1. Lupski JR. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 1998;14:417–422. PMID:
9820031.
2. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y,
et al. Detection of large-scale variation in the human genome. Nat Genet 2004;36:949–951. PMID:
15286789.
3. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P,
et al. Large-scale copy number polymorphism in the human genome. Science 2004;305:525–528. PMID:
15273396.
4. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006;7:85–97. PMID:
16418744.
5. Lee C, Scherer SW. The clinical context of copy number variation in the human genome. Expert Rev Mol Med 2010;12:e8. PMID:
20211047.
6. Stankiewicz P, Lupski JR. Genome architecture, rearrangements and genomic disorders. Trends Genet 2002;18:74–82. PMID:
11818139.
7. Yagi H, Furutani Y, Hamada H, Sasaki T, Asakawa S, Minoshima S,
et al. Role of
TBX1 in human del22q11.2 syndrome. Lancet 2003;362:1366–1373. PMID:
14585638.
8. Paylor R, Glaser B, Mupo A, Ataliotis P, Spencer C, Sobotka A,
et al. Tbx1 haploinsufficiency is linked to behavioral disorders in mice and humans: implications for 22q11 deletion syndrome. Proc Natl Acad Sci U S A 2006;103:7729–7734. PMID:
16684884.
9. McDonald-McGinn DM, Sullivan KE. Chromosome 22q11.2 deletion syndrome (DiGeorge syndrome/velocardiofacial syndrome). Medicine (Baltimore) 2011;90:1–18. PMID:
21200182.
10. Breckpot J, Thienpont B, Bauters M, Tranchevent LC, Gewillig M, Allegaert K,
et al. Congenital heart defects in a novel recurrent 22q11.2 deletion harboring the genes CRKL and MAPK1. Am J Med Genet A 2012;158A:574–580. PMID:
22318985.
11. Lupski JR, de Oca-Luna RM, Slaugenhaupt S, Pentao L, Guzzetta V, Trask BJ,
et al. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 1991;66:219–232. PMID:
1677316.
12. Zhang F, Seeman P, Liu P, Weterman MA, Gonzaga-Jauregui C, Towne CF,
et al. Mechanisms for nonrecurrent genomic rearrangements associated with CMT1A or HNPP: rare CNVs as a cause for missing heritability. Am J Hum Genet 2010;86:892–903. PMID:
20493460.
13. Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 1996;6:743–748. PMID:
8994846.
14. Zhou W, Zhang F, Chen X, Shen Y, Lupski JR, Jin L. Increased genome instability in human DNA segments with self-chains: homology-induced structural variations via replicative mechanisms. Hum Mol Genet 2013;22:2642–2651. PMID:
23474816.
15. Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 1999;9:657–663. PMID:
10607616.
16. Eichler EE. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet 2001;17:661–669. PMID:
11672867.
17. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S,
et al. Recent segmental duplications in the human genome. Science 2002;297:1003–1007. PMID:
12169732.
18. Bailey JA, Eichler EE. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet 2006;7:552–564. PMID:
16770338.
19. Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW,
et al. A burst of segmental duplications in the genome of the African great ape ancestor. Nature 2009;457:877–881. PMID:
19212409.
20. Olson MV, Varki A. Sequencing the chimpanzee genome: insights into human evolution and disease. Nat Rev Genet 2003;4:20–28. PMID:
12509750.
21. Nelson PN, Hooley P, Roden D, Davari Ejtehadi H, Rylance P, Warren P,
et al. Human endogenous retroviruses: transposable elements with potential. Clin Exp Immunol 2004;138:1–9. PMID:
15373898.
22. Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F,
et al. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res 2008;18:1865–1874. PMID:
18842824.
23. Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X,
et al. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet 2007;39:1361–1368. PMID:
17922013.
24. Dittwald P, Gambin T, Gonzaga-Jauregui C, Carvalho CM, Lupski JR, Stankiewicz P,
et al. Inverted low-copy repeats and genome instability: a genome-wide analysis. Hum Mutat 2013;34:210–220. PMID:
22965494.
25. Fu W, Zhang F, Wang Y, Gu X, Jin L. Identification of copy number variation hotspots in human populations. Am J Hum Genet 2010;87:494–504. PMID:
20920665.
26. Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D,
et al. Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 2009;84:148–161. PMID:
19166990.
27. Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet 2011;12:363–376. PMID:
21358748.
28. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y,
et al. Origins and functional impact of copy number variation in the human genome. Nature 2010;464:704–712. PMID:
19812545.
29. Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY,
et al. NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits. Genome Res 2013;23:1395–1409. PMID:
23657883.
30. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C,
et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011;470:59–65. PMID:
21293372.
31. Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med 2010;61:437–455. PMID:
20059347.
32. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU,
et al. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 2005;77:78–88. PMID:
15918152.
33. Liu P, Lacaria M, Zhang F, Withers M, Hastings PJ, Lupski JR. Frequency of nonallelic homologous recombination is correlated with length of homology: evidence that ectopic synapsis precedes ectopic crossing-over. Am J Hum Genet 2011;89:580–588. PMID:
21981782.
34. Peng Z, Zhou W, Fu W, Du R, Jin L, Zhang F. Correlation between frequency of non-allelic homologous recombination and homology properties: evidence from homology-mediated CNV mutations in the human genome. Hum Mol Genet 2014 10 16 [Epub].
http://dx.doi.org/10.1093/hmg/ddu533.
35. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J,
et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860–921. PMID:
11237011.
36. Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet 2009;10:691–703. PMID:
19763152.
37. Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J. Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet 2007;23:158–161. PMID:
17307271.
38. Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002;3:370–379. PMID:
11988762.
39. Sasaki M, Lange J, Keeney S. Genome destabilization by homologous recombination in the germ line. Nat Rev Mol Cell Biol 2010;11:182–195. PMID:
20164840.
40. de Smith AJ, Walters RG, Coin LJ, Steinfeld I, Yakhini Z, Sladek R,
et al. Small deletion variants have stable breakpoints commonly associated with alu elements. PLoS One 2008;3:e3104. PMID:
18769679.
41. Gu W, Zhang F, Lupski JR. Mechanisms for human genomic rearrangements. Pathogenetics 2008;1:4. PMID:
19014668.
42. Erez A, Patel AJ, Wang X, Xia Z, Bhatt SS, Craigen W,
et al. Alu-specific microhomology-mediated deletions in CDKL5 in females with early-onset seizure disorder. Neurogenetics 2009;10:363–369. PMID:
19471977.
43. Matejas V, Huehne K, Thiel C, Sommer C, Jakubiczka S, Rautenstrauss B. Identification of Alu elements mediating a partial PMP22 deletion. Neurogenetics 2006;7:119–126. PMID:
16570190.
44. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F,
et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008;453:175–183. PMID:
18464734.
45. Higashimoto K, Maeda T, Okada J, Ohtsuka Y, Sasaki K, Hirose A,
et al. Homozygous deletion of DIS3L2 exon 9 due to non-allelic homologous recombination between LINE-1s in a Japanese patient with Perlman syndrome. Eur J Hum Genet 2013;21:1316–1319. PMID:
23486540.
46. Janoušek V, Karn RC, Laukaitis CM. The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family. BMC Evol Biol 2013;13:107. PMID:
23718880.
47. Yang N, Kazazian HH Jr. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol 2006;13:763–771. PMID:
16936727.
48. Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, Kinzler KW,
et al. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res 1992;52:643–645. PMID:
1310068.
49. Kazazian HH Jr, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 1988;332:164–166. PMID:
2831458.
50. Belancio VP, Deininger PL, Roy-Engel AM. LINE dancing in the human genome: transposable elements and disease. Genome Med 2009;1:97. PMID:
19863772.
51. Dangel AW, Mendoza AR, Baker BJ, Daniel CM, Carroll MC, Wu LC,
et al. The dichotomous size variation of human complement C4 genes is mediated by a novel family of endogenous retroviruses, which also establishes species-specific genomic patterns among Old World primates. Immunogenetics 1994;40:425–436. PMID:
7545960.
52. Shuvarikov A, Campbell IM, Dittwald P, Neill NJ, Bialer MG, Moore C,
et al. Recurrent HERV-H-mediated 3q132-q1331 deletions cause a syndrome of hypotonia and motor, language, and cognitive delays. Hum Mutat 2013;34:1415–1423. PMID:
23878096.
53. Hermetz KE, Surti U, Cody JD, Rudd MK. A recurrent translocation is mediated by homologous recombination between HERV-H elements. Mol Cytogenet 2012;5:6. PMID:
22260357.
54. Kamp C, Ditton H, Huellen K, Vogt PH. Complex human Y-chromosomal HERV sequence structure in the AZFa region: new candidate genes for the control of early germ cell proliferation? Eur J Hum Genet 2001;9(Suppl 1):C044.
55. Bosch E, Jobling MA. Duplications of the AZFa region of the human Y chromosome are mediated by homologous recombination between HERVs and are compatible with male fertility. Hum Mol Genet 2003;12:341–347. PMID:
12554687.
56. Arruda JT, Silva DM, Silva CC, Moura KK, da Cruz AD. Homologous recombination between HERVs causes duplications in the AZFa region of men accidentally exposed to cesium-137 in Goiania. Genet Mol Res 2008;7:1063–1069. PMID:
19048485.
57. Koh E. Male infertility and genome disease -mechanism of microdeletions in azoospermia factor (AZF) regions and genomic diversification of the Y chromosome through analysis of human endogenous retrovirus. Genes Genet Syst 2010;85:445.
58. Carvalho CM, Zhang F, Lupski JR. Structural variation of the human genome: mechanisms, assays, and role in male infertility. Syst Biol Reprod Med 2011;57:3–16. PMID:
21210740.
59. Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN. Complex gene rearrangements caused by serial replication slippage. Hum Mutat 2005;26:125–134. PMID:
15977178.
60. Carvalho CM, Ramocki MB, Pehlivan D, Franco LM, Gonzaga-Jauregui C, Fang P,
et al. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nat Genet 2011;43:1074–1081. PMID:
21964572.
61. Hastings PJ, Ira G, Lupski JR. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 2009;5:e1000327. PMID:
19180184.
62. Zhang F, Khajavi M, Connolly AM, Towne CF, Batish SD, Lupski JR. The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet 2009;41:849–853. PMID:
19543269.
63. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 2003;100:11484–11489. PMID:
14500911.
64. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
et al. Human-mouse alignments with BLASTZ. Genome Res 2003;13:103–107. PMID:
12529312.
65. Chen X, Shen Y, Zhang F, Chiang C, Pillalamarri V, Blumenthal I,
et al. Molecular analysis of a deletion hotspot in the NRXN1 region reveals the involvement of short inverted repeats in deletion CNVs. Am J Hum Genet 2013;92:375–386. PMID:
23472757.
66. Lieber MR. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 2010;79:181–211. PMID:
20192759.
67. Moore JK, Haber JE. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 1996;16:2164–2173. PMID:
8628283.
68. Conrad DF, Hurles ME. The population genetics of structural variation. Nat Genet 2007;39(7 Suppl):S30–S36. PMID:
17597779.
69. Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing. Nat Genet 2009;41:393–395. PMID:
19287383.
70. Yao NY, O'Donnell M. SnapShot: the replisome. Cell 2010;141:1088. PMID:
20550941.
71. Rhind N, Gilbert DM. DNA replication timing. Cold Spring Harb Perspect Biol 2013;5:a010132. PMID:
23838440.
72. Farkash-Amar S, Simon I. Genome-wide analysis of the replication program in mammals. Chromosome Res 2010;18:115–125. PMID:
20205353.
73. Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM. Genome-scale analysis of replication timing: from bench to bioinformatics. Nat Protoc 2011;6:870–895. PMID:
21637205.
74. Raghuraman MK, Brewer BJ. Molecular analysis of the replication program in unicellular model organisms. Chromosome Res 2010;18:19–34. PMID:
20012185.
75. Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR,
et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet 2012;91:1033–1040. PMID:
23176822.
76. Bechhoefer J, Rhind N. Replication timing and its emergence from stochastic processes. Trends Genet 2012;28:374–381. PMID:
22520729.
77. Desprat R, Thierry-Mieg D, Lailler N, Lajugie J, Schildkraut C, Thierry-Mieg J,
et al. Predictable dynamic program of timing of DNA replication in human cells. Genome Res 2009;19:2288–2299. PMID:
19767418.
78. Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, Yakhini Z,
et al. Global organization of replication time zones of the mouse genome. Genome Res 2008;18:1562–1570. PMID:
18669478.
79. Hansen RS, Canfield TK, Lamb MM, Gartler SM, Laird CD. Association of fragile X syndrome with delayed replication of the
FMR1 gene. Cell 1993;73:1403–1409. PMID:
8324827.
80. MacAlpine DM, Rodríguez HK, Bell SP. Coordination of replication and transcription along a
Drosophila chromosome. Genes Dev 2004;18:3094–3105. PMID:
15601823.
81. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW,
et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 2008;6:e245. PMID:
18842067.
82. Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD,
et al. Replication timing of the human genome. Hum Mol Genet 2004;13:191–202. PMID:
14645202.
83. Aran D, Toperoff G, Rosenberg M, Hellman A. Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 2011;20:670–680. PMID:
21112978.
84. Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J,
et al. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 2010;20:761–770. PMID:
20430782.
85. Cardoso-Moreira M, Emerson JJ, Clark AG, Long M.
Drosophila duplication hotspots are associated with late-replicating regions of the genome. PLoS Genet 2011;7:e1002340. PMID:
22072977.
86. Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM,
et al. The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Rep 2014;7:70–78. PMID:
24685138.
87. Watanabe Y, Maekawa M. Spatiotemporal regulation of DNA replication in the human genome and its association with genomic instability and disease. Curr Med Chem 2010;17:222–233. PMID:
20214565.
88. Litmanovitch T, Altaras MM, Dotan A, Avivi L. Asynchronous replication of homologous alpha-satellite DNA loci in man is associated with nondisjunction. Cytogenet Cell Genet 1998;81:26–35. PMID:
9691171.
89. Grinberg-Rashi H, Cytron S, Gelman-Kohan Z, Litmanovitch T, Avivi L. Replication timing aberrations and aneuploidy in peripheral blood lymphocytes of breast cancer patients. Neoplasia 2010;12:668–674. PMID:
20689761.
90. Fritz A, Sinha S, Marella N, Berezney R. Alterations in replication timing of cancer-related genes in malignant human breast cancer cells. J Cell Biochem 2013;114:1074–1083. PMID:
23161755.
91. Donley N, Thayer MJ. DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability. Semin Cancer Biol 2013;23:80–89. PMID:
23327985.
92. Woo YH, Li WH. DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nat Commun 2012;3:1004. PMID:
22893128.
93. De S, Michor F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat Biotechnol 2011;29:1103–1108. PMID:
22101487.
94. Burrell RA, McGranahan N, Bartek J, Swanton C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature 2013;501:338–345. PMID:
24048066.
95. Chen L, Zhou W, Zhang C, Lupski JR, Jin L, Zhang F. CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis. Hum Mol Genet 2014 11 14 [Epub].
http://dx.doi.org/10.1093/hmg/ddu572.