ライフサイエンスコーパス: copy number

1 sted for the covariates of age and MYCN gene copy number.

2 and selects for a progressively higher BRAF copy number.

3 types than other patients with the same SMN2 copy number.

4 hat maintain HPV-31 episomes increased viral copy number.

5 s that correspond to protein levels and gene copy number.

6 4 isolates correlated with plasmepsin 2 gene copy number.

7 sues but distributes in other tissues at low copy number.

8 rdings are not sensitive to decreased Chrna7 copy number.

9 parasites, in addition to variations in DNA copy-number.

10 ardless of the accuracy of the estimation of copy numbers.

11 stimated that decreases in mitochondrial DNA copy number, a measure of mitochondrial genome abundance

12 omas had a significantly higher frequency of copy number aberrations (67%) than other subgroups (P =

13 relationships of protein expression with DNA copy number aberrations and signatures of post-transcrip

14 igned to detect driver mutations, chromosome copy number aberrations, and mutation signatures.

15 ve from chemorefractory disease, we examined copy-number aberrations (CNAs) in circulating tumor cell

16 We utilized whole exome sequencing, copy number algorithm evaluation, and high-resolution wh

17 Copy number alteration (CNA) is a major contributor to g

18 tween immune metagene expression and somatic copy number alteration levels (rho = -0.484, P = 2 x 10-

19 utational load, neoantigen load, and somatic copy number alteration levels between immune-rich TNBC c

20 ncordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, an

21 We discovered six cases with copy number alterations (CNAs) at the IDH1 locus at recu

22 Here we monitored the dynamics of copy number alterations (CNAs) in 1,110 PDX samples acro

23 antity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis.

24 cer (BCa) cell lines and compared mutations, copy number alterations (CNAs), gene expression and drug

25 We stratify mutations and copy number alterations for important kidney cancer gene

26 netic basis for immune evasion: near-uniform copy number alterations of chromosome 9p24.1 and the ass

27 ct primary tumors and did not harbor similar copy number alterations or demonstrate significant mutat

28 Clustering copy number alterations shows that most cell lines resem

29 We identify somatic mutations and copy number alterations significantly associated with po

30 ssion landscape is determined by the somatic copy number alterations that drive expression in cis led

31 re frequently targeted by somatic mutations, copy number alterations, DE and AS, indicating their pro

32 aracterized by increased accumulation of DNA copy number alterations, greater genetic diversity and i

33 the GEMM genomic landscapes are dominated by copy number alterations, while protein-altering mutation

34 d did not show a bias to regions involved in copy number alterations.

35 ing antigen-specific CTLs in vivo results in copy-number alterations (CNAs) associated with DNA damag

36 t are essential in the context of particular copy-number alterations (copy-number associated gene dep

37 Extensive prior research focused on somatic copy-number alterations (SCNAs) affecting cancer genes,

38 somatic point mutations, but rather somatic copy-number alterations (SCNAs).

39 Cohort samples had extensive copy-number alterations and highly recurrent somatic mut

40 PCNSLs and PTLs exhibit frequent 9p24.1 copy-number alterations and infrequent translocations of

41 ad intratumor heterogeneity for both somatic copy-number alterations and mutations.

42 While cancer driver mutations and copy-number alterations have been studied at a systems-l

43 Multiple somatic mutations and copy-number alterations in genes that are therapeutic ta

44 ssess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in

45 After integration of somatic copy-number alterations, and clinical features specific

46 l burden (e.g., microsatellite instability), copy-number alterations, and specific somatic alteration

47 lted in parallel evolution of driver somatic copy-number alterations, including amplifications in CDK

48 we report the identification of chromosomal copy-number amplification at 1q21.3 that is enriched in

49 hromothriptic rearrangements occurred before copy number amplifications, and that rates of single-nuc

50 thereby leading to false-positive results in copy number-amplified regions.

51 Parallel DNA methylation and copy number analysis demonstrated that both genetic and

52 ration sequencing studies for mutational and copy number analysis.

53 in the group of participants with a low AMY1 copy number and a high dietary intake of starch.Our find

54 Then we analyzed interactions between AMY1 copy number and energy-adjusted starch intake (obtained

55 and its target genes (IL8, CSF2), and TRIB1 copy number and expression were predictive of clinical o

56 d with 528 genes having correlations between copy number and gene expression.

57 ecDNA amplification would increase oncogene copy number and intratumoural heterogeneity more effecti

58 Mitochondrial DNA (mtDNA) copy number and mtDNA deletions were increased significa

59 We investigated the association between AMY1 copy number and obesity traits, and the effect of the in

60 Notably, the mitochondrial DNA copy number and peroxisome proliferator-activated recept

61 phenome-wide association studies, as well as copy number and rare variant analyses.

62 c differences between the twin pairs-such as copy number and rare, single-nucleotide variants-did not

63 icant effect of the interaction between AMY1 copy number and starch intake on BMI (P-interaction = 0.

64 d the effect of the interaction between AMY1 copy number and starch intake on these obesity traits.We

65 nslated region (UTR), which affect both mRNA copy number and translation.

66 duction of viral transcription, viral genome copy number and virus yield.

67 and adenovirus receptor) expression and CVB3 copy number, and an improved left ventricular function i

68 the CVB3-induced inflammatory response, CVB3 copy number, and apoptosis in vitro.

69 mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints.

70 and analyzed mRNA and miRNA expression, DNA copy number, and DNA methylation in 117 Wilms tumors, fo

71 racterization (including DNA methylation and copy number, and RNA and protein expression).

72 es from 10 cases, the mutational signatures, copy number, and SNV mutational profiles reflect the exp

73 in bacterial strains containing the natural copy numbers ( approximately 40 monomers), as well as in

74 d by targeted next-generation sequencing and copy number array.

75 pan of Tk2-deficient mice and restored mtDNA copy number as well as respiratory chain enzyme activiti

76 These data provide a catalog of copy-number associated gene dependencies and identify pa

77 ntext of particular copy-number alterations (copy-number associated gene dependencies).

78 We hypothesised that EGFR copy number by fluorescence in-situ hybridisation (FISH)

79 tudy demonstrates how dynamic control of DNA copy number can serve as an effective strategy to progra

80 distinguished in part by rearrangements and copy number changes affecting chromosomal segments.

81 eneration sequencing analysis of chromosomal copy number changes and mutations is useful in distingui

82 The mutation signature of sgs1Delta reveals copy number changes flanked by repetitive regions with h

83 nts measured in the clinical cohort, such as copy number changes or mutations in protein coding genes

84 DNA copy number changes resulted in recurrent 1q gain, MYCN

85 In clonally related tumors, chromosomal copy number changes were more reliable than mutations fo

86 ancestry, overall mutational frequencies and copy number changes were not significantly different bet

87 Copy-number changes in 16p11.2 contribute significantly

88 lysis of SNVs in relation to allele-specific copy-number changes pinpoints the common ancestor to a p

89 sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only

90 cability to cancer samples with frequent DNA copy-number changes.

91 We detected significant alterations in DNA copy numbers (CN), gene expression levels, and DNA methy

92 a large number of genetic variants including copy number (CNV) and single nucleotide variant (SNV) in

93 nd S100A9 enhanced oxidative stress and CVB3 copy number compared with unstimulated infected cells.

94 We used gene expression and copy number data to infer pathway activities for cell li

95 Using this strategy, we integrated gene copy number data, drug exposure data and patient surviva

96 in respiratory activity: depletion of mtDNA copy number, decreases in mtRNA levels, and decreases in

97 Loss of heterozygosity and decreased copy number delimited interspersed monosomic and disomic

98 criptome impacted by allele preferential and copy number-dependent expression effects.

99 nd loci, CD274/PD-L1 and PDCD1LG2/PD-L2, and copy number-dependent increased expression of these liga

100 r NLP face, and further increases in v-SNARE copy numbers did not affect nucleation rate.

101 ome, totaling 1.7 Mbp, which show consistent copy number differences between marine and freshwater po

102 Neither the copy number differences nor the rearrangements were obse

103 e integrated mutations, gene expression, DNA copy numbers, DNA methylation and protein abundance, all

104 trotransposons (RTs) can rapidly increase in copy number due to periodic bursts of transposition.

105 ers), as well as in strains with much higher copy numbers due to LacI overexpression.

106 ne expression approach, we demonstrated that copy number elevations of catechol-O-methyl-transferase

107 Moreover, copy number elevations of COMT or Tbx1 reduced the proli

108 ovide evidence for the novel hypothesis that copy number elevations of these 22q11.2 genes alter the

109 ures, specific recurrent point mutations, or copy-number events in respect to chemotherapy status.

110 Interestingly, we do not observe the extreme copy number expansion of the AMY2B gene characteristic o

111 omplex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppressi

112 tional tool to determine HLA allele-specific copy number from sequencing data.

113 Copy number gain (3 copies) was also observed for MUC2,

114 tinib with that of placebo according to EGFR copy number gain (CNG) and EGFR, KRAS, BRAF, and PIK3CA

115 RKCI is targeted for frequent tumor-specific copy number gain (CNG) in both lung squamous cell carcin

116 Copy-number gain at 3q resulted in increased MAP3K13 mRN

117 -EPN-B) tumours display frequent large-scale copy number gains and losses but have favourable clinica

118 f human cancer revealed subtle but impactful copy number gains in E2F1 and E2F3 in hepatocellular car

119 F transcriptional output, we have shown that copy number gains in E2f1 or E2f3b resulted in dosage-de

120 Maternally derived copy number gains of human chromosome 15q11.2-q13.3 (Dup

121 NVs were found in <1.5% of brains, including copy number gains of PRPH that were overrepresented in A

122 amatically improved in GT mice with a vector copy number/genome higher than 1 in the BM and 2 in the

123 first assessed the association between AMY1 copy number (genotyped by digital droplet polymerase cha

124 he studies highlight the prognostic value of copy-number heterogeneity assessment in tumor biopsies a

125 Elevated copy-number heterogeneity was associated with an increas

126 gree of aneuploidy and is partly due to gene copy number imbalances, suggesting that subtle changes i

127 Gene copy number impacts on gene expression were detected wit

128 cal steady-state distribution of the protein copy number in a general kinetic model of stochastic gen

129 und to have overexpression and increased DNA copy number in a variety of human malignancies.

130 We observed decreased mitochondrial copy number in all the three FRDA models tested: cells,

131 ying the cell-to-cell variability of plasmid copy number in bacteria.

132 than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lin

133 body labeling efficiency to quantify protein copy number in cellular contexts using super-resolution

134 that it is nearly fixed (99.9%) for diploid copy number in contemporary humans.

135 rial fragmentation and reduced ATP and mtDNA copy number in FECD.

136 expression correlated with increased genomic copy number in SCLC lines.

137 curred during plant evolution, increased its copy number in some species.

138 Sal-1, one such fragment with the highest copy number in the infected cells, is derived from Salmo

139 (Rho = 0.3531; P = 0.0218) and the proviral copy number in the peripheral blood as an indirect measu

140 predictor of plasma viral load and proviral copy number in the peripheral blood.

141 Amplified copy number in the plasmepsin II/III genes within Plasmo

142 mple and accurate determination of transgene copy number in these six important crop species.

143 n Ts65DN mice; however, normalizing APP gene copy number in Ts65Dn mice fails to rescue plasticity.

144 positively correlated with proviral HIV-DNA copy numbers in peripheral blood mononuclear cells (PBMC

145 As a result, our study showed that copy number increase and overexpression of MCM8 may play

146 KG2C (KLRC2) gene is frequently deleted, and copy number influences the adaptive response of NKG2C(+)

147 l key factors, including variation in target copy number, inherent potency of sgRNA guides, and expre

148 DNA methylation and copy number integration with transcript levels yielded a

149 SMN2 copy number is a key positive modifier of the disease, b

150 First, the copy number is estimated by maximum likelihood and assoc

151 that statistical analysis with the expected copy number is more powerful than the statistic with the

152 repair factors that also regulate chromosome copy numbers is seen to increase DNA breaks in U2OS oste

153 The copy number loss (0-copy/1-copy) of nsv823469 significan

154 Furthermore, the copy number loss of nsv823469 in normal pulmonary tissue

155 The loss allele, inducing copy number loss of nsv823469, has a tendency to transmi

156 ity of NLRC5 caused by promoter methylation, copy number loss, or somatic mutations is associated wit

157 ctivity or, through incrementally increasing copy number, may be sites of secondary selective pressur

158 d volume were positively associated with CR1 copy number (mean number of CR1 molecules per erythrocyt

159 oplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citr

160 te that this approach can generate confident copy number measurements in independent transgenic lines

161 biological samples, such as gene expression, copy number, methylation etc.

162 appreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing in

163 Copy number modulation is a generalizable principle that

164 Mitochondrial DNA copy number (mtDNA-CN), which represents the number of m

165 ich can lead to changes in mitochondrial DNA copy number (mtDNAcn).

166 We analyzed RNA-Seq, DNA copy number, mutation and germline SNP data of 627 ER(+)

167 Copy number mutations implicate excess production of alp

168 Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each

169 The results indicate a copy number of 25 for FliG.

170 Somatic copy number of 8 genes frequently deleted in ALL (CDKN2A

171 l doublings, consistent with a measured LRV1 copy number of about 15.

172 revent this mother from dying by keeping the copy number of egl-1 mRNA below a critical threshold.

173 versal genetic strategy to precisely control copy number of fluorescently labeled molecules in a cell

174 We therefore suggest that the copy number of HIV in 8E5 extracts be established by dPC

175 h BRCAness score is associated with aberrant copy number of HR genes rather than somatic mutation and

176 ar to affect gene expression by altering the copy number of intergenic regulatory regions.

177 in single-nucleotide resolution and relative copy number of JC virus (JCV) clinical standards.

178 re observed in a clinical sample with a high copy number of JCV or a plasmid control.

179 Multiple copy number of PI 88788-type GmSNAP18, GmAAT, and GmWI12

180 ndividually, there are no limitations on the copy number of the protein under study; as a result, we

181 ve evolutionary strategy to rapidly increase copy numbers of genomes per cell at the expense of the t

182 rison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retro

183 Copy numbers of the FCGR2A and FCGR2C genes were signifi

184 te polymerase production will produce higher copy numbers of the improved partner gene.

185 We quantified gene copy numbers of the pyruvate kinase, liver, and red bloo

186 The distribution and copy numbers of the virus appear to correlate with urina

187 Our results showed that the copy numbers of viral nuclear DNA can vary by as much as

188 e interaction between starch intake and AMY1 copy number on obesity.

189 Single-cell copy number or mutational profiling was performed, in ad

190 g in Escherichia coli in the form of plasmid copy number oscillations via a modular design that can b

191 ggest that, in addition to plasmepsin II/III copy number, other loci, including pfcrt, may also be in

192 e subject to inherent random fluctuations in copy numbers over time.

193 limited application in the detection of low-copy-number pathogens in complex samples.

194 For high-copy-number plasmids, diffusion ensures that both daught

195 ns to actively segregate chromosomes and low copy-number plasmids.

196 In addition, we show copy number profiles can also be obtained from the same

197 onal changes are supported by mutational and copy number profiles in breast cancers.

198 a generated using whole-exome sequencing and copy number profiling of primary and multiple-matched me

199 accurate methodology to perform whole-genome copy-number profiling of single nuclei obtained from for

200 e PI3K/AKT/mTOR pathway (including mutation, copy number, protein, or RNA) were examined across 11,21

201 ed localization microscopy to studies of low-copy-number proteins in living bacteria.

202 STmiR sensors were also used to estimate the copy number range of miRNAs in total RNA extracts.

203 hood estimation (MPLE) model to identify the copy number ratio and CNV boundary.

204 d at boundaries between amplified and normal copy-number regions.

205 29 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression vari

206 In several cases bla KPC was found on high copy number, small Col-like plasmids, previously associa

207 ssentiality screens while accounting for the copy number-specific effect.

208 ed bees (7.45*10(12) +/- 1.62*10(12) average copy number +/- standard error) compared to other tested

209 Therefore, after correction for CR1 copy number, the Sl and McCoy polymorphisms did not infl

210 ailure and heart failure, we estimated GSTM1 copy number using exome sequencing reads in the Atherosc

211 Copy number variable genes tended to be evolutionarily r

212 on of novel variants among smaller and rarer copy number variable segments.

213 Computational copy number variant (CNV) prediction pipelines and an ex

214 ress this, we performed exome sequencing and copy number variant analysis on 1511 frozen human brains

215 n be used in training and testing of somatic copy number variant calling tools.

216 We also identified copy-number variant (CNV) eQTLs, including some that app

217 Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-alle

218 are under-represented in neurodevelopmental copy number variants (CNVs) (P<2.2 x 10(-10)), suggestin

219 Copy number variants (CNVs) have been strongly implicate

220 to examine the effect of neurodevelopmental copy number variants (CNVs) on the cognitive performance

221 The effect of Copy Number Variants (CNVs) on Type 2 Diabetes (T2D) rem

222 We show that copy number variants (CNVs) show a variety of genetic si

223 microscopic genomic rearrangements including copy number variants (CNVs).

224 fitting the minor component are enriched for copy number variants and low complexity regions, which c

225 jority of the insulinomas display mutations, copy number variants and/or dysregulation of epigenetic

226 consistent with the emerging effects of rare copy number variants associated with intellectual disabi

227 Rare copy number variants contribute significantly to the ris

228 Analysis of copy number variants detected 5.2 deletions and 10.3 amp

229 ndly R package, modSaRa, designed to perform copy number variants identification.

230 These included copy number variants in 14% (n=54, 15% are novel), and p

231 tified de novo loss of function mutations or copy number variants in high-confidence ASD-associated g

232 Duplication and triplication of copy number variants of 22q11.2 are consistently and rob

233 rences in single-nucleotide polymorphisms or copy number variants, respectively, for differential dis

234 ute to the pathogenicity of rare, multigenic copy-number variants (CNVs) that have been observed in p

235 y-matched controls for rare (< 1% frequency) copy-number variants (CNVs) using SNP microarray data.

236 Africa, we identify a diverse array of large copy-number variants affecting the host invasion recepto

237 Rare copy-number variants conferring moderate to high risk of

238 analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (

239 Causal copy-number variants were found in 12 patients (11.9%) w

240 ngle-cell libraries for detection of somatic copy-number variants.

241 Oncogenomic studies indicate that copy number variation (CNV) alters genes involved in tum

242 iant could be accelerated by the presence of copy number variation (CNV) at the K3L locus, which in m

243 Gene copy number variation (CNV) has been shown to be associa

244 Recently copy number variation (CNV) has gained considerable inte

245 Copy number variation (CNV) is an important cause of neu

246 In some species copy number variation (CNV) of target site loci (e.g. th

247 Chromosomal copy number variation (CNV) refers to a polymorphism tha

248 y platform and established methods to assess copy number variation (CNV), the authors compared the ge

249 We performed a genome-wide copy number variation analysis of 343 ASD trios, 203 pat

250 sponding region in horse shows extraordinary copy number variation and different relative location an

251 The resulting DNA copy number variation and patterns of chromosome loss an

252 on, DNA methylation, noncoding microRNA, and copy number variation data available from the Gene Expre

253 Large-scale whole-genome studies of copy number variation in Han Chinese samples are still l

254 ceptibility to IAV segregates independent of copy number variation in multicopy ChrY gene families th

255 reception, detoxification and digestion, and copy number variation in the two latter gene families, s

256 ic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repe

257 Single nucleotide polymorphisms and copy number variation of the FCGR2/3 gene cluster were s

258 We screened additional patients for copy number variation of the putative regulatory element

259 Copy number variation of the target loci may be another

260 3A/E6AP-dependent ASD.SIGNIFICANCE STATEMENT Copy number variation of the UBE3A gene and aberrant ove

261 orroborative pattern between the chromosomal copy number variation profiles of the AH cfDNA and tumor

262 latform, followed by genome-wide chromosomal copy number variation profiling to assess the presence o

263 Copy number variation was rampant with between 16 098 an

264 assesses gene expression, somatic mutation, copy number variation, and methylation, we for the first

265 athways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics.

266 considerable presence/absence variation and copy number variation.

267 rovides an evolutionary alternative for gene copy number variation.Eukaryotic cells rely on the ubiqu

268 ocyte antigen (HLA) alleles, exome array and copy-number variation (CNV) analyses.

269 (WGA) methods are limited by low accuracy of copy-number variation (CNV) detection and low amplificat

270 Although several tools for copy-number variation calling in whole genome sequencing

271 We found no recurrent non-NF1 locus copy-number variation in PN.

272 ses that adversely affect genotyping include copy-number-variation, paralogous sequences, library pre

273 neity, total mutation load, neoantigen load, copy number variations (CNV), gene- or pathway-level som

274 hed array data from the 60 samples show that copy number variations (CNVs) and alterations in DNA met

275 Shank mutations and copy number variations (CNVs) are linked to several psyc

276 Copy number variations (CNVs) contribute significantly t

277 Copy number variations (CNVs) have recently been linked

278 It is highly possible that copy number variations (CNVs) in susceptible regions hav

279 microdeletion is among the most common gene copy number variations (CNVs) known to confer risk for i

280 Copy number variations (CNVs) often include noncoding se

281 , which parallels the effects of human Shank copy number variations (CNVs) on Autism spectrum disorde

282 ingle-nucleotide polymorphisms (SNPs) and 43 copy number variations (CNVs) with in-vitro piperaquine

283 sensing, the scaling in cancer of chromosome copy number variations and other mutations with tissue s

284 ould be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities,

285 quences by Illumina paired-reads sequencing, copy number variations by qPCR, RNA concentrations by qR

286 Liu et al. now show that multiple smaller copy number variations may also arise in in-vivo-conceiv

287 K2 is one of the genes in the 16p11.2 locus, copy number variations of which are associated with auti

288 we report the first observation of abundant copy number variations on neuropeptides and receptors, w

289 and 12.6 de novo insertions and deletions or copy number variations per ASD subject.

290 AMY1 and AMY2 show copy number variations that affect differences in amylas

291 les, 215 genes spanning rare and replication copy number variations, 99 genes overlapping with linkag

292 are significantly correlated with their gene copy number variations.

293 ation was lost when the strong effect of CR1 copy number was included in the model.

294 x (BMI) and body fat percentage.Results:AMY1 copy number was not associated with BMI (P = 0.80) or bo

295 Moreover, the ATP6V1A copy number was positively correlated with its mRNA leve

296 Myometrial mitochondrial copy number was reduced in older mice, although there we

297 Variations in copy number were minimal in samples amplified using the

298 The means of PKLR, FCGR2A, FCGR2C, and FCGR3 copy numbers were significantly higher among children wi

299 ers a unique opportunity to quantify protein copy number with nanoscale resolution.

300 m likelihood and association of the expected copy number with the phenotype is tested.