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 Missing covariates were imputed.

3 he proportions of undetected infections were imputed.

4 leukocyte antigen (HLA) serotypes were also imputed.

5 Missing data were imputed.

6 ion to treat, and missing data were multiply imputed.

7 In the GALA II study WBC types were imputed.

8 Missing covariate data were imputed.

9 GICS population); genotypes of two SNPs were imputed.

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

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

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

13 puting genotype probabilities first and then imputing.

14 Here we impute 1,380,133 indels based on the latest 1,000 Genome

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

16 When imputing 10 Mb of sequence data from 50,000 reference sa

17 genetic model in an association analysis of imputed 2.5 million single-nucleotide polymorphism dosag

18 We imputed 24 million single-nucleotide polymorphisms and i

19 We impute 4,315 high-resolution signal maps, of which 26% a

20 emely low sequencing coverage, by accurately imputing 5.7 million SNPs at a mean r(2) value of 0.98 i

21 Using the latest software, we imputed 7 million single-nucleotide polymorphisms (SNPs)

22 We imputed 8,961 classical HLA alleles, amino acids, and SN

23 It is well known that the ability to impute a rare variant is dependent both on the array cho

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

25 We first imputed all possible genotypes across the LMO1 locus and

26 To further study this locus, we imputed alleles at classical leukocyte antigen (HLA) loc

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

28 The primary imputed analysis showed that compared with the control g

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

30 included calculating the correlation between imputed and observed allelic dosage in a subset of sampl

31 he human leukocyte antigen (HLA) region were imputed and tested.

32 Missing genotypes and SNPs were imputed and, after quality exclusions, 501 typed and 123

33 nalysis pipeline can be applied to sequence, imputed, and genotyping array, e.g., "exome chip," data,

34 d, whether or not missing urine screens were imputed as cocaine positive.

35 n summary statistics, have been proposed for imputing association summary statistics.

36 Additional genotypes were imputed based on the 1000 Genomes reference panel.

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

38 tes multiple input formats including BAM and imputed beagle genotype probability files.

39 lly for the Malays and Indians but even when imputing between northern and southern Han Chinese.

40 ,000-5,500 g) were linked to daily PM2.5 via imputed birth days.

41 t of genetic variance when missing loci were imputed by the method proposed in this paper.

42 One missing study was imputed by trim and fill analysis, suggesting only sligh

43 from SLE genome-wide association studies was imputed by use of 1000 Genomes data.

44 ts on isolated cell types, it is possible to impute cell proportions and adjust for them, but there i

45 s and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) ge

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

47 t random forest imputation may be useful for imputing complex epidemiologic data sets in which some p

48 lected as the primary procedure, the overall imputed cost ranged from $5802 to $7931.

49 was used as a primary procedure, the overall imputed cost was $5828 to $8098.

50 asmin was the primary procedure, the overall imputed cost was $8767 to $10 977.

51 and Medicaid Services, was used to calculate imputed costs for each primary treatment modality in a f

52 ing growth curve models, which enabled us to impute data at missing time points for each participant.

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

54 genome-wide significance in combination with imputed data from a GWAS in nsCPO triads (p = 2.73 x 10(

55 further discover new susceptibility loci, we imputed data from four GWAS of Asian non-smoking female

56 Imputed data in 608 Japanese cases and 737 controls furt

57 We used imputed data on 3,782 women and 3,753 men of the Nationa

58 efficient approach to combining observed and imputed data on rare variants.

59 This imputed data set will enable us to better study the rela

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

61 additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for c

62 s such, we demonstrate filtering methods for imputed data that improve genotype concordance from 79.3

63 We use the imputed data to detect low-quality experimental datasets

64 used multivariable regression with multiply imputed data to estimate associations while controlling

65 value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-inf

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

67 ean ancestry participants using 1000 Genomes imputed data.

68 l women with logistic regression of multiply imputed data.

69 ht-association threshold of P < 5E-06 in the imputed dataset were followed up in an independent sampl

70 r controlling for baseline utility and using imputed dataset, treatment was associated with a reducti

71 Our imputed datasets provide the most comprehensive human re

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

73 hierarchical linear models with 20 multiply imputed datasets.

74 Finally, reanalysis of the European HapMap imputed Diabetes Genetics Replication and Meta-Analysis

75 ose a novel, fast and yet accurate method to impute diploid genotypes.

76 cause and effect (i.e., left atrial dynamics impute disease events as consequences), disease classifi

77 We used a mixed linear model to impute DNA methylation (DNAm) levels of four brain tissu

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

79 These imputed drug response data are then associated with soma

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

81 PCPT (end-of-study biopsy supplemented with imputed end points).

82 est for the joint effect of all measured and imputed eQTLs in a gene.

83 t by using GTEx data as a reference, one can impute expression levels in inaccessible tissues in non-

84 expression imputation and that incorporating imputed expression data can improve power to detect phen

85 This imputed expression quantitative trait locus, termed impe

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

87 Main analyses were imputed for missing data.

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

89 These missing values were imputed from other characteristics.

90 ailable, the 2012 cesarean delivery rate was imputed from other years.

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

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

93 ERAP1 haplotypes imputed from the International Genetics of AS Consortium

94 ghting, and in models using cognitive scores imputed from the Telephone Interview for Cognitive Statu

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

96 arean rate data were available, the rate was imputed from total health expenditure per capita, fertil

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

98 est for the joint effect of all measured and imputed functional variants which are associated with a

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

100 We imputed gene expression into GWAS data from over 900,000

101 individual's genetic profile and correlates 'imputed' gene expression with the phenotype under invest

102 The procedures these technologies use to impute genetic data, therefore, greatly affect downstrea

103 ined analyses using >10 million genotyped or imputed genetic markers.

104 oximately 9 m '1000 Genomes Reference Panel' imputed genetic variants.

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

106 Here we extend that work to imputed genome-wide genotypes and conduct new RNA sequen

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

108 p imputation, and lastly how the clusters of imputed genotype are pieced together as the final imputa

109 We applied variance-component methods to imputed genotype data for 11 common diseases to partitio

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

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

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

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

114 ROH measurements were analyzed using raw or imputed genotype data.

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

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

117 SNPs using the 'iCOGS' genotyping array and impute genotypes for a further 1,284 using 1000 Genomes

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

119 FEV1/FVC with 1000 Genomes Project (phase 1)-imputed genotypes and followed up top associations in 54

120 nt generation of imputation methods provides imputed genotypes at the marginal accuracy.

121 the combined reference panel increased well-imputed genotypes by from 49.8% to 61.8%.

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 ved genotypes for sequenced subjects and the imputed genotypes for nonsequenced subjects is unbiased.

125 We then examined the entire data set using imputed genotypes from 1917 cases and 3858 control indiv

126 We expect that the use of imputed genotypes in swine breeding will yield highly ac

127 We used imputed genotypes of common variants in a discovery samp

128 ation analysis in the discovery cohort using imputed genotypes of the major histocompatibility comple

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

130 tudy we investigated the impact of employing imputed genotypes when using more elaborated models of p

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

132 no additional information to be gained from imputed genotypes.

133 pendent samples using de novo genotyping and imputed genotypes.

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

135 Imputing genotypes from reference panels created by whol

136 The 1KJPN was effective for imputing genotypes of the Japanese population genome wid

137 es and 9,979 controls of European ancestry), imputing genotypes utilising the 1000 Genomes Project.

138 tical tests were applied to the 1000 Genomes imputed genotypic data.

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

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

141 h excessive missing data, and approaches for imputing highly skewed continuous distributions that are

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

143 We also imputed HLA alleles using dense SNP data in the MHC regi

144 We also imputed HLA data with a previously validated imputation

145 ize interactions between raltegravir and the imputed HLA molecule.

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

147 Using a validated prediction algorithm, we imputed HLA-C cell surface levels in 228 individuals fro

148 elation was confirmed between the actual and imputed HLA-match groups.

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

150 of asparaginase-induced immune responses, we imputed human leukocyte antigen (HLA) alleles in patient

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

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

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

154 r each selected SNP those untyped SNPs to be imputed in the add-one two-step imputation, and lastly h

155 An imputed intention-to-treat analysis of 414 patients show

156 ome sequencing (WGS) of 8,453 Icelanders and imputed into 1,840 cases and 129,016 control women, foll

157 le-genome sequencing of 2,636 Icelanders and imputed into 4,572 BCC patients and 266,358 controls.

158 ome sequencing of 2,636 Icelanders that were imputed into 5,419 kidney stone cases, including 2,172 c

159 were estimated with data for training costs imputed into a regression analysis with health-care expe

160 6 Icelanders and found variants that we then imputed into the genomes of approximately 398,000 Icelan

161 al observed in European subjects was for the imputed intronic SNP rs1830298 in ALS2CR12 (telomeric to

162 thium-responsive patients with controls, two imputed markers attained genome-wide significant associa

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

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

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

166 Imputed Medicaid, private insurance, and informal care c

167 Based on imputed metagenomic profiles, Kyoto Encyclopedia of Gene

168 We did a multilevel meta-analysis to impute missing country-specific listeriosis incidence ra

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

170 pproaches of using regularized regression to impute missing values of high-dimensional data that can

171 d at least one post-baseline assessment, and imputed missing data with the last observation carried f

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

173 After imputing missing data and applying NHANES sampling weigh

174 hained equations (MICE) is commonly used for imputing missing data in epidemiologic research.

175 Imputing missing disease phenotypes for patients via co-

176 Here we present an approach for imputing missing disease phenotypes given the genotype o

177 teractions among bZIP transcription factors, imputing missing present-day interactions among the bZIP

178 Such pseudo-array staircases are able to impute more accurately than the classic one-step imputat

179 l as from other omics, and 2) simultaneously impute multiple missing omics datasets by an iterative a

180 Here we impute nine large Dutch biobanks (~35,000 samples) with

181 e-nucleotide polymorphisms (SNPs) (including imputed ones) fall into non-coding regions, making it di

182 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotyp

183 (Stage 1) or approximately 200 000 (Stage 2) imputed or genotyped single variants and BMI, and summar

184 Compared with Mendel-Impute, our low-rank based method achieves similar accur

185 completion (LRMC) model is similar to Mendel-Impute, our matrix co-clustering factorization (MCCF) mo

186 etion" (MID) method, which involves deleting imputed outcomes prior to analysis.

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

188 on HR: 0.92; 95% CI: 0.84 to 1.01; p = 0.10; imputed population HR: 0.97; 95% CI: 0.92 to 1.03; p = 0

189 dence interval [CI]: 0.71 to 1.06; p = 0.16; imputed population HR: 0.99; 95% CI: 0.89 to 1.09; p = 0

190 on HR: 0.92; 95% CI: 0.79 to 1.07; p = 0.26; imputed population HR: 0.99; 95% CI: 0.92 to 1.06; p = 0

191 ifferences in survival between the naive and imputed populations at 30 days (naive population hazard

192 or patients with unknown race, we multiplied imputed race to calculate age-, race-, and serotype-spec

193 s, looking at studies that have been able to impute rare variants, methods behind merging reference p

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

195 However, ignoring the uncertainties of imputed rare variants in downstream association analysis

196 ind merging reference panels, approaches for imputing rare variants, and methods for analyzing rare v

197 ew the additional challenges that arise when imputing rare variants, looking at studies that have bee

198 ciation with rs1830298 was replicated in the imputed results from the combined GWAS (P = 3 x 10(-6)),

199 15), effect -1.24 years of maternal life per imputed risk allele in parent; sex difference, P=0.011),

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

201 In addition, we imputed sequence variants for MICA, an MHC HLA-like gene

202 es for milk production and curly coat, using imputed sequence variants, and identified variants assoc

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

204 Imputed signal tracks show overall similarity to observe

205 an in a prior national civilian survey (with imputed/simulated age at enlistment), whereas post-enlis

206 osome 20q11 [P= 1.72 x 10(-8) for rs3746446; imputed Single Nucleotide Polymorphism (SNP) rs6088703 P

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

208 I and approximately 2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 ind

209 Data on genotyped or imputed single-nucleotide polymorphisms most significant

210 ted for association with 27.7 M genotyped or imputed single-nucleotide polymorphisms separately in th

211 yped (Illumina Omni2.5 BeadChip) or reliably imputed single-nucleotide polymorphisms.

212 ents using 472 450 genotyped and 6.9 x 10(6) imputed single-nucleotide polymorphisms.

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

214 co fine-mapping approach using genotyped and imputed SNP data for 6,608 endometrial cancer cases and

215 Analyses of imputed SNP data from the entire data set confirmed the

216 8), RBBP8 (OR 0.76; 95% CI 0.62-0.94) and an imputed SNP near CDKN2B-AS1 (OR 0.79; 95% CI 0.64-0.98)

217 oid the genotype imputation step by directly imputing SNP statistics, e.g. Directly Imputing summary

218 We impute SNPs, classical HLA alleles and amino-acid residu

219 puted to 1000 Genomes Project data, and well-imputed SNPs (>0.01 minor allele frequency) were analyse

220 ed an average of 79% (SE = 8%) of hg(2) from imputed SNPs (5.1x enrichment; p = 3.7 x 10(-17)) and 38

221 es (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained a

222 an additive genetic model, revealed several imputed SNPs (eg, rs115231074: odds ratio [OR], 1.22 [P

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

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

225 ive genetic model was applied to 2.5 million imputed SNPs for each gene.

226 erage and to interrogate additional SNPs, we imputed SNPs from the 1000 Genomes Project reference pan

227 Analysis of 1184 genotyped and imputed SNPs in 6608 Caucasian cases and 37 925 controls

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

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

230 e strongest associations uncovered were with imputed SNPs residing within the FGFR2 (rs1219515, P = 1

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

232 explained (PVE) for DMA% by all measured and imputed SNPs was 16% (p = 0.08), which was reduced to 5%

233 after quality exclusions, 501 typed and 1232 imputed SNPs were included in logistic regression models

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

235 rce-specific health associations from the 10 imputed source contribution time series were combined, r

236 Behavioral studies show that humans impute structure into simple learning problems, even whe

237 es of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could no

238 ectly imputing SNP statistics, e.g. Directly Imputing summary STatistics (DIST) proposed by our group

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

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

241 We were able to impute the genomes of 1,317 South Dakota Hutterites, who

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

243 representation of the fluxes and ability to impute the missing data in between the measurements.

244 ge of these additional related phenotypes to impute the phenotype of interest or target phenotype and

245 In addition, our method can impute the summary statistic of the target phenotype as

246 ich uses only GWAS summary statistics to (i) impute the summary statistics at unmeasured eQTLs and (i

247 EGMIX uses this accurate LD estimates to (i) impute the summary statistics at unmeasured functional v

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

249 two-step imputation may improve accuracy by imputing the low density genotyped study animals to a me

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

251 By imputing the presence and timing of unobserved infection

252 By imputing the sequencing data from the GWAS data for the

253 he disease burden of rare variants may be to impute them into existing large datasets.

254 We imputed these variants into 104,220 individuals down to

255 Genotype data were imputed to 1000 Genomes Project data, and well-imputed S

256 using single nucleotide polymorphisms (SNPs) imputed to 1000 Genomes.

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

258 P and single nucleotide polymorphisms (SNPs) imputed to HapMap2.

259 alytic activity and/or selectivity have been imputed to non-covalent interaction between the reaction

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

261 nome-wide association analysis of 34 studies imputed to the 1000 Genomes Project reference panel and

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

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

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

265 Genotype data in each study were imputed to the 1000 Genomes reference.

266 Additionally, after imputing to 1000 Genomes, two less common independent SN

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

268 orts by starting with genotyped variants and imputing to all common variants spanning ETS1.

269 Multiple imputation was used to impute tumor markers for those missing data on 1-3 marke

270 Demographic estimators impute two ancestral population bottlenecks: one >100,00

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

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

273 uses a relevant reference panel to directly impute unmeasured SNP statistics based only on statistic

274 risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal varian

275 he Infinium Omni Express bead microarray and imputed up to reference panels from the 1000 Genomes Pro

276 SNPs (minor allele frequency>0.05) that were imputed using 1000 Genomes Phase 1 European data (R(2)>0

277 enotypes for six million common variants are imputed using 1000 Genomes Project and UK10K as the refe

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

279 nucleotide polymorphisms (SNPs) are commonly imputed using large multi-ethnic reference panels.

280 an 5,000,000 SNPs were directly genotyped or imputed using the 1000 Genomes Project reference panels.

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

282 testing gene-gene interaction on marginally imputed values of untyped SNPs.

283 gnitive score at 2 years of age (childhood), imputing values for deaths.

284 association between 8,114,394 genotyped and imputed variants across the genome and risk for developi

285 We tested for association between these imputed variants and non-HDL cholesterol levels in 119,1

286 ndividuals that all approximately 17 million imputed variants explain 56% (standard error (s.e.) = 2.

287 We tested the imputed variants for association with SCr.

288 ion and meta-analysis on close to 15 million imputed variants from three large collections of AD fami

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

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

291 lly more powerful than the use of accurately imputed variants only and the use of sequencing data alo

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

293 s (NHLBI) Exome Sequencing Project (ESP), we imputed whole-exome sequence data into 13 719 African Am

294 with SNP imputation, common HLA alleles were imputed with greater accuracy than low-frequency variant

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

296 Missing data were imputed with multiple imputation methods.

297 Additional genotypes were imputed with the 1000 Genomes reference panel.

298 llumina Human 660WQuadv1C BeadChip array and imputed with the Markov Chain Haplotyping algorithm usin

299 on of some individuals is based on genotypes imputed with the same accuracy as our Yorkshire populati

300 s and gave higher predictive accuracies than imputing with the mean.

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