ライフサイエンスコーパス: impute

1 on VCF files using a new approach, called LB-Impute.

2 4 days and the remainder had clinical status imputed.

3 riteria are based on a variable that must be imputed.

4 in Pediatric Health Information System were imputed.

5 weights for the remaining participants were imputed.

6 end-point data (39 participants, 3.7%) were imputed.

7 Missing covariates were imputed.

8 y, and SNPs that could not be genotyped were imputed.

9 Missing data were imputed.

10 In the GALA II study WBC types were imputed.

11 age, and Karnofsky score, with missing data imputed.

12 st one dose of study drug, with missing data imputed.

13 nction responses, with missing data multiply imputed.

14 When imputing 10 Mb of sequence data from 200,000 reference s

15 sensitivity of this approach, and show that imputed 1x WGS recapitulates 95.2% of variants found by

16 pped the classical MHC (chr6: 29.6-33.1 Mb), imputing 216 human leukocyte antigen (HLA) alleles and 4

17 n adjusted difference with missing responses imputed, 6.5 points; 95% CI, 1.1 to 11.9).

18 tability of this method by showing that, for imputing a target sample from a certain tissue, SampleLA

19 ve US survey, we used multiple imputation to impute ABP-defined hypertension status for NHANES partic

20 root mean square errors between the true and imputed abundance, we compare its performance to K-neare

21 The hazard ratio (HR) for the imputed aggregate treatment effects of comprehensive dis

22 The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C da

23 After imputing AMY1-CN for ~1,000 subjects, we identified taxa

24 At age 24 years, in the imputed analysis sample, the severity of personality dis

25 AnnotBoost, a machine learning framework to impute and denoise pathogenicity scores using a broad se

26 adjustment for confounders, in both multiply imputed and complete case samples.

27 h and became worse as more observations were imputed and more subjects were excluded from the analysi

28 a mean nonreference discordance rate between imputed and sequenced genotypes of 3.2% compared to 1.6%

29 s who switched to open-label ixekizumab were imputed as non-responders in logistic regression analysi

30 in which all missing data after 56 days were imputed as treatment failure (with reexpansion in 129 of

31 ysis of LTL by pooling densely genotyped and imputed association results across large-scale European-

32 440 control datasets from 107 cell types to impute background signal.

33 ata for patients with no resistance test was imputed based on the patient's risk of harboring drug-re

34 In summary, our imputed BrainSpan transcriptomic data provide a valuable

35 n them, work only against the immodest codes imputed by neuroscientists to the signals they study; th

36 igenome analysis and display, a new tool for imputing causal genes from genome-wide association studi

37 e methods in terms of the similarity between imputed cell profiles and bulk samples and whether these

38 (HLA) region was comprehensively studied by imputing classical alleles and polymorphic amino acid po

39 ified ethnic/national populations be used to impute complete HLA types.

40 The total imputed costs (all in 2019 United States dollars) for pr

41 After addition of imputed costs, first year of life costs were not signifi

42 We also introduce methods for imputing covariates in held-out data and for evaluating

43 hole genome bisulfite sequencing datasets by imputing CpG methylation states on individual sequencing

44 By analyzing imputed data for a large number of human traits, we empi

45 exome arrays and augmented this dataset with imputed data from the UK Biobank.

46 Imputed data in 608 Japanese cases and 737 controls furt

47 ion with 9 different ways to handle multiply imputed data in a derivation sample to develop logistic

48 variable selection strategies with multiply imputed data on the external performance of derived prog

49 The other 8 approaches to handling multiply imputed data resulted in prognostic models with performa

50 of the correlations was generally reduced in imputed data sets, and this effect increased with the am

51 other sources (administrative, modelled, and imputed data).

52 ifficulty with speaking (P = .049) and using imputed data, less interference of neurologic symptoms i

53 Based on the cartographies constructed from imputed data, we showed that the antigenic evolution of

54 Instead of relying on imputed data, we use an expectation-maximization approac

55 ean ancestry participants using 1000 Genomes imputed data.

56 l women with logistic regression of multiply imputed data.

57 made by digitalizing existing knowledge, by imputing data from related species with similar life his

58 tics using propensity score matching in each imputed dataset.

59 tic regression analyses on complete-case and imputed datasets to investigate sociodemographic and CSE

60 nd ~7% between the WGS and the 1000G and HRC imputed datasets, respectively.

61 sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Refer

62 Imputed dosage of the FTO SNP rs9939609 was used.

63 RNA-seq drop-out correction (scDoc) method, imputing drop-out events by borrowing information for th

64 t introduces an ensemble learning method for imputing dropout events in scRNA-seq data.

65 novel computational method that allows us to impute drug response in very large clinical cancer genom

66 These imputed drug response data are then associated with soma

67 This yields an imputed drug response for every drug in each patient.

68 rom this analysis, we found that a number of imputed EC pathways responsible for the production of im

69 c distribution data [1, 8], phylogenetically imputed ecological traits, and an amphibian phylogeny [9

70 We use this learned representation to impute epigenomic data more accurately than previous met

71 eier (KM) estimator of the survival function imputes event times for right-censored and left-truncate

72 Using these models, we impute expression in independent data from CBCS and TCGA

73 odels of prostate tissue gene expression and impute expression transcriptome-wide for 233,955 Europea

74 ifferent ancestral populations, we evaluated imputed expression levels for predictive accuracy genome

75 This imputed expression quantitative trait locus, termed impe

76 entified HLA alleles that are challenging to impute for each of the populations separately.

77 analysis, patients who died had a value of 0 imputed for 24-week peak VO2.

78 Although variance was imputed for some studies, these conclusions did not chan

79 The imputed founder viruses in women were genetically simila

80 ses from males were compared to those of the imputed founding virus population in their female partne

81 Multiple imputed fractional logistic regression models that accou

82 s. claims variables; in the primary dataset, impute frailty status from claims variables and conduct

83 s claims variables; in the primary data set, impute frailty status from claims variables, and conduct

84 Based on the 1961 non-imputed FRNT results classified as dengue seronegative o

85 HLA alleles were imputed from genome-wide genotype data for 1326 patients

86 ug repositioning by comparing transcriptomes imputed from GWAS data with drug-induced gene expression

87 rating the expression regulatory information imputed from multiple tissues, and made significant achi

88 These missing values were imputed from other characteristics.

89 Analysis of classical HLA alleles (imputed from SNP genotypes) revealed an interaction with

90 virus in equilibrium-that cannot be directly imputed from structure alone.

91 ERAP1 haplotypes imputed from the International Genetics of AS Consortium

92 We then imputed from these sequences into new and existing genom

93 These results highlight the utility of re-imputing from denser reference panels, until whole-genom

94 duce a multi-task learning method to jointly impute gene expression in 44 human tissues.

95 developed multi-tissue imputation methods to impute gene expression in uncollected or inaccessible ti

96 nent of this approach is to build a model to impute gene expression levels from genotypes by using sa

97 udy, we developed a tensor-based approach to impute gene expression on a transcriptome-wide level.

98 , which is based on two linked approaches to impute gene function and bridge genes with biological pr

99 ptome-wide association study (TWAS) based on imputed gene expression from whole blood and liver.

100 AS identified 5 additional genetic loci with imputed gene expression levels differing between cases a

101 association between the study trait and the imputed gene expression levels from cis-acting expressio

102 Here, we present GIGSEA (Genotype Imputed Gene Set Enrichment Analysis), a novel method th

103 The resulting matrix factorization imputes gene abundance for both zero and nonzero counts

104 d RESCUE, to mitigate the dropout problem by imputing gene expression levels using information from o

105 variant in a low-level biological trait with imputed genetic data has implications for the study of h

106 meta-analysis was applied to 8,016,731 well-imputed genetic markers from large-scale meta-analyses o

107 To explore the value of imputed genetically regulated gene expression (GReX) mod

108 HapMap imputed genome-wide association studies (GWAS) have reve

109 anagement approaches for rapid production of imputed genome-wide data.

110 The signal cannot be recapitulated by imputing genome-wide genotype data on a large reference

111 imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib famil

112 Fine mapping using sequence and imputed genotype data has revealed strong candidates for

113 Using 1000 Genomes Project-imputed genotype data in up to approximately 370,000 wom

114 f bone using a combination of WGS and deeply imputed genotype data, we have identified five novel gen

115 Using 1000 Genomes-imputed genotype data, we identified 47,587 cis-expressi

116 f principal components of ancestry, age, and imputed genotype data, with meta-analysis performed usin

117 ciation study using Affymetrix 6.0 array and imputed genotype data.

118 All data, including the imputed genotype matrix used for GWAS, are easily downlo

119 are, and uses a new method to combine the LD imputed genotype probabilities with IBD configurations t

120 We impute genotypes across the locus, finding the single nu

121 the combined reference panel increased well-imputed genotypes (with imputation quality score >/=0.4)

122 e large scale genome-wide data, allowing for imputed genotypes by modelling time to event outcomes un

123 agnosed individuals, and that our study used imputed genotypes for a subset of HLA genes.

124 To do so, we used imputed genotypes from 401,460 white British UK Biobank

125 However, imputed genotypes in underrepresented populations incur

126 categorical phenotypes, and can accommodate imputed genotypes under a dosage model.

127 We analysed directly obtained and imputed genotypes, and followed-up associated loci in 1,

128 rd progression from low-coverage sequence to imputed genotypes, overcoming barriers that at present r

129 Leveraging 1000 Genomes imputed genotypes, we carried out genome-wide associatio

130 pendent samples using de novo genotyping and imputed genotypes.

131 stage 2 associations (P < 5 x 10(-8)) using imputed genotypes.

132 g the Revised NEO Personality Inventory, and imputed GTF2I rs13227433 from saliva-derived DNA using c

133 low-depth WGS is an efficient alternative to imputed GWAS chip designs, allowing the discovery of up

134 true association signals than the classical imputed GWAS design.

135 hen meta-analysed with those from two deeply imputed GWAS replication cohorts (n = 1610 and 13 749).

136 WGS recapitulates 95.2% of variants found by imputed GWAS with an average minor allele concordance of

137 high-resolution HLA typing and 'HLA-2-Haplo' imputes haplotype pairs and provides additional function

138 0; #2) impute SFOL (population median); #3) impute Hct (population median); #4) estimate Hct (Hb/MCH

139 single nucleotide polymorphisms, as well as imputed HLA alleles and amino acids.

140 ic data generated by a customized SNP array, imputed HLA alleles, and multiple linear regression.

141 ize interactions between raltegravir and the imputed HLA molecule.

142 Only 35.6% of the HaploStats imputed HLA-A, -B, -C, -DRB1, and -DQB1 haplotypes had n

143 We imputed HLA-A, -B, and -DRB1 alleles and corresponding A

144 After imputing HLA variants into 6,805 case subjects and 13,46

145 an and median observed and missing at random-imputed HRQOL scores were calculated, followed by sensit

146 ingle-Nucleotide Polymorphisms (SNPs) and 38 imputed Human Leukocyte Antigen (HLA) alleles were analy

147 ough a genome-wide association study (GWAS), imputed human leukocyte antigen (HLA) alleles, exome arr

148 tumor immunity and corresponding with higher imputed immune cell scores and histologically detected t

149 athologists' estimate of lymphocyte density, imputed immune cell subtypes, and pathway analyses.

150 This trend was replicated in the imputed Immunochip data for the two K528-bearing haploty

151 G2 risk alleles were genotyped in BioMe and imputed in BioVU/NUgene participants.

152 pplied to PRSs with SNPs either genotyped or imputed in the validation dataset.

153 on maximum transverse diameter (measured or imputed) in 113 patients (88%) in the doxycycline group

154 6 Icelanders and found variants that we then imputed into the genomes of approximately 398,000 Icelan

155 onstrate the feasibility of this approach to impute lncRNA transcriptome of normal and cancer tissues

156 This study used measured and genetically imputed Lp(a) molar concentration, kringle IV type 2 (KI

157 performed on the genotyped and 1000 Genomes-imputed markers separately for each study, and combined

158 INTERMACS profile 1 alone, missing at random-imputed mean and median HRQOL scores were similar to obs

159 hs (6 months: 22.5 [SD 17.1] vs 24.2 [17.2], imputed mean difference -0.3 [95% CI -3.5 to 3.0]; 12 mo

160 ]; 12 months: 21.9 [SD 19.3] vs 21.5 [19.3], imputed mean difference -1.9 [95% CI -5.6 to 1.7]).

161 ence (6 months: 27.5 [SD 5.1] vs 28.1 [4.4], imputed mean difference 1.3 [95% CI 0.3 to 2.3]; 12 mont

162 .3]; 12 months: 27.8 [SD 5.4] vs 29.0 [5.0], imputed mean difference 1.6 [95% CI 0.5 to 2.7]).

163 nd 3 months after implantation, whereas MNAR-imputed mean scores were lower (>/=5 points) at baseline

164 We also employed PICRUSt2 to impute MetaCyc Enzyme Consortium (EC) pathway abundances

165 Based on imputed metagenomic content, US samples have a relative

166 Our method uses smoothing to impute methylation levels at strain-specific sites, ther

167 or association between depression status and imputed MHC variants, applying both a region-wide signif

168 We explored the validity of imputing migraine days on migraine-locked entries, and e

169 ates programs such as PLINK, SHAPEIT, Eagle, IMPUTE, Minimac, and several R packages, to create a sea

170 option to utilize predicted miRNA targets to impute miRNA activity from independent test PCG datasets

171 Here, we present iMIRAGE (imputed miRNA activity from gene expression), a convenie

172 e create a series of random forest models to impute missing beta activity concentrations at each RadN

173 urther show that our approach can accurately impute missing data after genome segmentation, reversing

174 arkov Chain Monte-Carlo simulation method to impute missing data and then fed the selected variables

175 lter for confident genotypes as the input to impute missing genotypes.

176 cribe a software pipeline and application to impute missing information in experimentally determined

177 AR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, per

178 MICE imputation allowed us to impute missing values for clinically informative feature

179 issing data mechanism, and use this model to impute missing values or obtain direct estimates of mode

180 sparse single-cell DNA methylation data and impute missing values.

181 t or no systolic blood pressure data, and we imputed missing systolic blood pressure data in 23 (1%)

182 We imputed missing values on anti-JCV antibody status (3912

183 MI is computationally intensive when imputing missing covariates with high-dimensional outcom

184 After imputing missing features, a predictive model was develo

185 Imputing missing values separately for each variable was

186 The median genetic distance of the imputed most recent common ancestor of the women's found

187 on package specially designed to efficiently impute multiple GWAS in parallel.

188 risk of 1.01 (95% CI: 0.99, 1.04) and an HR(imputed) of 1.02 (95% CI: 1.00, 1.04) per 5-nmol/L incre

189 the maximum transverse diameter (measured or imputed) of the aorta and also if they underwent aneurys

190 bserved migraine attacks satisfactorily, and imputing on migraine-locked days was consistent with the

191 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotyp

192 100 000 Icelanders with genetic information (imputed or whole-genome sequencing).

193 e cell-type heterogeneity is resolved, while imputing or normalizing heterogeneous data can introduce

194 on-the-fly for each new target sample to be imputed, outperform models based on fixed gene relations

195 In the first step, it phases and imputes parental genotypes based on the segregation stat

196 often results in many genotypes being poorly imputed, particularly in studies where the individuals a

197 ity analysis, in which missing data were not imputed, peak VO2 at 24 weeks decreased by -0.63+/-0.375

198 The imputed percentage of patients with a decrease of at lea

199 The imputed percentage of patients with a decrease of at lea

200 oach, SNIPER (Subcompartment iNference using Imputed Probabilistic ExpRessions), based on denoising a

201 Avocado shows significant improvements in imputing protein binding compared to the top models in t

202 and potential of larger reference panels to impute rare variants, while recognizing that increasing

203 is is a useful fiction - fiction, because it imputes reason to non-rational psychological processes;

204 uctural variants and common variants in well-imputed regions with few genes implicated from exome seq

205 DP HaploStats and HLA Matchmaker programs to impute/reproduce the measured high-resolution HLA type,

206 Of those with an imputed result, only 10.3% of Caucasians and 4.8% of non

207 , in which missing primary outcome data were imputed, resulted in a similar finding (relative rate, 1

208 ted with FRNT, and 1035 samples (34.5%) with imputed results, we found that 320 (10.7%) of 2996 child

209 urse from young adulthood to later life, and imputed risk factor trajectories for low-density lipopro

210 ction.The proposed method, TOBMIkNN reliably imputed RNA-seq data by borrowing information from DNA m

211 gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair.

212 o a limited sample size, we further analyzed imputed rs2735383 genotypes (r(2) > 0.999) of 47,640 bre

213 The study, however, cannot directly impute sepsis causation to the viruses identified.

214 a more than 14-fold increase compared to the imputed sequence.

215 Genome-wide, imputed, sequence, and structural data are now available

216 plied 6 approaches: #1) assume SFOL = 0; #2) impute SFOL (population median); #3) impute Hct (populat

217 wide association study found rs557874766, an imputed single nucleotide polymorphism located within a

218 ects and more than 7.8 million genotyped and imputed single nucleotide polymorphisms (SNPs) were anal

219 genome-wide association studies using 1000-G imputed single-nucleotide polymorphisms.

220 n study for VTE with approximately 9 000 000 imputed single-nucleotide polymorphisms.

221 We used imputed SNP to HLA typing data from these cohorts to fur

222 With data for 3,365 genotyped and imputed SNPs across a 1 Mb region (positions 44,394,495-

223 ciation between 1000 Genomes Project (1000G) imputed SNPs and electrocardiographically measured QT we

224 with approximately 2.5 million genotyped and imputed SNPs in 9,055 participants of European descent a

225 SNPs in CYP19A1 and CYP1B1 using TaqMan and imputed SNPs in estrogen receptor 1 using genome-wide ma

226 imputation analysis in the region, with 562 imputed SNPs included in the statistical analyses.

227 summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near

228 white, of which, 434,839 typed and 7,423,250 imputed SNPs were used as the discovery.

229 ent-based approach that would recover 99% of imputed SNVs.

230 Methods imputing solely using subsets of sites identified by the

231 ction with deep neural network (cTP-net), to impute surface protein abundances from scRNA-seq data by

232 The imputed survival across a range of dose levels (AUC) was

233 ng a Boosted Regression Tree (BRT) model, we imputed survival outcomes (i.e. survival or death) when

234 Using a boosted regression tree model, we imputed survival outcomes (ie, survival or death) when u

235 usion of tract identifiers based on multiply imputed, synthetic data.

236 brian to Triassic biodiversity curve with an imputed temporal resolution of 26 +/- 14.9 thousand year

237 rage (0.15x) sequencing with a new method to impute the ancestral haplotype space in 1,887 commercial

238 rior to and following PCV use can be used to impute the indirect protection afforded by PCV in unvacc

239 We proposed a new computational strategy to impute the methylation value at the unmeasured CpG sites

240 on due to technical artifacts and attempt to impute the missing information, other recent studies arg

241 ues in the context of clustering is to first impute the missing values, and then apply the clustering

242 ercepts for cohorts was the best approach to impute the systematically missing predictor.

243 Preliminary chemical reactivity studies imputed the bioactivity of these natural products to a D

244 In the second step, it phases and imputes the offspring genotypes by detecting which haplo

245 in partially-measured microarray samples by imputing the expression of unmeasured genes.

246 that BayesMetab has improved performance in imputing the missing values and performing statistical i

247 KNN-TN generally has improved performance in imputing the missing values of the different datasets co

248 ng serological endpoints in a 10% sample and imputing the remaining infection statuses yields unbiase

249 correction by predicting the false zeros and imputing their values by making use of the interrelation

250 PrediXcan imputes tissue-specific expression levels from genetic v

251 based on millions of samples with array data imputed to a large fully sequenced reference panel and o

252 Missing data were imputed to account for variable response and ensure a re

253 meability in subjects with ASD should not be imputed to HP2 but to other members of the zonulin famil

254 rom the ALSPAC cohort who were genotyped and imputed to Phase 1 version 3 of the 1000 Genomes Project

255 e Illumina HumanCoreExome array and variants imputed to the 1000 Genomes Project and UK10K haplotypes

256 single-nucleotide polymorphism (SNP) arrays imputed to the 1000 Genomes Project reference panel.

257 ina (San Diego, CA) arrays and statistically imputed to the 1000 Genomes Project.

258 Genome-wide genotypes were imputed to the 1000 Genomes reference panel.

259 t) were genotyped on a genome-wide array and imputed to the 1000 Genomes reference panel.

260 WAS) for plasma FXI levels, using novel data imputed to the 1000 Genomes reference panel.

261 All individuals had genotypes imputed to the Haplotype Reference Consortium 1.1 Panel.

262 naire data on perceived age and genetic data imputed to the Haplotype Reference Consortium imputation

263 ontrols) and one with genome-wide genotyping imputed to the Haplotype Reference Consortium panel (9,3

264 MegaChip genotypes were imputed to Thousand Genomes data.

265 mpirically evaluate imputation accuracy when imputing to a 1000 Genomes Phase 3 versus a Phase 1 refe

266 Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin mode

267 experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative method

268 egrated Genetic Association Resource), which imputes transcriptomic data and performs subsequent TWAS

269 es and by performing linear interpolation to impute ungenotyped variants.

270 provides a flexible and transparent means to impute univariate missing data under general missing-not

271 pression patterns between lncRNA and PCGs to impute unknown lncRNA profiles.

272 efining computational methods for inferring (imputing) unknown interactions.

273 Missing payment data were imputed using a generalized linear model to estimate ove

274 ysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes

275 sed aerosol optical depth (AOD) product were imputed using a spatiotemporal land-use random-forest (R

276 n of six cell type-specific chromatin marks (imputed using ChromImpute) performed best, with an 58% i

277 e find, for example, that the transcriptome, imputed using genotype data, explains a significant prop

278 ymorphism panel of soybean with missing data imputed using various methods, (2) evaluate the imputati

279 e, so that there is a need for techniques to impute values for genotypes whose phenotypes have not be

280 ultiple imputation with chained equations to impute values for missing data.

281 s variables and conduct inference with those imputed values in place of the unobserved frailty measur

282 variables, and conduct inference with those imputed values in place of the unobserved frailty measur

283 We imputed variants in 200 genes across the HLA region, one

284 fying by ancestry, we analysed genotyped and imputed variants in Melanesians (607 cases and 1,229 con

285 ive genetic model and associated ~35 million imputed variants with natural log-transformed phenotype

286 11,923 bulls and 32,347 cows with 17,669,372 imputed variants.

287 otal of ~ 18 million autosomal genotyped and imputed variants.

288 h variables were selected using the multiply imputed versions of the derivation sample.

289 establish a robust pipeline for calling and imputing very low-depth WGS genotypes from standard bioi

290 Analysis of multiply imputed, weighted data (mean n = 1866) showed that 168 (

291 Further, few have addressed how GIs can be imputed when data are scarce.

292 acids (VFAs) indicators and VFA traits using imputed whole-genome sequence data in Iranian Holstein c

293 This study used imputed whole-genome sequencing from the Trans-Omics for

294 Missing data were multiply imputed with chained equations.

295 articularly for those genotypes that Impute2 imputed with low certainty.

296 Genotypes with missing values imputed with methods that make use of genealogic informa

297 seline to the final month; missing data were imputed with the use of multiple imputation.

298 Full reproductive histories were imputed, with the status of unobserved animals estimated

299 NA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch length

300 n the Y chromosomes of father-son pairs, and imputed Y-STR genotypes.