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 to mediate rapid, directional ribosomal DNA copy number change.

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

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

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

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

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

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

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

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

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

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

15 intronic and intergenic regions to identify copy number changes.

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

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

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

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

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

21 ifying mutation percentage and integer value copy number changes.

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

23 ology-mediated chromosome rearrangements and copy number changes.

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

25 us recombination dysfunction, and widespread copy number changes.

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

27 of normalized read depth delineates relative copy number changes.

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

29 omparative genomic hybridization revealed 18 copy number changes.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

62 Chromosomal copy number changes are frequently associated with harmf

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

82 Copy-number changes detected in NIPT sequencing data in

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

148 3 enhanced RLGS fragments, indicative of DNA copy number changes, including gains of single alleles,

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

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

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

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

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

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

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

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

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

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

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

160 For copy number changes larger than three the effective reso

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

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

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

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

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

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

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

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

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

170 Copy number changes of 9 minimal regions significantly c

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

197 15 with losses) as well as miRNA genes with copy number changes that were unique to each tumor type.

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

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

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

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

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

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

204 Analysis of DNA copy number changes using comparative genomic hybridizat

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

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

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

208 Single copy number change was successfully detected and the res

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

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

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

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

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

214 No copy number changes were associated exclusively with met

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

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

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

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

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

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

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

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

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

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

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

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

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

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