ライフサイエンスコーパス: copy number change

1 evolved in a similar manner with respect to copy number change.

2 whose expression is consistently altered by copy number change.

3 l minimal common regions (MCRs) of recurrent copy number change.

4 er mutations in cancer genes and patterns of copy number change.

5 to mediate rapid, directional ribosomal DNA copy number change.

6 of normalized read depth delineates relative copy number changes.

7 cal importance for the accurate detection of copy number changes.

8 omparative genomic hybridization revealed 18 copy number changes.

9 A subset of pediatric HGGs showed minimal copy number changes.

10 mes 1, 3, 6, and 8 were tested with MLPA for copy number changes.

11 ent but still considerable (18%) large-scale copy number changes.

12 ed under purifying or positive selection for copy number changes.

13 food intake, can be associated with specific copy number changes.

14 ith more LOH changes had significantly fewer copy number changes.

15 ibit one of three 'signatures' based on gene copy number changes.

16 s caused by cancer-associated aneuploidy and copy number changes.

17 DNA and increase our ability to detect gene copy number changes.

18 ellite-stable CRCs, often in the form of HLA copy number changes.

19 us NAFLD/NASH biopsies did not harbor clonal copy number changes.

20 for point mutations, structural variants and copy number changes.

21 n levels as low as 0.1%, even in presence of copy number changes.

22 s in tumor samples, which frequently display copy number changes.

23 intronic and intergenic regions to identify copy number changes.

24 tion/deletions, and >6,000 genes affected by copy number changes.

25 ied to calculate probabilities (p-values) of copy number changes.

26 matched normal were analyzed for genome-wide copy number changes.

27 ction of genome altered and whole chromosome copy number changes.

28 here bulk allele frequencies are affected by copy number changes.

29 ciations with gene expression, sequence, and copy number changes.

30 ifying mutation percentage and integer value copy number changes.

31 umber of somatic mutations and the burden of copy number changes.

32 ology-mediated chromosome rearrangements and copy number changes.

33 cleotide variants, insertions, deletions and copy number changes.

34 ic hybridization to assess gross chromosomal copy number changes.

35 us recombination dysfunction, and widespread copy number changes.

36 rrently deleted regions with a high level of copy number changes.

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

38 y available genomic resource for mapping DNA copy-number changes.

39 lified and higher expression correlated with copy-number changes.

40 f genes that show common and highly variable copy-number changes.

41 EZH2 mutations or perturbed gene dosage for copy-number changes.

42 ty to detect all types of rearrangements and copy number changes; (2) straightforward integration of

43 ion by narrowing the spectrum of deleterious copy-number changes; (2) Environmental context and cispl

44 a widespread method for the analysis of DNA copy number changes across the human genome.

45 sis, we previously observed whole chromosome copy number changes affecting all lymphoma cells.

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

47 Copy number changes affecting chromosomes 15 and 19 occu

48 of ctDNA assays detecting fusion events and copy number changes, although ctDNA assays may be routin

49 er address these two issues, we assessed DNA copy number changes among affinity-purified tumor cells

50 d for greater resolution in detection of DNA copy number changes (amplifications or deletions) across

51 Comparing gene copy number change and RNA expression changes profiled o

52 data suggest that CIN is not synonymous with copy number change and some cancers have a specific tend

53 nt mutations, small insertions or deletions, copy number changes and chromosomal rearrangements.

54 astic leukemia (iAMP21-ALL) characterized by copy number changes and complex rearrangements of chromo

55 composition makes it possible to detect both copy number changes and copy-neutral loss-of-heterozygos

56 developed to recreate different scenarios of copy number changes and depth of coverage by altering a

57 ied subtypes characterized by concordant DNA copy number changes and gene expression as well as uniqu

58 Genome-wide analysis of DNA copy number changes and gene expression led to the ident

59 olorectal carcinomas that integrated genomic copy number changes and gene expression profiles.

60 high-resolution map of structural variants, copy number changes and global genome features including

61 high-resolution map of structural variants, copy number changes and global genome features including

62 The simultaneous measurement of DNA copy number changes and loss of heterozygosity events by

63 sociated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events.

64 y enrolled AML patients for acquired genomic copy number changes and loss of heterozygosity using Aff

65 Significance: Profiling of the genomic copy number changes and mutations in circulating tumor D

66 amine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of

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

68 genes and cellular pathways affected by both copy number changes and point alterations.

69 ily simplex families have implicated de novo copy number changes and point mutations, but are not opt

70 s a complex genomic landscape, with frequent copy number changes and point mutations, but genomic rea

71 the circadian genes' omics profile, such as copy number changes and RNA-sequence data along with the

72 -comparative genomic hybridization (CGH) for copy number changes and single-copy number polymorphism

73 clocks while accounting for the presence of copy number changes and structural alterations, we ident

74 tures related to genome stability, including copy number changes and telomerase activity.

75 These were the presence of gross chromosomal copy number changes and the presence of mutations in GNA

76 ffective and robust strategy for identifying copy number changes and translocations in tumor genomes

77 here was no significant relationship between copy number changes and tumor stage or grade, the linked

78 ormed an integrated, genome-wide analysis of copy-number changes and gene expression profiles in 90 t

79 eveloped for the genome-wide analysis of DNA copy-number changes and methylation patterns, chromatin

80 eningiomas harbored more complex patterns of copy-number changes and rearrangements, including one tu

81 ions, to chromosome-level changes, including copy-number changes and structural variants.

82 geneity despite thousands of rearrangements, copy-number changes, and retrotransposon insertions.

83 ologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome.

84 Genomic copy number changes are associated with antifungal drug

85 Chromosomal copy number changes are frequently associated with harmf

86 ucial tumour suppressor genes, and segmental copy number changes are key mechanisms underlying the tr

87 ecifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.

88 Genome-wide DNA copy number changes are the hallmark events in the initi

89 eases, we will end with a discussion of gene copy-number changes as therapeutic targets.

90 sensory gene repertoires revealed functional copy number changes associated with ecomorphological ada

91 tify, in high-resolution regions of DNA, the copy number changes associated with outcome in patients

92 defects included loss-of-function mutations, copy-number changes associated with reduced expression,

93 ion (array-CGH) and detected significant DNA copy number change at many loci on most or all chromosom

94 array technology has facilitated studies on copy number changes at a genome-wide scale with high res

95 implicated in generating translocations and copy number changes at CFSs in cancers.

96 ogression at the cellular level that include copy number changes at the scale of single genes, entire

97 on of new driver alterations and large-scale copy-number changes at TIC borders.

98 rtition the whole genome into segments where copy numbers change between contiguous segments, and sub

99 from either protoplasts or stem explants for copy number changes by comparison of Illumina read depth

100 ldrich, UK) and detailed analysis of genomic copy number changes by high-resolution array-CGH.

101 falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tum

102 e dominated by either mutations (M class) or copy number changes (C class).

103 nt evidence has demonstrated that chromosome copy number changes can function as point mutation-indep

104 ed by these CNVs, as strong candidates whose copy number change causally underlies approximately 46%

105 We observed mutations and copy number changes characteristic of cancer and chart t

106 stablished PME genes; three with intronic or copy-number changes (CLN6, GBA, NEU1) and two very rare

107 milar de novo deletions and duplications, or copy number changes (CNCs), are now known to be a major

108 d that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the K

109 Large-scale rearrangements and copy number changes combined with different modes of clo

110 b or 100 kb to detect statistically distinct copy-number changes compared to the reference.

111 egions of SNP-LOH occurred in the absence of copy number change, comprising an average per cell line

112 Our understanding of how DNA copy number changes contribute to disease, including can

113 This begins to establish how copy number changes could originate during tumorigenesis

114 nd that the number of genes altered by major copy number changes, deletion of all copies or amplifica

115 act of these changes; (3) Fitness effects of copy-number changes depend on parental karyotype; and (4

116 Copy-number changes detected in NIPT sequencing data in

117 obe set for the visualization of chromosomal copy number changes directly in thin-layer cervical cyto

118 useful technique for identifying chromosomal copy number changes during tumor progression, and that t

119 to identify if small regions of genomic DNA copy number changes exist by using a high density, gene-

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

121 The reduction in copy-number changes, following shRNA treatment, was conf

122 Low-level copy number changes for two of the lines under analysis

123 A comparison of DNA copy number changes found in the cell lines with those r

124 of an otherwise wild-type sample, as well as copy number changes from cancers even in the context of

125 ed a new tool, Canvas, for identification of copy number changes from diverse sequencing experiments

126 e an R package, "ELViS," that analyzes viral copy number changes from DNA sequencing of whole viral g

127 ent quantitation of arm and chromosome-level copy-number changes from targeted sequencing data.

128 lue) or less than 11% (third quartile) total copy number changes had a better overall survival (log-r

129 oughout the genome, both high- and low-level copy number changes had a substantial impact on gene exp

130 Although some regions of copy number change harbor known oncogenes and tumor supp

131 Targeting copy number change has been disappointing; it is crucial

132 Detection of genomic copy number changes has been an important research area,

133 The ability to determine allele-specific copy number changes has only recently been described.

134 Enzymes capable of promoting site-specific copy number changes have yet to be identified.

135 y presented a major challenge when assessing copy number changes; however, ploidy-corrected copy numb

136 Cluster analysis based on copy number changes identified a large group of cancers

137 We compared the performance of CNVkit to copy number changes identified by array comparative geno

138 nsupervised hierarchical clustering based on copy number changes identified four clusters.

139 nal methodology to identify drivers of broad copy number changes, identifying PDGFA (chr7) and PTEN (

140 nother low-rate mutation process that causes copy number change in part or all of the duplicon.

141 ssor genes DBC2, CDH1, and TP53 to visualize copy number changes in 13 cases of synchronous DCIS and

142 can be of diagnostic help we determined DNA copy number changes in 186 melanocytic tumors (132 melan

143 We have analyzed copy number changes in 2419 patients referred for clinic

144 erial artificial chromosome clones to assess copy number changes in 44 archival breast cancers.

145 oximately 1 Mb, has been used to investigate copy number changes in 48 colorectal cancer (CRC) cell l

146 velop AneuFinder, which allows annotation of copy number changes in a fully automated fashion and qua

147 tion of the observed gene and chromosome arm copy number changes in a larger cohort of primary and me

148 DNA-based genomic microarrays to examine DNA copy number changes in a panel of prostate tumors and fo

149 sion, cfDNA sequencing revealed mutations or copy number changes in all patients tested, including cl

150 bstantiated by an intratumoral comparison of copy number changes in areas with radial and vertical gr

151 y, most cancer genes show less mutations and copy number changes in AYAs, including the noncoding TER

152 We have performed a genome-wide analysis of copy number changes in breast and colorectal tumors usin

153 provide tools to quantitatively measure DNA copy number changes in cancer and to map those changes d

154 tasets makes the identification of recurrent copy number changes in cancer, an important issue that c

155 th DNA microarray technology to measure gene copy number changes in cancer.

156 Here, we examine chromosome copy number changes in cancers from more than 1800 self-

157 27); however, in patients with a light iris, copy number changes in chromosome 3 and 8q had a greater

158 ession profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative g

159 ods and enables prioritization of pathogenic copy number changes in duplicated genes.

160 Here, we describe copy number changes in five previously unreported loci w

161 nucleotide polymorphism arrays to screen for copy number changes in glioblastoma multiforme (GBM), we

162 challenge to identify small genuine somatic copy number changes in high-resolution cancer genome pro

163 , genome-wide measurements of subchromosomal copy number changes in highly purified DNA from sorted C

164 ) to study gene amplifications and low-level copy number changes in HNSCC in order to locate previous

165 We found that selective copy number changes in immune-related genes may contribu

166 emonstrate the use of this array to identify copy number changes in mouse cancers, as well to determi

167 we highlight the causes and consequences of copy number changes in normal physiologic processes as w

168 , confirming and mapping clinically relevant copy number changes in patients with CDH+.

169 addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1-

170 unequal segregation can result in more rapid copy number changes in response to therapy than is possi

171 t mutations, amplifications, and chromosomal copy number changes in retinoblastoma.

172 nt probe amplification identified intragenic copy number changes in several samples including two whi

173 MO and to a lesser extent through concurrent copy number changes in SUFU and GLI2.

174 We examined copy number changes in the genomes of B cells from 58 pa

175 onstrate that HR-CGH allows the detection of copy number changes in the human genome at an unpreceden

176 were used to analyze DNA from patients with copy number changes in the pericentromeric region of chr

177 In these two patients, mutations and DNA copy number changes in the primary tumors appear to have

178 We compared gene copy number changes in the tumors based on histologic su

179 he spatial organization of DNA-level somatic copy number changes in tumors can provide insight to und

180 que that gives information about chromosomal copy number changes in tumors.

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

182 Copy-number changes in 1q, 16q, and 1p, and single-nucle

183 comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat synd

184 entify gene orientation, gene order and gene copy-number changes in a collection of genomes.

185 t analytic approach (SW-ARRAY) for detecting copy-number changes in array CGH data.

186 nucleotide polymorphism arrays to screen for copy-number changes in glioblastoma multiforme samples a

187 ogy has been applied to the detection of DNA copy-number changes in malignant tumors.

188 In a screen for gene copy-number changes in mouse mammary tumors, we identifi

189 DECIPHER catalogs common copy-number changes in normal populations and thus, by e

190 s that significantly correlated with genomic copy-number changes in primary HRS cells.

191 Genome-wide copy-number changes in the original NIPT samples and in

192 populations, the degree of the complexity of copy-number changes in those populations, and measures o

193 ns, including somatic sequence mutations and copy number changes, in breast, colon, and pancreatic ca

194 nt for the utility of technologies assessing copy number changes include the ability to interrogate r

195 gated, we observed localization and multiple copy number changes including deletions, duplications, a

196 We found 160 individuals that carry >10 Mb copy number changes, including 56 with whole chromosome

197 3 enhanced RLGS fragments, indicative of DNA copy number changes, including gains of single alleles,

198 cancer-associated loss of heterozygosity and copy number changes, including homozygous deletion and g

199 as are characterized by somatically acquired copy number changes, including loss of heterozygosity (L

200 We identified 14 regions of nonrandom copy-number change, including 7 regions of amplification

201 We show multiple regions of copy-number change, including alterations common in pros

202 Correlations among the regions with copy number changes indicate that losses of chromosomes

203 To uncover how chromosome copy number changes influence the cancer proteome, we co

204 rstanding the forces that drive and regulate copy number change is fundamental.

205 orithm the effective resolution for +/-1 DNA copy number changes is about 2 Mb.

206 The overall pattern of regions affected by copy number changes is consistent with cytogenetic data

207 The ability to accurately determine such copy number changes is critical in tracing and understan

208 Characterization of these DNA copy number changes is important for both the basic unde

209 cates that a specific pattern of chromosomal copy number changes is maintained in cell culture.

210 Characterization of these DNA copy-number changes is important for both the basic unde

211 For copy number changes larger than three the effective reso

212 those multiple colorectal cancer-associated copy number changes, many of which were also present in

213 imately 80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination.

214 that can lead to gene dysfunction, including copy number change, methylation, abnormal expression, mu

215 interface, investigators can easily observe copy number changes, mutations, and structural events in

216 Our comparison of copy-number changes, mutations and mRNA expression profi

217 The most frequent DNA copy number changes observed were losses of 9/9p (83%),

218 plied and optimized to infer locations where copy number changes occur.

219 mutations, in the form of large chromosomal copy number changes, occur in a small fraction of cases

220 ral variants in the human genome: 41% of all copy number changes occurred at sites of such copy numbe

221 hlights the role of structural variation and copy number change of susceptibility genes like ACAs in

222 Whilst copy number changes of 16q12 are common in breast cancer

223 analysis of recurrent somatic mutations and copy number changes of 720 genes.

224 Copy number changes of 9 minimal regions significantly c

225 aneuploid phenotypes are the consequence of copy number changes of a few especially harmful genes th

226 e confirmed recurrent and specific low-level copy number changes of chromosomes 7, 8, 13, 18, and 20,

227 ovo CNVs that we identified, three generated copy number changes of entire genes.

228 We assessed copy number changes of genes associated with hepatocarci

229 cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes

230 Analysis of cloned chromosome termini and of copy number changes of loci genome-wide using tiling arr

231 ue for neuroblastoma, where multiple genomic copy number changes of proven prognostic value exist.

232 umber states of two cells given evolution by copy number changes of single probes, all probes on a ch

233 Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both

234 e a quantitative and high-resolution view of copy number changes on a genome-wide scale.

235 icable means for systematic detection of DNA copy number changes on a genomic scale.

236 he potentially compensatory effects of mtDNA copy number changes on the process.

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

238 omic features in terms of somatic mutations, copy-number changes or structural variations.

239 oncordance in global gene expression and DNA copy number changes (P = 2.2 x 10(-16)).

240 ched' cluster showed significantly increased copy number changes (P=0.04).

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

242 outgrowth persistence or loss of sub-clones, copy number changes, polyclonality and/or spatial geneti

243 The identification of DNA copy number changes provides insights that may advance o

244 e than 16,000 insertion/deletion (indel) and copy number changes, providing an unprecedented genetic

245 d primarily focus on more prevalent stepwise copy number changes rather than large expansions.

246 lation of driver aberrations, including gene copy-number changes, rearrangements and mutations; howev

247 ers, but determining the clinically relevant copy number changes remains a challenge.

248 In particular, identification of copy number changes remains a challenging task due to th

249 ations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation

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

251 e and human CPC gene expression profiles and copy number changes revealed altered expression of genes

252 le-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signa

253 m mutation analysis (direct sequencing), DNA copy number changes (SNP-array), messenger RNA levels (q

254 subtypes also contained distinct genomic DNA copy number changes, some of which are similarly altered

255 de novo mutations, minisatellite mutations, copy-number changes, structural variants, genomic insert

256 to the group of genomic disorders caused by copy number changes that are mediated by the local genom

257 Common DNA copy number changes that are unlikely to be directly pat

258 The process of adaptation relies on gene copy number changes that arise at high rates, including

259 nsertions and deletions, rearrangements, and copy number changes that have been acquired over decades

260 s early genomic instability, specifically in copy number changes that may later be observed in EAC.

261 We identified 41 miRNA genes with gene copy number changes that were shared among the three can

262 15 with losses) as well as miRNA genes with copy number changes that were unique to each tumor type.

263 thresholds can be crossed by mass action of copy number changes that, on their own, are benign.

264 rther mechanistic insights into Alu-mediated copy-number change that are extendable to other loci.

265 mutational mechanism underlying such genomic copy number changes, the sequence determinants of NAHR l

266 However, when detecting low-level DNA copy number changes this technology requires the use of

267 very little consistent contribution of gene copy number change to RNA expression changes.

268 oes further transcriptomic reprogramming and copy number changes to acquire full resistance.

269 sing a bioinformatics pipeline that exploits copy number changes to quantify the emergence of treatme

270 urothelium-derived cell line for genome-wide copy number changes using array comparative genomic hybr

271 Analysis of DNA copy number changes using comparative genomic hybridizat

272 d that our new algorithm is suitable to call copy number changes using data from PCR-enriched samples

273 The pattern of copy number change was complex with multiple interstitia

274 The overall pattern of copy number change was strikingly similar between cell l

275 Single copy number change was successfully detected and the res

276 Tumor mutational load, with exclusion of copy number changes, was determined for each case and co

277 Twenty-three percent of the abnormal copy number changes we found are immediately flanked by

278 Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin

279 g, chromatin structure, DNA methylation, and copy number changes, we suggest that the major contribut

280 Deletion of 7q11.21 is a benign copy number change well represented in control populatio

281 Genome-wide copy number changes were analyzed in 70 primary human lu

282 No copy number changes were associated exclusively with met

283 Frequent copy number changes were associated with concordant chan

284 Copy number changes were detected in cfDNA of 10 patient

285 One hundred and five putative copy number changes were identified by aCGH in our cohor

286 Consistent copy number changes were identified, including gain of c

287 Genome-wide copy number changes were monitored using array comparati

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

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

290 Copy number changes were rapid and dynamic during adapta

291 SNP loci with LOH and copy number changes were validated by sequencing and qua

292 re-replication may be a contributor to gene copy number changes, which are important in fields such

293 on framework to identify regions of discrete copy-number changes while simultaneously accounting for

294 The systematic comparison of segments of copy number change with gene expression profiles showed

295 available and correlate frequently occurring copy number changes with disease outcome.

296 osome 6 tile path array is useful in mapping copy number changes with high resolution and accuracy.

297 ion lines of Caenorhabditis elegans for gene copy-number changes with array comparative genomic hybri

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

299 ipotent stem cells and induced neurons, gene copy number change within the 15q13.3 microdeletion was

300 ions, including mutations, gene fusions, and copy number changes, within this well-defined cohort of