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

3 rs are characterized by widespread recurrent copy number alterations.

4 analyses of breast cancer transcriptome and copy number alterations.

5 A-HNC) and correlate outcomes with EGFR gene copy number alterations.

6 by a modest number of recurrent or 'driver' copy number alterations.

7 ate and high-grade dysplasia showed frequent copy number alterations.

8 elic ratios to enhance the interpretation of copy number alterations.

9 nvestigated 108 adult astrocytic tumours for copy number alterations.

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

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

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

13 highly associated with specific mutations or copy number alterations.

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

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

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

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

18 alternative to DNA microarrays for detecting copy-number alterations.

19 entified 50 minimal common regions (MCRs) of copy number alterations, 28 amplifications, and 22 delet

20 H) calls was 96% (range, 91-99%) and for raw copy number alterations, 71% (range, 43-87%).

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

22 ofiling was developed to identify genes with copy number alterations, aberrant mRNA expression, and r

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

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

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

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

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

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

29 Copy number alteration analysis disclosed distinguishabl

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

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

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

33 iver genes within recurrent broad regions of copy number alteration and to delineate distinct oncogen

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

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 iations between alternative MYC/chromosome 8 copy number alterations and differential benefit of adju

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

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

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

41 ms of hepatocarcinogenesis, we characterized copy number alterations and gene expression profiles fro

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

43 te lymphoblastic leukemia samples, including copy number alterations and gene expression profiles.

44 arcinomas by integrating genome-wide data on copy number alterations and gene expression with full an

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

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

47 We examined DNA copy number alterations and loss of heterozygosity (LOH)

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

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

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

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

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

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

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

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

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

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

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

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 ons in key genes, including point mutations, copy-number alterations and structural rearrangements.

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

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

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

68 A subset of HNSCC manifests EGFR copy number alterations, and this is associated with a p

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

70 34% of the leukemias lacked any identifiable copy-number alterations, and 28% of the leukemias with r

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

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

73 Chromosomal copy number alterations (aneuploidy) define the genomic

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

75 Copy number alterations are independently and reiterativ

76 Copy-number alterations are widespread in animal and pla

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

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

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

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

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

82 We identified, in total, 159 copy number alterations at presentation and 231 at relap

83 apse by comparing the profiles of genomewide copy number alterations at presentation in 21 patients w

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

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

86 Copy-number alterations became prevalent only in invasiv

87 mias being characterized by a high number of copy-number alterations but rare point mutations.

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

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

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

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

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

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

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

95 DNA copy number alterations (CNA) frequently underlie gene e

96 Unsupervised cluster analysis of DNA copy number alterations (CNA) identified recurrent aberr

97 ive genomic hybridization (aCGH) to identify copy number alterations (CNA) in 58 ALL patients.

98 eported whole genome profiling of chromosome copy number alterations (CNA) in gliomas, and now presen

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

100 stability in cancer leads to abnormal genome copy number alterations (CNA) that are associated with t

101 urately both copy number variation (CNV) and copy number alterations (CNA).

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

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

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

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

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

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

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

109 lso has multiple ( approximately 6 per case) copy number alterations (CNAs) as revealed by genome-wid

110 Copy number alterations (CNAs) associated with cancer ar

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

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

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

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

115 tide polymorphism arrays to identify somatic copy number alterations (CNAs) in 20 diagnosis/relapse p

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

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

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

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

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

121 sed screening approaches permit detection of copy number alterations (CNAs) of less than 5 Mb in size

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

123 Among three loci demonstrating recurrent copy number alterations (CNAs) specific to the acquired

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

125 Acquired copy number alterations (CNAs) were confirmed using an u

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

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

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

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

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

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

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

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

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

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

136 enome-wide is the occurrence of regional DNA copy number alterations (CNAs), which may lead to deleti

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

154 Significant differences in copy number alterations distinguish childhood and adult

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

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

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

158 ound a strong enrichment in these regions of copy number alterations for 11 genes associated with the

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

160 eously surveying known somatic mutations and copy number alterations for translational studies in can

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

162 nomic hybridization data that considers both copy number alteration frequencies and the occurrence of

163 Somatic copy number alterations frequently occur in the cancer g

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

165 identify genomic regions that show recurrent copy-number alterations (gains and losses) in tumor geno

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

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

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

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

170 Integrated analysis of somatic mutations and copy number alterations identified another 35 significan

171 viously shown to be targets of recurring DNA copy number alteration in ALL.

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

173 To investigate this issue, we characterized copy number alterations in 191 breast tumors using dense

174 establish expression profiles and delineate copy number alterations in 30 primary neuroblastomas.

175 olymorphism array to analyze genome-wide DNA copy number alterations in 31 high-grade ovarian serous

176 In parallel, we analysed genome-wide DNA copy number alterations in 701 primary tumours.

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

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

179 ntified in these screens with an analysis of copy number alterations in colon cancer specimens.

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

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

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

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

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

185 In a screen for gene copy number alterations in mouse mammary tumors initiate

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

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

188 ic loci containing miRNA genes exhibited DNA copy number alterations in ovarian cancer (37.1%), breas

189 d several frequent, high-magnitude focal DNA copy number alterations in SCLC.

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

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

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

193 ve genomic hybridization" method to identify copy number alterations in the tumor samples.

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

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

196 report a large-scale project to characterize copy-number alterations in primary lung adenocarcinomas.

197 The known role of copy-number alterations in sporadic genomic disorders, c

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

199 Using a high-resolution screen for DNA copy-number alterations in Wilms tumor, we identified so

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

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

202 Somatic copy number alterations involving the ESR1 gene occur in

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

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

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

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

207 that pathway analysis of genes in regions of copy number alterations may uncover molecular mechanisms

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

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

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

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

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

213 cancer (72.8%), and melanoma (85.9%), where copy number alterations observed in >15% tumors were con

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

215 ecimens indicated that related AR intragenic copy number alterations occurred in CRPCa in the context

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

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

218 ate 376 known somatic mutations and quantify copy number alterations of genes commonly implicated in

219 In contrast, we observed frequent copy number alterations of genes in the pathway, includi

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

221 uction of p53 mutant protein, and finally by copy number alterations of PTEN and EGFR.

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

223 statistical analysis of the power to detect copy-number alterations of a given size; (ii) SegSeq, an

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

225 No copy-number alterations of MBD5 were observed in 7878 co

226 assays designed to detect these chromosomal copy number alterations on a genome-wide and high-resolu

227 through indirect gene activation rather than copy number alteration or mutation involving the MET gen

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

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

230 Patients whose tumors had EGFR copy number alterations (particularly patients with incr

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

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

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

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

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

236 lterations, with a mean of only 2.38 somatic copy-number alterations per leukemia, and less than 1 no

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

238 stimates, and may offer a simple solution to copy number alteration quantification for cancer sequenc

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

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

241 ese findings, analysis of regional recurrent copy number alterations revealed many more events unique

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

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

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

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

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

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

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

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

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

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

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

253 tive) selection, on the landscape of somatic copy-number alterations (SCNAs) in cancer.

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 We have addressed the issue of whether copy number alterations seen in tumor-derived cell lines

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

259 Clustering copy number alterations shows that most cell lines resem

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

261 This showed non-random patterns of copy number alterations significantly linked to EGFR and

262 Structural variants, copy number alterations, single-nucleotide variants, and

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

264 .0001) and by a higher frequency of specific copy number alterations, such as -5/5q-, -7/7q-, -16/16q

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

266 d patterns of DNA sequence, methylation, and copy number alterations support a model of ordered molec

267 Copy number alterations target multiple tumour suppressi

268 Most copy number alterations targeted chromosome 21, reinforc

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

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

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

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

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

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

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

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

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

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

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

280 Our study shows the feasibility of using copy number alterations to predict patient prognostic ou

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

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

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

284 e results define the major impact of genomic copy number alterations upon transcription within neurob

285 erations in this tumor type, we searched for copy number alterations using high-density microarrays a

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

287 1 (ERBB2) amplicon, the overall frequency of copy number alterations was higher in invasive tumors th

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

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

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

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

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

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

294 onclude that cigarette smoking leads to more copy number alterations, which may be mediated by the ge

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 We hypothesized that tumor DNA copy number alterations would allow the identification o

299 These CYCLOPS (copy number alterations yielding cancer liabilities owin

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