ライフサイエンスコーパス: segmental duplication

1 n events were frequently found in regions of segmental duplication.

2 version accounts for less than 10% of recent segmental duplication.

3 by massive sequence loss and divergence, and segmental duplication.

4 in a single diploid genome are the result of segmental duplication.

5 ted degree of recent (<35 million years ago) segmental duplication.

6 ng high-identity and copy-number-polymorphic segmental duplication.

7 me has been subjected to the highest rate of segmental duplication.

8 tion, whereas most snaR genes have spread by segmental duplication.

9 attributable to whole genome duplication and segmental duplication.

10 gone two rounds of large-scale genome and/or segmental duplication.

11 nome is relatively repetitive but has little segmental duplication.

12 ge arrays of satellite DNA and surrounded by segmental duplications.

13 ed with high GC content, repeat elements and segmental duplications.

14 mplex mosaics of fragments of numerous other segmental duplications.

15 esence of highly homologous intrachromosomal segmental duplications.

16 gene families with genomic features, such as segmental duplications.

17 homologous groups that resulted from recent segmental duplications.

18 duplication and subsequent species-specific segmental duplications.

19 resulted from unequal crossing-over between segmental duplications.

20 he gene family has evolved through local and segmental duplications.

21 genes, disease loci, functional elements and segmental duplications.

22 clustered and preferentially associated with segmental duplications.

23 quences (Srpt),and an additional 2.11 Mb are segmental duplications.

24 n genome is particularly enriched for recent segmental duplications.

25 elopmental delay and epilepsy are flanked by segmental duplications.

26 thin the human genome, providing evidence of segmental duplications.

27 E transposable elements and those containing segmental duplications.

28 ents between low-copy repeats, also known as segmental duplications.

29 and identified 8 new large interchromosomal segmental duplications.

30 g to determine breakpoints that occur within segmental duplications.

31 of the CNVRs (108/177) directly overlap with segmental duplications.

32 ed the relationships between pseudogenes and segmental duplications.

33 hereas the proximal breakpoint falls between segmental duplications.

34 can contain mosaic patterns of thousands of segmental duplications.

35 ons, respectively, and 18-55% and 39-77% for segmental duplications.

36 ctional elements and regions known to harbor segmental duplications.

37 , mediated by flanking repeated sequences or segmental duplications.

38 gions (10-44 kb) of high methylation were at segmental duplications.

39 chromosome") showed a marked enrichment for segmental duplication (45% of 75.2 Mb), indicating that

40 ticularly rich in low-copy repeats (LCRs) or segmental duplications (5%-10%), and this characteristic

41 pes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turno

42 of the mouse genome is part of recent large segmental duplications (about half of what is observed f

43 Segmental duplications account for up to 6% of the human

44 We have characterized a segmental duplication adjacent to the Xp/Yp telomere, ea

45 and interchromosomal duplications, including segmental duplications adjacent to both the centromere a

46 apid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and p

47 es in the mitochondrion, a very high rate of segmental duplication and deletion in the nuclear genome

48 ense mutations as well as FOXC1-encompassing segmental duplication and deletion revealed white matter

49 Phylogenetic analysis also revealed recent segmental duplication and extensive rearrangement and re

50 In addition, both segmental duplication and whole-genome duplication contr

51 s recombination between approximately 4.9 kb segmental duplications and allows the deletion breakpoin

52 ements, disease/trait associated loci, known segmental duplications and artifact prone regions, there

53 first systematic and genome-wide analysis of segmental duplications and associated copy number varian

54 w that UCEs are significantly depleted among segmental duplications and copy number variants.

55 monstrated all previously known heterozygous segmental duplications and deletions (3 Mb to 18 kb) loc

56 mmalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

57 utionarily unstable regions that harbor more segmental duplications and interspecies genomic rearrang

58 Segmental duplications and other highly repetitive regio

59 density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of

60 tags alone, including transposable elements, segmental duplications and peri-centromeric regions.

61 omplex relationship between the evolution of segmental duplications and rearrangements associated wit

62 ers may also play a role in the emergence of segmental duplications and the evolution of new genes by

63 ixed structural variants, specifically large segmental duplications and their polymorphic precursors

64 n turn, initiated the expansion of gene-rich segmental duplications and their subsequent role in nona

65 as a result of human-specific expansions of segmental duplications and two independent inversion eve

66 ns are enriched for structural variation and segmental duplication, and can be resolved in the future

67 out expression in moderately-sized (1-50 Mb) segmental duplications, and about the response of small

68 heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integra

69 ic features such as repetitive DNA elements, segmental duplications, and genes.

70 elineation of structural variants, including segmental duplications, and is able to return all possib

71 d nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are div

72 erspersed nuclear elements and LTR elements, segmental duplications, and subtelomeric regions, but si

73 Repetitive elements, segmental duplications, and syntenic tandem DNA repeats

74 ential artefacts emanating from pseudogenes, segmental duplications, and template switching, and outp

75 d with other sequenced animal genomes, human segmental duplications appear larger, more interspersed,

76 The segmental duplication architecture surrounding the MS lo

77 trol BACs (P < .000001), which suggests that segmental duplications are a major catalyst of large-sca

78 Given that tandem and segmental duplications are common in both animal and pla

79 Segmental duplications are common in mammalian genomes,

80 Primate-specific segmental duplications are considered important in human

81 Our analysis reveals that human segmental duplications are frequently organized around '

82 Human segmental duplications are hotspots for nonallelic homol

83 We observe that CNPs in segmental duplications are more likely to be population

84 nomic duplication and demonstrate that these segmental duplications are most likely the result of anc

85 Low-copy repeats, or segmental duplications, are highly dynamic regions in th

86 microsyntenic region, we conclude that these segmental duplications arose independently after the sep

87 Whereas H1 and H2 segmental duplications arose independently and before hu

88 ates provide additional evidence implicating segmental duplications as a major mechanism of chromosom

89 f reconstructing the evolutionary history of segmental duplications as an optimization problem on the

90 ion and ectopic rearrangements that involved segmental duplications as well as microscale events.

91 tions, we did not find evidence of extensive segmental duplications, as has been documented in primat

92 into the structure and formation of primate segmental duplications at sites of genomic rearrangement

93 e polymorphic patchworks of interchromosomal segmental duplications at the ends of chromosomes.

94 Our specialized segmental duplication BAC microarray and associated data

95 Using our segmental duplication BAC microarray, we screened a pane

96 obal comparison of differences in content of segmental duplication between human and chimpanzee, and

97 al differences in the architecture of recent segmental duplications between human and mouse.

98 ly duplicated segments can be distinguished: segmental duplications between nonhomologous chromosomes

99 requency recombination sites, and tandem and segmental duplications between related species.

100 All 26 Populus OMT genes were located in segmental duplication blocks and two third of them were

101 high sequence identity, and mosaic nature of segmental duplication blocks.

102 one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric

103 SVs are significantly enriched in regions of segmental duplication, but that this effect is largely i

104 human chromosomes, contain a high density of segmental duplications, but relatively little is known a

105 n is notable because recombination among the segmental duplications can result in deletions causing P

106 meres are concentrations of interchromosomal segmental duplications capped by telomeric repeats at th

107 species have been enriched for interspersed segmental duplications compared with representative Old

108 ediated by a chimpanzee-specific increase in segmental duplication complexity.

109 Because segmental duplications comprise a significant proportion

110 canine reference sequence, we estimate that segmental duplications comprise approximately 4.21% of t

111 Low copy repeats (LCRs; segmental duplications) constitute approximately 5% of t

112 highly similar repeats by comparison of the segmental duplication content of two different human gen

113 Analysis of gene, repetitive element, and segmental duplication content show this assembly to be o

114 is strongly correlated with gene, repeat and segmental duplication content.

115 ficantly enriched for structural variations (segmental duplications, copy number variants, and indels

116 Notably, these segmental duplications correspond closely to the sites o

117 We show that this region is composed of segmental duplications corresponding to 14 ancestral seg

118 Furthermore, these data suggest that segmental duplications could lead to evolution of novel

119 rounding ERBB2 in the normal genome, such as segmental duplications, could promote the locus-specific

120 Large segmental duplications cover much of the Arabidopsis tha

121 We have constructed a mouse segmental duplication database to aid in the characteriz

122 Our study demonstrates that segmental duplications define hotspots of chromosomal re

123 Genome structural variation includes segmental duplications, deletions, and other rearrangeme

124 lication, among the largest interchromosomal segmental duplications described in humans, is not accou

125 ansion and fixation of some intrachromosomal segmental duplications during great-ape evolution has be

126 pulation differences in the copy number of a segmental duplication encompassing the gene encoding CCL

127 expanded through tandem gene duplication and segmental duplication events as demonstrated by two geno

128 Thus, a series of consecutive segmental duplication events during primate evolution re

129 Nevertheless, base per base, large segmental duplication events have had a greater impact (

130 ervations support the contention that serial segmental duplication events might have orchestrated pri

131 extant Aux/IAA loci arose primarily through segmental duplication events, in sharp contrast to the A

132 s along with the characterization of complex segmental duplications flanking the deletion regions sug

133 me-wide duplication, tandem duplication, and segmental duplication followed by dispersal and diversif

134 RV integration in males for chromosome Y and segmental duplication for chromosome 19.

135 Because of the abundance of segmental duplications, genome comparisons require the i

136 We interrogated 120 regions flanked by segmental duplications (genomic hotspots) for events >50

137 Segmental duplications > 1 kb in length with >or= 90% se

138 changes we found are immediately flanked by segmental duplications > or =10 kb in size and > or =95%

139 ularly enriched for large, highly homologous segmental duplications (> or =90% sequence identity and

140 the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > o

141 breakpoints co-localized to highly identical segmental duplications (>51 kb in length, > 94% identity

142 at approximately 57% of all highly identical segmental duplications (>or=90%) were misassembled or co

143 m by which the interspersed pattern of human segmental duplications has evolved is unknown.

144 This dynamism of segmental duplications has important implications in dis

145 Taken together, these data suggest that segmental duplications have been an ongoing process of p

146 uplication (45% of 75.2 Mb), indicating that segmental duplications have been problematic for sequenc

147 ggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count o

148 repetitive elements such as transposons and segmental duplications; however, our analysis of the C57

149 tomated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer

150 c regions: in animals they contain extensive segmental duplications implicated in gene creation, and

151 omosomes II and IV also revealed evidence of segmental duplication in Arabidopsis.

152 omes but are highly correlated with sites of segmental duplication in human and chimpanzee.

153 nome, lending support to a two-step model of segmental duplication in the genome.

154 e is remarkable in having the lowest rate of segmental duplication in the genome.

155 q14 showing that CHRFAM7A is part of a large segmental duplication in the opposite orientation to CHR

156 years ago, after proliferation of the TBC1D3 segmental duplication in the primate lineage.

157 Segmental duplications in chromosome 15 are largely clus

158 A large number of the segmental duplications in mammalian genomes have been ca

159 However, an assessment of the role of segmental duplications in normal variation has not yet b

160 The extent of segmental duplications in other mammalian genomes is unk

161 Segmental duplications in the human genome are selective

162 heuristic to solve the problem for a set of segmental duplications in the human genome in both parsi

163 c disease and in the enrichment of gene-rich segmental duplications in the human genome, and they for

164 istance, and we use the algorithm to analyze segmental duplications in the human genome.

165 le studying large genomic rearrangements and segmental duplications in the human genome.

166 crodeletions, the expansion of chromosome 15 segmental duplications in the human lineage and independ

167 me 10L and is part of the most recent set of segmental duplications in the maize genome.

168 Invertase family members reside on segmental duplications in the near-colinear genomes of t

169 als possible ancestral relationships between segmental duplications including numerous examples of du

170 Interchromosomal segmental duplications including OR genes have also occu

171 Active rounds of segmental duplication, involving single genes or larger

172 ributed across 11 out of the 13 chromosomes; segmental duplication is a predominant duplication event

173 egration of active elements, suggesting that segmental duplication is an important process for CRR ac

174 impaired fertility that is characteristic of segmental duplications is due to inactivation by RIP of

175 A major difficulty in analyzing segmental duplications is that many duplications are com

176 genome (largely low-complexity sequence and segmental duplications) is challenging.

177 f primate genomes, we show that a particular segmental duplication (LCR16a) has been the source locus

178 e pair fractionation following polyploidy or segmental duplication leaves a genome enriched for "conn

179 es formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements.

180 mbination secondary to the presence of large segmental duplications (macrohomology) in this region.

181 sociated with genomic disorders with complex segmental duplications mapping at the breakpoints.

182 ding the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy num

183 vel of concerted evolution in the 5-7 MY-old segmental duplication may reflect the behavior of many g

184 haploid strains, most events involved tandem segmental duplications mediated by nonallelic homologous

185 d our initial analysis on 48 recurrent CNVs (segmental duplication-mediated 'hotspots') from 24 loci

186 led to an explosion in the discovery of new segmental duplication-mediated deletions and duplication

187 repeat architecture of the genome to target segmental duplication-mediated rearrangement hotspots (n

188 Segmental duplications, most of them part of polyploidy

189 examined from crosses heterozygous for long segmental duplications obtained using insertional or qua

190 ps reveal several evolutionarily independent segmental duplications occurring over the last 600+ mill

191 nic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-

192 Our results also indicate that segmental duplication of large arrays of satellite repea

193 ximately 2.2 Mb in size and flanked by large segmental duplications of >98% sequence identity and in

194 Whereas the segmental duplications of chromosome 16 are enriched in

195 e parsimonious than models that invoke large segmental duplications of the molecule.

196 ions composed of transposon termini flanking segmental duplications of various lengths.

197 ct that recently duplicated sequences (e.g., segmental duplications) often coincide with breakpoints.

198 Notably, of the UCEs that are found in segmental duplications or copy number variants, the majo

199 s overlap with genes, and many coincide with segmental duplications or gaps in the human genome assem

200 Segmental duplications or low-copy repeats (LCRs) consti

201 g that Arabidopsis has undergone a number of segmental duplications or possibly a complete genome dup

202 nomic duplication results from intraallelic (segmental duplication) or interallelic recombination wit

203 Segmental duplications overlap 841 genes and are signifi

204 Segmental duplications play fundamental roles in both ge

205 descriptions of large insertion/deletion or segmental duplication polymorphisms (SDs) in the human g

206 We found that segmental duplications populate the majority of primate-

207 morphism arose from the rapid integration of segmental duplications, precipitating two local inversio

208 structed the origin and history of a 127-kbp segmental duplication, R2d, in the house mouse (Mus musc

209 It is also enriched in segmental duplications, ranking third in density among t

210 We further show that the segmental duplication region encompassing the IgG heavy

211 cy (up to 30%) and that CNVs residing within segmental duplication regions (higher reference copy num

212 phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable.

213 etection, ranging 39-77% and 86-100% for non-segmental duplication regions, respectively, and 18-55%

214 ified many novel protein-DNA interactions in segmental duplication regions.

215 ions and/or a higher rate of gene loss after segmental duplication relative to genes in both low-copy

216 Although regions of large, high-identity segmental duplications remain largely unresolved, this c

217 ence continuity of complex regions of recent segmental duplication remains one of the major challenge

218 Taken together the above data indicate that segmental duplications represent a significant impedimen

219 Current sequence annotation of segmental duplications requires computationally intensiv

220 This microarray contained CNPs in segmental duplication-rich regions and insertions of seq

221 rated that nonexonic UCEs are depleted among segmental duplications (SDs) and copy number variants (C

222 ied the CNVs mediated by NAHR between paired segmental duplications (SDs) and further revealed the co

223 recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human

224 Segmental duplications (SDs) are operationally defined a

225 Large segmental duplications (SDs) constitute at least 3.6% of

226 Segmental duplications (SDs) play an important role in g

227 00-kb and is flanked by approximately 147-kb segmental duplications (SDs) that are >99% identical, a

228 s are >95% identical and reside within large segmental duplications (SDs) with a high level of simila

229 n increase in the proportion of interspersed segmental duplications (SDs) within the genomes of human

230 cture, especially low copy repeats (LCRs) or segmental duplications (SDs).

231 milarity>/=90% and length>/=1 kb) are termed segmental duplications (SDs); here, we analyze the inter

232 ichment was most pronounced for interspersed segmental duplications separated by > or =1 Mb of interv

233 the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of trans

234 n 1q21.1, 15q13, 15q24 and 17q12 to flanking segmental duplications, suggesting that these are also s

235 Twenty-seven percent of all segmental duplications terminated within an Alu repeat.

236 iched more significantly by recent rounds of segmental duplication than by original integration of ac

237 In addition, we provide evidence for a human segmental duplication that may have provided a mechanism

238 distance, we also identify a small number of segmental duplications that appear to have seeded many o

239 oximately 5% of the human genome consists of segmental duplications that can cause genomic mutations

240 ation is consistent with the large number of segmental duplications that compose the Arabidopsis geno

241 ex organization composed of specific sets of segmental duplications that have hyperexpanded in concer

242 re characterized by the presence of flanking segmental duplications that predispose these regions to

243 ugh the human sequence has a high density of segmental duplication, the mouse sequence has a very low

244 Importantly, segmental duplications themselves were also significantl

245 omosomes IV, X and XIV, similar to mammalian segmental duplications, was 'at risk' for participating

246 seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed an

247 -processed pseudogenes that were included in segmental duplications; we find 53 RPL23A pseudogenes in

248 previous reports, surprisingly high rates of segmental duplication were also found throughout the gen

249 s that approximately 30% of the recent human segmental duplications were caused by a recombination-li

250 We found that segmental duplications were significantly enriched at ma

251 size and is flanked on the distal side by a segmental duplication, whereas the proximal breakpoint f

252 a recent gene family expansion by tandem or segmental duplications, whereas wave II, a rapid paralog

253 of nonredundant consensus sequences of human segmental duplications, wherein a majority of the ancest

254 ene, whereas TBC1D3 is derived from a recent segmental duplication, which is absent in most other mam

255 Segmental duplications, which comprise approximately 5%-

256 ats composed of repetitive gene clusters and segmental duplications, which corresponded to regions of

257 hese loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formati

258 chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding

259 sites localized to areas of intrachromosomal segmental duplication within the human genome.