has remained largely inaccessible across m

237 We argue that STR variants are more likely than single-nucleotide vari

238 tic studies on individual STRs suggests that STR variation profoundly affects phenotype and contribut

239 ritability and highlight the challenges that STRs pose due to their repetitive nature.

240 We discovered that STRs sequenced with a PCR-free protocol have up to ninef

241 The STR catalysis of reactions of small aldehydes gives an u

242 The STR profiles demonstrated that the samples originated fr

243 Additionally, the STR profile of GM09947 cells could be deduced even in th

244 lso clarify the roles played by Top3 and the STR complex as a whole during the resolution of replicat

245 mation of the (R)-configured products by the STR enzyme from Ophiorrhiza pumila (OpSTR) using a combi

246 Our method will be valuable for the STR analysis of samples containing mixtures of cells/DNA

247 cer cell lines and not a replacement for the STR method.

248 ocated outside the STR were required for the STR to function as eSTR.

249 leads to recruitment of Sgs1 as part of the STR (Sgs1-Top3-Rmi1) complex, mediated by two SUMO-inter

250 ctra can be obtained for close to 90% of the STR loci in the genome.

251 e mechanism how the number of repeats of the STR regulates gene transcription.

252 n by direct binding to a repeat motif of the STR.

253 that these adjacent SNPs located outside the STR were required for the STR to function as eSTR.

254 ranscriptional complexes located outside the STR, rather than by direct binding to a repeat motif of

255 Additionally, we validated the STR calls against known allele sizes in a set of GeT-RM

256 Here, we examine the STRs and phylogenetic-time relationships (PTRs) of soil

257 While the STRs and PTRs were significantly shifted by altered prec

258 atHMM-DB with normal repeat ranges for these STRs.

259 9 to 24 hours posttransfusion; none of these STRs had been reported by passive surveillance.

260 er, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences,

261 In addition to STR targets, this approach also generates large, genome-

262 ect monosynaptic connections from the PFC to STR.

263 aptasensor showed a high selectivity toward STR with a limit of detection (LOD) as low as 54.5 nM.

264 Traditional STR analyses were based on the PCR amplification of STR

265 ymes (FatM and RAM2) and an ABC transporter (STR) that are required for symbiosis and conserved uniqu

266 ration of two PAM-resident ABC transporters, STR and STR2, is limited.

267 e several disease-related long trinucleotide STRs.

268 We used STR-FM to study STR error rates and patterns in publicly

269 Whether STRs directly contribute to the regulation of glucose ho

270 Our data support a model in which STR length in eukaryotic genomes results from a balance

271 A genome-wide STR and SNP based linkage analysis was performed in one

272 the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human

273 de the cost, effort and time associated with STR analysis.

274 ed decreased mortality for GTR compared with STR at 1 year (RR, 0.62; 95% CI, 0.56-0.69; P < .001; nu

275 ression was decreased with GTR compared with STR at 6 months (RR, 0.72; 95% CI, 0.48-1.09; P = .12; N

276 Compared with STR, GTR substantially improves overall and progression-

277 The required read depth increases with STR length and is lower for a PCR-free protocol.

278 At 3 years, patients with STR<30% experienced a higher rate of major adverse cardi

279 Y-STR data were used to test different out-of-Africa migra

280 We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic scien

281 Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogeneti

282 ur males living in southern Xinjiang at 26 Y-STR loci.

283 The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+.

284 none of pedigree samples shares identical Y-STR haplotype.

285 romosomes of father-son pairs, and imputed Y-STR genotypes.

286 Interestingly, Y-STR analyses showed a closer affinity of Gujjars to othe

287 identification of pedigree from mismatched Y-STR haplotypes.

288 es, resulting in the largest collection of Y-STR mutation rates to date.

289 s studies on the Iraqi population based on Y-STR markers were limited by a restricted number of marke

290 Global and regional Y-STR analysis demonstrated regional genetic continuity am

291 hes with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations.

292 Twenty-three Y-STR loci included in the PowerPlex Y23 (Promega, Madison

293 However, when two Y-STR haplotypes have a few mismatched loci, it is difficu

294 Y-STRs have emerged as important forensic and population g

295 We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the

296 Finally, we identified Y-STRs with potential applications in forensics and geneti

297 neage because of the high mutation rate of Y-STRs.

298 ion, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increase

299 e the mutation rates of Y chromosome STRs (Y-STRs) with 2-6 bp repeat units that are accessible to Il

300 equencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (