ライフサイエンスコーパス: segmental duplication

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

2 nome is relatively repetitive but has little segmental duplication.

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

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

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

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

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

8 attributable to whole genome duplication and segmental duplication.

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

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

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

12 hereas the proximal breakpoint falls between segmental duplications.

13 can contain mosaic patterns of thousands of segmental duplications.

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

15 ctional elements and regions known to harbor segmental duplications.

16 , mediated by flanking repeated sequences or segmental duplications.

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

18 improve the accuracy of long-read mapping in segmental duplications.

19 mplex mosaics of fragments of numerous other segmental duplications.

20 esence of highly homologous intrachromosomal segmental duplications.

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

22 homologous groups that resulted from recent segmental duplications.

23 resulted from unequal crossing-over between segmental duplications.

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

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

26 clustered and preferentially associated with segmental duplications.

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

28 n genome is particularly enriched for recent segmental duplications.

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

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

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

32 iched for AGRs and more generally containing segmental duplications.

33 etecting subexonic CNVs and variation within segmental duplications.

34 rearrangements and gene expansions linked to segmental duplications.

35 duplication and subsequent species-specific segmental duplications.

36 elopmental delay and epilepsy are flanked by segmental duplications.

37 E transposable elements and those containing segmental duplications.

38 complex (MHC) variants, satellite DNAs, and segmental duplications.

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

40 and identified 8 new large interchromosomal segmental duplications.

41 g to determine breakpoints that occur within segmental duplications.

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

43 ed the relationships between pseudogenes and segmental duplications.

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

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

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

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

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

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

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

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

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

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

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

55 which contain extensive regions of paralogy, segmental duplication and high copy-number repeats, but

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

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

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

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

60 ct the insertion locus of large interspersed segmental duplications and characterize translocations.

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

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

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

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

65 uman genome assembly, which resolves complex segmental duplications and large tandem repeats, includi

66 Segmental duplications and other highly repetitive regio

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

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

69 ut of 341 validation BACs sampled from known segmental duplications and provides the first preliminar

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

71 intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric

72 the presence of repetitive sequences such as segmental duplications and tandem repeat arrays.

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

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

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

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

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

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

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

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

81 ally associating domains across centromeres, segmental duplications, and human disease-associated gen

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

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

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

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

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

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

88 The segmental duplication architecture surrounding the MS lo

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

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

91 Segmental duplications are common in mammalian genomes,

92 Primate-specific segmental duplications are considered important in human

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

94 Human segmental duplications are hotspots for nonallelic homol

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

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

97 gene conversion events that include inverted segmental duplications are often characterized as simple

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

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

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

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

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

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

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

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

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

107 Our specialized segmental duplication BAC microarray and associated data

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

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

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

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

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

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

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

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

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

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

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

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

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

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

122 Because segmental duplications comprise a significant proportion

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

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

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

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

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

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

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

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

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

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

133 Large segmental duplications cover much of the Arabidopsis tha

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

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

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

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

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

139 being identified, all NAHR events contain a segmental duplication encompassing FAM230 gene members s

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

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

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

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

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

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

146 A total of 14 SlPP2Cs have arisen from segmental duplication events, while no tandem duplicatio

147 associated with independent lineage-specific segmental duplications flanking LCR16a leading to the em

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

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

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

151 er analyses revealed that gene duplications, segmental duplication, gene amplification, and point mut

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

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

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

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

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

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

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

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

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

161 This dynamism of segmental duplications has important implications in dis

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

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

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

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

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

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

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

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

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

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

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

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

174 Segmental duplications in chromosome 15 are largely clus

175 The complex interspersed pattern of segmental duplications in humans is responsible for rear

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

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

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

179 Segmental duplications in the human genome are selective

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

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

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

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

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

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

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

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

188 Interchromosomal segmental duplications including OR genes have also occu

189 that may include whole-genome duplications, segmental duplications, independent gene duplications or

190 lgorithms to characterize large interspersed segmental duplications, inversions, deletions, and trans

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

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

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

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

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

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

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

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

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

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

201 Local tandem and segmental duplications mainly contributed to the expansi

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

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

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

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

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

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

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

209 Segmental duplications, most of them part of polyploidy

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

211 f LCN lines appears unaffected, a chromosome segmental duplication occurred in one of the lines.

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

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

214 The -4 kb upstream site falls in a segmental duplication of a nearly identical intronic reg

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

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

217 Whereas the segmental duplications of chromosome 16 are enriched in

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

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

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

221 ypes, including small insertion or deletion, segmental duplication or deletion, and chromosome gain o

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

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

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

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

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

227 mbinations occur between FAM230 and specific segmental duplication orientations within LCR22A and LCR

228 Segmental duplications overlap 841 genes and are signifi

229 Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy numbe

230 trate that a significant fraction of PSVs in segmental duplications overlaps with variants and advers

231 Segmental duplications play fundamental roles in both ge

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

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

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

235 of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (<5% for the t

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

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

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

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

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

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

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

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

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

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

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

247 Current sequence annotation of segmental duplications requires computationally intensiv

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

249 f the current GRCh38 reference is defined by segmental duplication (SD) and simple repeat (SR), yet 9

250 nonallelic homologous recombination between segmental duplication (SD) pairs with varying similarity

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

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

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

254 e in disease and evolution, highly identical segmental duplications (SDs) are among the last regions

255 Segmental duplications (SDs) are operationally defined a

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

257 The quest for segmental duplications (SDs) in the reference sequence r

258 s of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons.

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

260 00-kb and is flanked by approximately 147-kb segmental duplications (SDs) that are >99% identical, a

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

277 Importantly, segmental duplications themselves were also significantl

278 It analyzes reads mapped to segmental duplications using existing long-read aligners

279 ize tandem, direct and inverted interspersed segmental duplications using short read whole genome seq

280 mosomes, and syntenic analysis revealed that segmental duplication was prevalent.

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

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

283 With the improved assembly of segmental duplications, we discovered new lineage-specif

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

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

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

287 nanopore coverage (such as cases where large segmental duplications were immediately adjacent to (TTA

288 We found that segmental duplications were significantly enriched at ma

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

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

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

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

293 Segmental duplications, which comprise approximately 5%-

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

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

296 aligned an additional 8-21% of the reads in segmental duplications with high confidence relative to

297 n potentially overcome this limitation, long segmental duplications with high sequence identity pose

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

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

300 quence reads to resolve collapsed regions of segmental duplications within genome assemblies.