ライフサイエンスコーパス: copy number

1 ly estimates the cancer cell fraction and SV copy number.

2 restriction was highly related to enFeLV-LTR copy number.

3 gene expression, DNA replication, and genome copy number.

4 utions and, finally, contraction of the gene copy number.

5 sposition, as well as independent of genomic copy number.

6 y level of infection, virus titer and genome copy number.

7 ated mtDNA transcription and a reduced mtDNA copy number.

8 C580Y) plus increased plasmepsin2 and Pfmdr1 copy numbers.

9 associated with local variations in genomic copy numbers.

10 on of SOX18 caused a decrease of KSHV genome copy numbers.

11 urviving patients demonstrated stable vector copy numbers (0.4-1.8 copies per neutrophil) and the per

12 tant isolates also had increased plasmepsin2 copy number (75.9%; 85/112).

13 nd MYD88(L265P) mutation and the genome-wide copy number aberration (CNA) profiles of individual vitr

14 Significantly higher somatic copy number aberration and allelic imbalance burdens are

15 that contain the 17q23 amplicon, a recurrent copy number aberration that defines about 9% of all prim

16 ifferent molecular events, including somatic copy number aberration, may be a common characteristic o

17 DNA copy number aberrations (CNA) are frequently observed in

18 Somatic copy number aberrations (CNAs) have been implicated in t

19 Copy number aberrations (CNAs), which are pathogenic cop

20 detect single nucleotide variants (SNVs) and copy number aberrations (CNAs), while MutSigCV (SNVs) an

21 at molecular subtypes are linked to specific copy number aberrations in genes such as mutant KRAS and

22 syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to vari

23 reveal acquisition of somatic mutations and copy number aberrations over time.

24 s limited their use to the analysis of large copy-number aberrations (CNAs) in individual cells.

25 We identified extensive allele-specific copy-number aberrations (CNAs) in these samples, includi

26 arch studies to identify clinically relevant copy number abnormality (CNA) profiles.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

45 Copy number alterations often occur in mitotic crises, a

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

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

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

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

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

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

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

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

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

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

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

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

58 genes and pathways preferentially mutated or copy-number altered in metastases compared with the pair

59 Four regions were preferentially copy-number altered: loss of STK11 and CDKN2A/B, as well

60 f the built environment with leukocyte mtDNA copy number among 5,502 Mexican American adults enrolled

61 l DNA (ecDNA) as the primary driver of focal copy number amplification (fCNA) - enabling gene amplifi

62 n more than 40% of cancer cells and that MYC copy number amplification correlates with enhanced trans

63 link observed between salivary amylase gene copy number (AMY1 CN) and weight management is likely mo

64 disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and

65 Allele-specific copy number analysis of tumors (ASCAT) assesses copy num

66 ing a novel integrative analysis of absolute copy-number analysis and gene expression in The Cancer G

67 eveal the average replication dynamics using copy-number analysis in any proliferating asynchronous c

68 able ultrasensitive molecular imaging of low-copy number analytes in biospecimens with high autofluor

69 rthermore, specific pattern and abundance of copy number and DNA methylation changes at these TFs and

70 ifying species- and cell-type-specific mtDNA copy number and dynamics in any normal or diseased tissu

71 correlation between endogenous FeLV (enFeLV) copy number and exogenous FeLV (exFeLV) infection outcom

72 approach that concurrently measures genomic copy number and exome mutations from archival cryostored

73 here was a positive correlation between ADAR copy number and expression.

74 We analyzed the variation in NLR gene copy number and identified plants with a low number of N

75 Allele-specific copy number and serial sampling analyses allowed for the

76 of single nucleotide polymorphisms and many copy number and structural variants.

77 muscle fibers without altering mitochondrial copy number and the abundance of proteins for oxidative

78 uctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphis

79 ses to transgenes and autoantibodies, vector copy number, and integration were evaluated.

80 exposures, we measured cell viability, mtDNA copy number, and mitochondrial bioenergetics utilizing t

81 are increases in mitochondrial size, genome copy number, and transcript levels.

82 length, accounts for the numerical nature of copy numbers, and accommodates between- and within-locus

83 D. melanogaster, TART-A is present at higher copy numbers, and nxf2 shows reduced expression, compare

84 suggest that parasites with increased pvdbp copy number are able to infect individuals with naturall

85 ns in mitochondrial DNA (mtDNA) sequence and copy number are implicated in aging and organ dysfunctio

86 MGMT promoter methylation were determined by copy-number arrays and/or Illumina 450K array, respectiv

87 pproach, including targeted gene sequencing, copy-number arrays, and gene expression profiling.

88 d conserved in canonical sequence motifs and copy numbers as in E. maclovinus, showing limited impact

89 transposable elements, independent of their copy number, as well as microbiome composition.

90 Given their high copy numbers, B2 and ALU may represent the predominant r

91 ful segregation, or "partition," of many low-copy number bacterial plasmids is driven by plasmid-enco

92 nd domestic cats had similar exFeLV proviral copy numbers, but Florida panther tissues have higher Fe

93 By clustering copy number calls, we reconstructed histories of chromos

94 ing 3 to 20 copies of NPNA revealed that low copy number can reduce the abundance of low-affinity mon

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

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

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

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

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

100 This effect increases with decreasing copy number, closely associated with the amplification f

101 systems that other than loss of RB1 few gene-copy number (CN) alterations are associated with irrever

102 DNA copy number (CN) profiling of ensembles of tumors allows

103 escribe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal d

104 stently high, with some AMR genes present at copy numbers comparable to the bacterial 16S rRNA gene.

105 Changes in gene copy number contribute to genomic instability, the onset

106 By analyzing patient copy-number data, we demonstrate that specific aneuploid

107 ctious in liver-humanized mice with high RNA copy numbers detectable in serum and feces.

108 The dPCR-based SMA copy number determination was accomplished in 90 min wit

109 fining epiclones that can match or transcend copy number-determined clonal lineages and opening up an

110 pular model for copy number evolution is the copy number distance (CND), defined as the length of a s

111 riation in timings between replicates at low copy number due to the LAMP amplification mechanism.

112 mutations in RAS and KIT and the widespread copy number events by which TGCT is characterised.

113 it challenging to accurately detect abnormal copy number events in a cost-effective manner in clinica

114 However, modeling copy number evolution is a substantial challenge, becaus

115 A recent popular model for copy number evolution is the copy number distance (CND),

116 Copy number expansion of auxin-related genes from duplic

117 tly increase antigen diversity and to enable copy number expansion of genes that contribute to drug r

118 data are consistent with a model in which 3B copy number expansion within the FMDV genome has allowed

119 lay evolution experiments revealed transient copy number expansions, the contingency of lineage outco

120 ABC-transporter copy number, expression and activity were examined using

121 XRN2 alterations (mutations, copy number/expression changes) are frequent in cancers.

122 The median copy numbers for peak shedding were 1.99 x 107 (interqua

123 geting repetitive elements-ranging in target copy number from about 32 to 161 000 per cell.

124 ylation of these segments associated with AR copy number gain.

125 Focal copy-number gain in CCNE1 and CDKN2A deletion was enrich

126 the optimal diagnostic cut-off point for MET copy number gains identified using fluorescence in situ

127 ce in control subjects, complete coverage in copy number gains, and presence in the minimal region co

128 onstrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and

129 varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements.

130 kin lymphomas (cHLs), which exhibit frequent copy-number gains of CD274 (PD-L1) and PDC1LG2 (PD-L2) o

131 s postulates that there is selection on gene copy number (gene dosage) to preserve the stoichiometric

132 l lines for TERT promoter mutational status, copy number, gene expression, and telomere length to pro

133 pplied to other polyploid cell lines or high-copy-number genes.

134 The burden of large and rare copy number genetic variants (CNVs) as well as certain s

135 copy number group (< median) and high mtDNA copy number group (>= median).

136 udy population was stratified into low mtDNA copy number group (< median) and high mtDNA copy number

137 Low copy numbers (>=500 copies/reaction) of SARS-CoV-2 RNA w

138 for Measuring Plasmid Retention) to measure copy number heterogeneity and 2mu plasmid loss in live c

139 ) within the tumor mass; the extent to which copy number heterogeneity impacts breast cancer genomes

140 somal amplifications; and the association of copy number heterogeneity with clinical and biological p

141 duce HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity), an algorithm that infers all

142 ike the highly polymorphic UAA UDA has a low copy number in elasmobranchs but is multicopy in the hol

143 section ratio) may influence levels of mtDNA copy number in leukocytes in Mexican Americans.

144 We found that the HER2 gene copy number in liquid biopsy was higher in GC and EGJC p

145 Genetic reduction of Cx43-copy number in mdx/WT-Cx43(+/-) chimeras protected them

146 gnificantly affect levels of leukocyte mtDNA copy number in Mexican Americans.

147 exing dPCR assay for measuring SMN1 and SMN2 copy numbers in spinal muscular atrophy (SMA) samples ha

148 by an accordion mechanism in which the gene copy number increases followed by base substitutions and

149 Focal copy-number increases (genomic amplification) pinpoint o

150 e computation, and mitochondrial DNA (mtDNA) copy number inference.

151 V using the segmentation function to measure copy number inflection points throughout the genome.

152 uantification of nucleic acid targets at low copy number is problematic with the limit of detection a

153 In addition, greater repeat copy number is significantly enriched in three independe

154 Centriole copy number is tightly maintained by the once-per-cycle

155 paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequen

156 rom the meiotic mobilization of specific low-copy number long-terminal repeat (LTR) retrotransposons,

157 Copy number loss of chromosome 22q, leading to loss of h

158 RNA variations among subtypes correlate with copy number loss of RP genes.

159 and in female subjects de novo heterozygous copy number loss or truncating mutations cause haploinsu

160 cantly greater in invasive ADC, whereas more copy number loss was observed in AIS and MIA.

161 levels of oncogene transcription compared to copy number-matched linear DNA, coupled with enhanced ch

162 Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that

163 Analysis of TME cell composition, DNA copy number, mutations and gene expression showed that i

164 tected by cytogenetics, and their associated copy number neutral loss of heterozygosity (CN-LOH) were

165 ncreased odds of having high levels of mtDNA copy number [Odds ratio (OR) = 1.24, 95% confidence inte

166 n reducing the level of infection and genome copy number of all viruses investigated than either pre-

167 While the total copy number of large multi-megabase segments can be deri

168 Here, we determine by mass spectrometry the copy number of nineteen chemosensory signaling proteins

169 Reduced copy number of ribosomal protein (Rp) genes adversely af

170 of studies, our knowledge about the protein copy number of TFs in the nucleus is limited.

171 We found that patients with a high copy number of the HER2 gene in the tumor tissue assesse

172 DNA image cytometry profiles, enumeration of copy numbers of eight breast cancer genes by multicolor

173 plication events have significant impacts on copy numbers of genes related to terpene and benzenoid/p

174 Although lower copy numbers of HIF1A (encoding HIF1alpha, located at 14

175 HPC-treated wastewater showed higher copy numbers of intI1 in the irrigated soil than chlorin

176 that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations o

177 e in the hardening behavior when the correct copy numbers of proteins are used.

178 e allowed for quantification of the absolute copy numbers of total and circular HBV DNA, and calculat

179 We show that copy numbers of triptolide biosynthetic pathway genes ar

180 und negative dose-response associations with copy number on intracranial volume and on regional cauda

181 cer target antigen (Ag) is expressed at high copy numbers on neoplastic cells, absent on normal tissu

182 exon 14 alteration, concurrent increased MET copy number or the detection of a MET exon 14 alteration

183 -type (WT) gene, due to either variations in copy number or transcriptional regulation, have also bee

184 ncreased odds of having high levels of mtDNA copy number (OR = 1.12, 95% CI 1.01, 1.27).

185 icant between groups with low and high mtDNA copy number (P < 0.001 and 0.002, respectively).

186 s was accompanied by lower mitochondrial DNA copy numbers (p < 0.001), mtND1 expression (p < 0.001) a

187 Analysis of copy numbers per cell of >7000 proteins provides new und

188 are carried almost exclusively on large, low-copy-number plasmids (pCRE).

189 ession by incrementally increasing GPCR gene copy number potentiates Galpha coupling of the pharmacol

190 a new kernel-based test called CONCUR (i.e., copy number profile curve-based association test) that i

191 CONCUR is built on the proposed concepts of "copy number profile curves" to describe the CNV profile

192 ation of the IGH, MYD88(L265P) mutation, and copy number profile enables VRL diagnosis.

193 atistics were used to summarize mutation and copy number profile.

194 otype associations by comparing individuals' copy number profiles across the genomic regions.

195 ods is very important for obtaining accurate copy number profiles from single-cell DNA sequencing dat

196 present the mutational, transcriptional, and copy number profiles of 560 Malaysian breast tumours and

197 Clustering analysis of the copy number profiles revealed that malignant B cells der

198 Copy number profiles, representing the number of copies

199 Deep-exome sequencing and genomic copy number profiling are performed on 23 patients, incl

200 We perform DNA copy number profiling on mixtures of cell lines, nuclei

201 Genome-wide copy number profiling revealed a high degree of similari

202 ly, the cellular mechanisms regulating mtDNA copy number remain poorly understood.

203 reater estimated N-cycle gene and transcript copy numbers, respectively, in AM relative to ECM soil.

204 tibility and FeLV long terminal repeat (LTR) copy number, similar to observations in natural FeLV inf

205 However, the effects of antigen copy number, spacing and affinity, as well as the dimens

206 is profiles display oscillations between two copy-number states, a considerable fraction of events in

207 allele frequency patterns, to infer the true copy number status of genes and genomic regions from who

208 n does not, however, correlate with FeLV env copy number, suggesting that this effect is specific to

209 NA replication results in an increase in DNA copy number that can be measured by high-throughput sequ

210 of mitochondrial activity and altered mtDNA copy number that result in organ dysfunction in aging an

211 Based on the median levels of mtDNA copy number, the study population was stratified into lo

212 espite a significant increase in bla(TEM-1B) copy number, the TZP-resistant isolate does not incur a

213 CoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution).

214 rley, there is evidence that changes in gene copy number underlie important agronomic traits.

215 shed common variant, rare coding variant and copy number variant data, we examined the relationship b

216 ion and performed whole-exome sequencing and copy-number variant (CNV) analysis of the tumors.

217 actions from these samples with whole-genome copy-number variant (CNV), whole-exome sequencing, and A

218 Some rare copy number variants (CNVs) are associated with schizoph

219 Deleterious copy number variants (CNVs) are identified in up to 20%

220 Copy number variants (CNVs) are pervasive in several ani

221 Copy number variants (CNVs) are suggested to have a wide

222 Copy number variants (CNVs) are the gain or loss of DNA

223 16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism

224 Carriers of large recurrent copy number variants (CNVs) have a higher risk of develo

225 Specific copy number variants (CNVs) have been robustly associate

226 licated numerous risk loci including several copy number variants (CNVs) of large effect and hundreds

227 Functional impact of copy number variants (CNVs) stems from both the proporti

228 inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods

229 DFT1 gradually accumulates copy number variants (CNVs), and its telomere lengths ar

230 in the minimal region common to overlapping copy number variants (CNVs), as well as on protein-prote

231 e biologically important information such as copy number variants (CNVs).

232 th facial morphological variants and genetic copy number variants (CNVs).

233 SNVs), recessive/homozygous SNVs, or de novo copy number variants (CNVs); however, most ASD cases con

234 variants/indels (dnSNVs/indels) and de novo copy number variants (dnCNVs).

235 De novo genic and copy number variants are enriched in patients with conge

236 egmental duplications overlap with recurrent copy number variants associated with neurocognitive diso

237 n polymorphisms that predispose to recurrent copy number variants associated with neurodevelopmental

238 participants carrying at least one of the 12 copy number variants associated with schizophrenia in UK

239 e-learning algorithms, we identified de novo copy number variants at 15q25.2 and 15q11.2 as being ass

240 ms through which highly penetrant, multigene copy number variants contribute to disease risk.

241 Furthermore, csa1 copy number variants differ in their immunostimulatory c

242 s and individual genes through which 22q11.2 copy number variants may confer risk for each disorder.

243 individuals who did not carry any of the 93 copy number variants reported to be pathogenic.

244 These assemblies reveal structural and copy number variants that differentiate the subspecies a

245 , and 13 fall within loci recurrently hit by copy number variants.

246 Large copy-number variants (CNVs) are strongly associated with

247 Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for

248 Gene copy number variation (CNV) could be detected in these p

249 ability of somatic point mutation (SPM) and copy number variation (CNV) data, gene-level and pathway

250 Cancer associated copy number variation (CNV) events provide important inf

251 Copy number variation (CNV) has been examined in many sp

252 Accurate interpretation of genomic copy number variation (CNV) remains a challenge and has

253 These results show that gene copy number variation affect the parasite's ability to e

254 Mutational and copy number variation analysis of a large cohort of pati

255 t assessed by next-generation sequencing and copy number variation analysis, 3 molecular subtypes wit

256 scribe a computational method HiNT (Hi-C for copy Number variation and Translocation detection), whic

257 apacity, revealing a mechanism by which gene copy number variation can modulate the host immune respo

258 nvolution of subclones that have independent copy number variation events within the same chromosome

259 Gene copy number variation is a predominant mechanism used by

260 Here, we demonstrate that copy number variation of TdDof, a gene encoding a putati

261 of this study is to evaluate expression and copy number variation of the ADAR gene in advanced GC an

262 Copy number variation of the peripheral nerve myelin gen

263 The authors combined data from 11 published copy number variation studies in 6,176 individuals with

264 n parallel with technology, from analyses of copy number variation to whole-exome sequencing (WES) an

265 ADAR gene expression and copy number variation were measured by real-time PCR and

266 next-generation sequencing and whole-genome copy number variation.

267 ic cells is revealed by analyses of inferred copy-number variation and trajectory.

268 y number analysis of tumors (ASCAT) assesses copy number variations (CNV) while accounting for aberra

269 Some copy number variations (CNV), associated with novel subt

270 urodevelopmental disorders caused by genomic copy number variations (CNVs) and gene expression data f

271 nables simultaneous detection of whole-exome copy number variations (CNVs) and point mutations in cod

272 functional effects of somatic mutations and copy number variations (CNVs) not evident in transcripto

273 Copy number variations (CNVs) of the human 16p11.2 genet

274 22q11.2 deletions and duplications are copy number variations (CNVs) that predispose to develop

275 karyotyping analysis, none of the predicted copy number variations (CNVs) were identified, which con

276 cleotide variations (SNVs) to large, complex copy number variations (CNVs), have been reported in pat

277 tory genes (SRGs) uncovers prevalent genomic copy number variations (CNVs), leading to mis-expression

278 ber aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in

279 e generated from 13 individuals with 16p11.2 copy number variations (CNVs).

280 and Translocation detection), which detects copy number variations and interchromosomal translocatio

281 ogenic mutations, whole genome mutations and copy number variations between primary and metastatic tu

282 3, and ATM SNVs), and MYC (translocations or copy number variations) were all independent risk factor

283 oci to detect mutations, translocations, and copy number variations, along with histomorphological an

284 e nucleotide variants, insertions/deletions, copy number variations, and translocations at a single t

285 ngs demonstrate a mechanism by which smaller copy number variations, not including the Pmp22 gene, ar

286 e human 16p11.2 gene locus is a hot spot for copy number variations, which predispose carriers to a r

287 g rare genomic events leading to HL, such as copy number variations.

288 e, there was no evidence of chromosome-level copy number variations.

289 s), small insertions and deletions (indels), copy-number variations (CNVs), loss of heterozygosity (L

290 pression data, with optional corrections for copy-number variations and able to run on signatures gen

291 erived cells with NF1 mutations also carried copy-number variations in CDKN2C, PTEN, and REL genes.

292 Mitochondrial copy number varies greatly within and across cancers and

293 anges in microbiome diversity, mean AMR gene copy number was consistently high, with some AMR genes p

294 PHIP copy number was elevated in the classical glioblastoma s

295 No further increase in mtDNA copy number was observed upon depletion of Pim1 in Delta

296 in mean HFMSE score, whereas gender and SMN2 copy number were not.

297 SMN1 and SMN2 copy numbers were completely concordant with previous re

298 at enFeLV env and long terminal repeat (LTR) copy numbers were determined for each individual and com

299 Total DNA was isolated and mtDNA copy numbers were determined using absolute quantificati

300 Changes in TE copy numbers were not predicted by the level of evolutio