ライフサイエンスコーパス: copy number alteration

1 tion, viral-human transcript fusion, and DNA copy number alteration.

2 non-randomly targeted by somatic mutation or copy number alteration.

3 genetic analysis of the tumor, including DNA copy number alterations.

4 an cancer, and results in widespread somatic copy number alterations.

5 ted as clonally related based on overlapping copy number alterations.

6 highly associated with specific mutations or copy number alterations.

7 used to detect point mutations, indels, and copy number alterations.

8 rs are characterized by widespread recurrent copy number alterations.

9 analyses of breast cancer transcriptome and copy number alterations.

10 form on oncogenic driver genes and recurrent copy number alterations.

11 cal pathways, clinicopathologic factors, and copy number alterations.

12 methylation, respectively, independently of copy number alterations.

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

14 re, we discuss the costs and benefits of DNA copy-number alterations.

15 g., normal CD4 counts, contained significant copy-number alterations.

16 haracterize their exomes, transcriptomes and copy-number alterations.

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

18 the frequencies of actionable mutations and copy number alterations/aberrations (CNAs) in the two mo

19 r results highlight the rarity of chromosome copy number alterations across mammalian tissues and arg

20 This can potentially generate correlated copy-number alterations across hundreds of linked genes,

21 The proliferation class has specific copy number alterations, activation of oncogenic pathway

22 ellular and multicellular subnetworks, while copy-number alterations affected downstream target genes

23 by oncogenic mutations, translocations, and copy number alterations affecting key components the NF-

24 In two independent data sets, copy-number alterations affecting either <25% or >75% of

25 ear to have multiple clones distinguished by copy number alterations alone.

26 Whole-chromosome copy number alterations, also known as aneuploidy, are a

27 ncrease of ploidy, intratumor heterogeneity, copy-number alteration, altered expression of 37 miRNAs,

28 Copy number alteration analysis disclosed distinguishabl

29 of interest for further evaluation, such as copy-number alteration analysis.

30 after controlling for background effect from copy number alteration and DNA methylation.

31 Mutation, copy number alteration and gene expression data from The

32 s can be attributed to both a combination of copy number alteration and promoter methylation at the D

33 of somatic mutations, the burden of genomic copy number alterations and aberrations in known oncogen

34 thod to analyze the relationship between DNA copy number alterations and an archive of gene expressio

35 nonhypermutated group with multiple somatic copy number alterations and aneuploidy in approximately

36 Our study therefore links focal copy number alterations and chromothripsis with poor out

37 l surface proteins by flow cytometry and for copy number alterations and differential gene expression

38 d identified significantly mutated genes and copy number alterations and discovered putative tumor su

39 F2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, pr

40 somatic sequence mutations with genome-wide copy number alterations and gene expression profiles rev

41 d ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-

42 Regions of copy number alterations and germline DNA variants are so

43 two types of sequencing information-somatic copy number alterations and loss of heterozygosity-withi

44 genes are altered we tested how expression, copy number alterations and mutation status varied acros

45 ntified a large number of previously unknown copy number alterations and mutations, requiring experim

46 ng 5 G1 tumors) was characterized by limited copy number alterations and mutations.

47 nce in situ hybridization were used to study copy number alterations and MYB rearrangements.

48 atic aberrations in breast cancer, including copy number alterations and point mutations.

49 ve that HAMPs have a high frequency of focal copy number alterations and recurrent mutations, whereas

50 ns, short insertions and deletions (indels), copy number alterations and selected fusions across 287

51 nary phylogeny of a tumor using both somatic copy number alterations and single-nucleotide alteration

52 d next-generation sequencing data of somatic copy number alterations and somatic mutations in 303 met

53 atient samples for identification of somatic copy number alterations and translocations.

54 quency of whole chromosome or chromosome arm copy number alterations and were associated with an incr

55 tion of tumor gene expression, while somatic copy-number alteration and CpG methylation accounted for

56 assively parallel sequencing, which identify copy-number alterations and breakpoint junctions, but th

57 We also analyzed a large dataset of somatic copy-number alterations and gene expression levels measu

58 ypes, which are based on patterns of genomic copy-number alterations and gene expression(12,13)).

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

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

61 ionated VE-cadherin-positive cells uncovered copy-number alterations and mutated TP53, confirming hum

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

63 sion, alternative splicing, point mutations, copy-number alterations and premature truncation) or red

64 re derived more commonly from mutations than copy number alterations, and compared the prevelence of

65 icant higher numbers of structural variants, copy number alterations, and driver changes than nnMCL,

66 enetic alterations (somatic point mutations, copy number alterations, and gene fusions) in ALK(-) ALC

67 These include mutations in TP53, arm-level copy number alterations, and HLA loss of heterozygosity.

68 Mutations, copy number alterations, and Merkel cell polyomavirus (M

69 tures consistent with aging tissues, minimal copy number alterations, and no genomic rearrangements.

70 enetic abnormalities: chimeric gene fusions, copy number alterations, and single-nucleotide variants.

71 etic alterations -somatic mutations, somatic copy number alterations, and structural variants-in a co

72 requency of single-nucleotide variations and copy number alterations, and underline the importance of

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

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

75 Chromosomal copy number alterations (aneuploidy) define the genomic

76 average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-leve

77 Acquired chromosomal instability and copy number alterations are hallmarks of cancer.

78 While chromosome 9p24.1 copy-number alterations are ubiquitous in cHL, they also

79 Copy-number alterations are widespread in animal and pla

80 than 75% of the genome is subject to somatic copy number alterations, are associated with a potential

81 c events, including intragenic mutations and copy number alterations, are required.

82 We also identify higher number of copy number alterations as a risk factor for recurrence,

83 lated genes in HCCs, we integrated their DNA copy-number alterations as determined by aCGH data and c

84 Set Enrichment Analysis coupled with genomic copy number alteration assessment revealed that YY1-asso

85 replication stress and an abundance of focal copy-number alterations associated with activation of th

86 e expression and array CGH data revealed DNA copy number alterations at the ATF4 locus, an important

87 acterized by a distinct immunophenotype, DNA copy number alterations at the rearrangement sites, olde

88 Copy-number alterations became prevalent only in invasiv

89 and, studies in microorganisms show that DNA copy-number alterations can be beneficial, increasing su

90 We compared gene expression profiles and DNA copy number alteration (CNA) data from 29 normal prostat

91 ation between relapse and the pattern of DNA copy number alteration (CNA) in 168 primary tumors, rais

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

93 cer and normal cells makes the estimation of copy number alteration (CNA) possible, even at very low

94 Specifically, copy number alteration (CNA) profiles generated by next-

95 is of analysis of both somatic mutations and copy number alterations (CNA) across a 641 cancer-associ

96 Somatic copy number alterations (CNA) are found in most aggressi

97 paired gene expression profiles and somatic copy number alterations (CNA) information on the same pa

98 ool (Linux commandline or web-interface) for copy-number alteration (CNA) analysis and tumor purity e

99 SERTING), an algorithm for detecting somatic copy-number alteration (CNA) using whole-genome sequenci

100 We identified differential copy-number alterations (CNA), mutations, DNA methylatio

101 patients with a marrow relapse for selected copy number alterations (CNAs) and mutations.

102 Identification of somatic DNA copy number alterations (CNAs) and significant consensus

103 WGS also delineated copy number alterations (CNAs) and structural variants i

104 otide polymorphism array profiling to detect copy number alterations (CNAs) and uniparental disomies

105 Whether somatic copy number alterations (CNAs) are a frequent cause of a

106 Somatic copy number alterations (CNAs) are a hallmark of cancer,

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

108 cell malignancy driven in part by increasing copy number alterations (CNAs) during disease progressio

109 Quantitative analysis of somatic copy number alterations (CNAs) has broad applications in

110 Both gene expression levels (GEs) and copy number alterations (CNAs) have important biological

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

112 Copy number alterations (CNAs) in cancer patients show a

113 , for the detection of somatic mutations and copy number alterations (CNAs) in exome data from tumor-

114 The accurate detection of copy number alterations (CNAs) in human genomes is impor

115 ic value of frequently detected somatic gene copy number alterations (CNAs) in mantle cell lymphoma (

116 We hypothesized that copy number alterations (CNAs) of intergenic nonprotein-

117 ere genomically unstable, with a median of 9 copy number alterations (CNAs) per case, many of such CN

118 Copy number alterations (CNAs) play an important role in

119 DLBCLs, we identified a comprehensive set of copy number alterations (CNAs) that decreased p53 activi

120 DNA copy number alterations (CNAs) were defined by using arr

121 than 99% for genotyping DNA samples without copy number alterations (CNAs), almost all of these algo

122 ubstitutions, insertions/deletions (indels), copy number alterations (CNAs), and a wide range of gene

123 matic mutations, chromosomal rearrangements, copy number alterations (CNAs), and associated driver ge

124 2 (28%) gene mutations, recurrent arm-length copy number alterations (CNAs), and focal alterations su

125 nd investigate the relationship between SVs, copy number alterations (CNAs), and mRNA expression.

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

127 R337H+ patients presented a higher number of copy number alterations (CNAs), compared to the R337H-.

128 e-wide single nucleotide alterations (SNAs), copy number alterations (CNAs), DNA methylation, and RNA

129 calized genes resulting from the presence of copy number alterations (CNAs), for which analysis of th

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

131 d in 12 patients; 3 of them showed identical copy number alterations (CNAs), in another 3 cases, MRD

132 Chaos3 tumors underwent recurrent copy number alterations (CNAs), particularly deletion of

133 th high ARID1A mutation rates typically lack copy number alterations (CNAs).

134 ina Omni 2.5 platforms were used to evaluate copy-number alterations (CNAs) and determine their assoc

135 Aneuploidy and copy-number alterations (CNAs) are a hallmark of human c

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

137 use their tumors share some chromosome-scale copy-number alterations (CNAs) but little-to-no single-n

138 fluencing folate pathway genes (mRNA, miRNA, copy number alterations [CNAs], SNPs, single nucleotide

139 significantly higher level of aneuploidy and copy number alterations compared with the carcinogen-ind

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

141 Neither MYB-NFIB fusion nor any copy number alteration correlated with survival.

142 , USO1, and ZNF668) in which NM/SSM-specific copy number alterations correlated with differential gen

143 oor outcome (reduced survival time); somatic copy number alterations correlated with expression of 27

144 It is commonly assumed that copy number alteration data can be modeled as piecewise

145 btypes, we analyzed exome, transcriptome and copy number alteration data from 167 primary human tumor

146 Human gene copy number alteration data, microarray expression data,

147 or mutations based on mutant allele data and copy number alteration data.

148 Furthermore, analyzing copy number alterations data from 1,547 cancer patients

149 Here, we obtained exome, transcriptome and copy-number alteration data from approximately 53 sample

150 Therefore, we integrated copy-number alteration data from the 8 most commonly del

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

152 t mutations, small insertions/deletions, and copy number alterations detected in the initial TNBC hum

153 Remarkably, we observe that copy number alteration detection could identify the geno

154 m 29 tissues (integrating somatic mutations, copy number alterations, DNA methylation, and gene expre

155 rvival using diverse molecular data (somatic copy-number alteration, DNA methylation and mRNA, microR

156 ive elongation factor E (NELFE), via somatic copy-number alterations enhanced MYC signaling and promo

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

158 equires "third-hit driver" mutations/somatic copy-number alterations found in non-DS leukemias.

159 Somatic copy number alterations frequently occur in the cancer g

160 , we performed a genome-wide analysis of DNA copy number alterations from 34 unique surgical CRPC spe

161 utomated tool that integrates SV candidates, copy number alterations, gene expression, and genome ann

162 e the growth of pediatric cancers, including copy number alterations, gene fusions, enhancer hijackin

163 We identify somatic copy number alterations, gene mutations and the basal ex

164 etic features, we identified several somatic copy-number alterations, gene mutations, and the basal e

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

166 ide variations However, detection of somatic copy number alteration has been substantially less explo

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

168 ng, we comprehensively map out the facets of copy number alteration heterogeneity in a cohort of brea

169 ss-species comparative analysis of recurrent copy number alterations identifies several candidate dri

170 s reveals the convergent effects of distinct copy number alterations impacting on common downstream p

171 s mutated in various diseases and regions of copy number alteration in cancer.

172 ype p53 harboring 1q gain, the most frequent copy number alteration in cancer.

173 LOY) is the most frequently detected somatic copy number alteration in leukocytes of men.

174 ultiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these ge

175 ptional responses to long-term selection for copy number alterations in cancer cells.

176 ivity (n = 52) as a framework to analyze DNA copy number alterations in combination with data from a

177 the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as e

178 ve identified large numbers of mutations and copy number alterations in human cancers.

179 ve in vitro and in vivo studies, we identify copy number alterations in key extracellular matrix prot

180 ncer genes to compare the gene mutations and copy number alterations in MCV-positive (n = 13) and -ne

181 de, high-resolution assessment of chromosome copy number alterations in mouse and human tissues.

182 We assessed single nucleotide variants and copy number alterations in mutDNA using Tagged-Amplicon-

183 ignaling pathway gene mutations (n = 10) and copy number alterations in MYC/MYCN (n = 6) and cell cyc

184 identified a distinctive pattern of somatic copy number alterations in Sezary syndrome, including hi

185 combined detection of single-nucleotide and copy number alterations in single cells in intact archiv

186 cing prognosis across all tumor types, while copy number alterations in the electron transport chain

187 Prevalent somatic copy number alterations in the MICA and MICB genes relat

188 ction and quantification of the absolute DNA copy number alterations in tumor cells is challenging be

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

190 ckpoint regulators, chromatin modifiers, and copy-number alterations in mediating selective response

191 y associated with an increase in genome-wide copy-number alterations in multiple human cancers.

192 TEN, TP53, STK11 and KRAS as well as several copy-number alterations in the pathogenesis of cervical

193 CTCs revealed a wide range of copy number alterations including those previously repor

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

195 We identify spatially distinct evolution of copy number alterations influencing local immune composi

196 Somatic copy number alterations involving the ESR1 gene occur in

197 int mutations or structural variants such as copy-number alterations is associated with an ~10-fold i

198 Somatic copy number alterations leading to allelic imbalance (AI

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

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

201 e highly similar at the level of global gene copy number alterations, loss of heterozygosity and sing

202 rated analysis of somatic mutations, somatic copy number alterations, low pass copy numbers, and gene

203 reast cancer heterogeneity by modeling mRNA, copy number alterations, microRNAs, and methylation in a

204 older age, genomic complexity, specific DNA copy number alterations, MK, and dismal outcome.

205 r mutation burden, frequency of mutations or copy number alterations, mutation signatures, intratumor

206 Somatic mutations, copy-number alterations, mutation load, and mutation sig

207 tory checkpoints, genome-wide frequencies of copy number alterations, mutational signatures in whole

208 s retain the histology, gene expression, DNA copy number alterations, mutations and treatment respons

209 kely to be missed, such as genes affected by copy number alterations, mutations in noncoding regions,

210 have been described, including mutations and copy number alterations, notably ERBB2 amplifications, t

211 y is a critical issue in the analyses of DNA copy number alterations obtained from microarrays.

212 Copy number alterations of 9p24.1/CD274(PD-L1)/PDCD1LG2(

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

214 Immune infiltration is correlated with copy number alterations of chromosome arm 6p, suggesting

215 Focal copy number alterations of ERG, IKZF1, PAX5, ETV6, RB1,

216 ent on the extra chromosome or are caused by copy number alterations of many genes that confer no obs

217 vating TP53 mutations, whereas 75% exhibited copy number alterations of TP53 or its upstream modifier

218 es that are due to the cumulative effects of copy-number alterations of many genes simultaneously.

219 Copy number alterations often occur in mitotic crises, a

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

221 have recently been shown to commonly harbor copy number alterations or mutations in the tumor suppre

222 ed; approximately 60% of patients carried no copy number alterations other than those detected by flu

223 ted with the acquisition of disease-relevant copy number alterations over time.

224 bility was partly explained by heterogeneous copy number alteration patterns or expression of a stemn

225 genomic rearrangements, and 323 segments of copy number alteration per tumour.

226 We identified a mean of 1.28 copy number alterations per case at diagnosis in both pa

227 ompared with t(14;18)(-) FL (mean, 0.77 vs 9 copy number alterations per case; P <001).

228 red-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; app

229 elevant somatic mutations and one high-level copy-number alteration per sample (range, 0-5 and 0-6, r

230 Taken together, our comprehensive view of copy number alterations provides a framework for underst

231 onsideration of additional features, such as copy number alteration, quantitative protein expression,

232 ith oncogenes, tumor suppressors and somatic copy number alterations related to cancer development.

233 andom patterns of clustered breakpoints with copy-number alterations resulting in interspersed gene d

234 ntegrative analysis of mutations and somatic copy-number alterations revealed frequent genetic altera

235 ected pituitary adenomas showed that somatic copy number alteration (SCNA) rather than mutation is a

236 transcriptomic data is confounded by somatic copy number alterations (SCNA), which produce co-express

237 Somatic copy-number alterations (SCNA) are a hallmark of many ca

238 characterized by the accumulation of somatic copy number alterations (SCNAs) and point mutations (PMs

239 er gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal.

240 Many cancer-associated somatic copy number alterations (SCNAs) are known.

241 line copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant impor

242 cale, we surveyed haplotype-specific somatic copy number alterations (sCNAs) in 1,708 normal-appearin

243 of driver loci underlying arm-level somatic copy number alterations (SCNAs) in cancer has remained c

244 PBRM1 mutations, del(14q) and other somatic copy number alterations (SCNAs) including amp(7), del(1p

245 oss of senescence, are of consistent somatic copy number alterations (SCNAs) involving chromosomal re

246 The resulting diversity in somatic copy number alterations (SCNAs) may provide the variatio

247 Determining how somatic copy number alterations (SCNAs) promote cancer is an imp

248 Detection of somatic copy number alterations (SCNAs) using high-throughput se

249 lation marks, somatic mutations, and somatic copy number alterations (SCNAs), among others - as predi

250 Here, we investigate ITH of somatic copy number alterations (SCNAs), DNA methylation, and po

251 Aneuploidy, also known as somatic copy number alterations (SCNAs), is widespread in cancer

252 Cancer genomes exhibit profound somatic copy number alterations (SCNAs).

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

254 In a genome-wide survey on somatic copy-number alterations (SCNAs) of long noncoding RNA (l

255 iR-4707-5p, PCAT1), were involved in somatic copy-number alterations (SCNAs) or structural variants (

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

257 Although copy number alterations showed strong cis- and trans-eff

258 Clustering copy number alterations shows that most cell lines resem

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

260 n), acquire somatic mutations and widespread copy number alterations similar to those observed in hum

261 ssion, exon expression, microRNA expression, copy number alteration, SNP, whole exome sequence, and D

262 .0001) and by a higher frequency of specific copy number alterations, such as -5/5q-, -7/7q-, -16/16q

263 lesions displayed numerous large chromosomal copy number alterations, suggesting they might precede s

264 Copy number alterations target multiple tumour suppressi

265 These cancers possessed copy number alterations targeting key loci in human T ce

266 s characterized by fewer mutations and fewer copy number alterations than LUADs from individuals of E

267 es, with fewer mutations, rearrangements and copy-number alterations than reported in other tumors in

268 ports an innovative analytical framework for copy number alterations that are oncogenic primarily owi

269 cancer is characterized by recurrent genomic copy number alterations that are presumed to contribute

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

271 s are characterized by non-random chromosome copy number alterations that presumably contain oncogene

272 after tumor initiation that largely reflect copy number alterations that target cellular processes o

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

274 K signaling, were among the most significant copy-number alterations that co-occurred with ERG genomi

275 ides a permissive landscape for selection of copy-number alterations that drive cancer proliferation.

276 DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-target

277 The presence of copy number alterations, the occurrence of multiple seed

278 oth exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altere

279 getable mutations but is defined by frequent copy-number alteration, the most common of which is gain

280 the detection of 'actionable' mutations and copy number alterations to guide treatment decisions, ac

281 We analyzed IR-induced tumors for copy number alterations to identify oncogenic changes th

282 e was pronounced intratumor heterogeneity in copy number alterations, translocations, and mutations a

283 n driver cancer gene alterations--mutations, copy number alterations, translocations, and/or chromoso

284 As DNA copy-number alterations underlie many human diseases, we

285 In animals, copy-number alterations usually exhibit dosage effects,

286 iver predictions with information on somatic copy number alterations, we find that the distribution a

287 In addition to copy number alterations, we observe a propensity of the

288 somatic structural variants, and 12 somatic copy number alterations were detected in the patient's l

289 Five recurrent copy number alterations were identified in PAs, includin

290 Co-occurring genomic mutations and copy number alterations were identified.

291 tion status, PTEN loss, EGFR expression, and copy number alterations were not associated with clinica

292 Significantly more copy number alterations were observed in the group with

293 AR mutations and/or copy number alterations were robustly detected in 48% (3

294 Somatic copy-number alterations were the major drivers of variat

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

296 this is a heterogeneous cancer dominated by copy number alterations with frequent large-scale rearra

297 The arrayCGH analysis revealed recurrent copy number alterations with losses involving 6q23-q27,

298 on associated with structure rearrangements, copy number alterations, with preferential amplification

299 These CYCLOPS (copy number alterations yielding cancer liabilities owin

300 er associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owin