1. FeukL, CarsonAR, SchererSW (2006) Structural variation in the human genome. Nat Rev Genet 7: 85–97.
2. ZhangF, GuW, HurlesME, LupskiJR (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10: 451–481.
3. CooperGM, ZerrT, KiddJM, EichlerEE, NickersonDA (2008) Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet 40: 1199–1203.
4. IafrateAJ, FeukL, RiveraMN, ListewnikML, DonahoePK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949–951.
5. KiddJM, CooperGM, DonahueWF, HaydenHS, SampasN, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56–64.
6. KorbelJO, UrbanAE, AffourtitJP, GodwinB, GrubertF, et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420–426.
7. McCarrollSA, HadnottTN, PerryGH, SabetiPC, ZodyMC, et al. (2006) Common deletion polymorphisms in the human genome. Nat Genet 38: 86–92.
8. McCarrollSA, KuruvillaFG, KornJM, CawleyS, NemeshJ, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166–1174.
9. RedonR, IshikawaS, FitchKR, FeukL, PerryGH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444–454.
10. SebatJ, LakshmiB, TrogeJ, AlexanderJ, YoungJ, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525–528.
11. TuzunE, SharpAJ, BaileyJA, KaulR, MorrisonVA, et al. (2005) Fine-scale structural variation of the human genome. Nat Genet 37: 727–732.
12. LupskiJR (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14: 417–422.
13. CarvalhoCM, ZhangF, LupskiJR (2010) Evolution in health and medicine Sackler colloquium: Genomic disorders: a window into human gene and genome evolution. Proc Natl Acad Sci U S A 107 Suppl 1: 1765–1771.
14. LiuP, CarvalhoCM, HastingsP, LupskiJR (2012) Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 22: 211–220.
15. LupskiJR (2009) Genomic disorders ten years on. Genome Med 1: 42.
16. StankiewiczP, LupskiJR (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18: 74–82.
17. LieberMR (2008) The mechanism of human nonhomologous DNA end joining. J Biol Chem 283: 1–5.
18. McVeyM, LeeSE (2008) MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends Genet 24: 529–538.
19. HanK, LeeJ, MeyerTJ, RemediosP, GoodwinL, et al. (2008) L1 recombination-associated deletions generate human genomic variation. Proc Natl Acad Sci U S A 105: 19366–19371.
20. SenSK, HanK, WangJ, LeeJ, WangH, et al. (2006) Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet 79: 41–53.
21. LeeJA, CarvalhoCM, LupskiJR (2007) A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131: 1235–1247.
22. HastingsPJ, IraG, LupskiJR (2009) A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5: e1000327 doi:10.1371/journal.pgen.1000327.
23. ChenJM, ChuzhanovaN, StensonPD, FerecC, CooperDN (2005) Complex gene rearrangements caused by serial replication slippage. Hum Mutat 26: 125–134.
24. SheenCR, JewellUR, MorrisCM, BrennanSO, FerecC, et al. (2007) Double complex mutations involving F8 and FUNDC2 caused by distinct break-induced replication. Hum Mutat 28: 1198–1206.
25. ShawCJ, LupskiJR (2004) Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum Mol Genet 13 Spec No 1: R57–64.
26. NobileC, ToffolattiL, RizziF, SimionatiB, NigroV, et al. (2002) Analysis of 22 deletion breakpoints in dystrophin intron 49. Hum Genet 110: 418–421.
27. ToffolattiL, CardazzoB, NobileC, DanieliGA, GualandiF, et al. (2002) Investigating the mechanism of chromosomal deletion: characterization of 39 deletion breakpoints in introns 47 and 48 of the human dystrophin gene. Genomics 80: 523–530.
28. InoueK, OsakaH, ThurstonVC, ClarkeJT, YoneyamaA, et al. (2002) Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females. Am J Hum Genet 71: 838–853.
29. VenturinM, GervasiniC, OrzanF, BentivegnaA, CorradoL, et al. (2004) Evidence for non-homologous end joining and non-allelic homologous recombination in atypical NF1 microdeletions. Hum Genet 115: 69–80.
30. ShawCJ, LupskiJR (2005) Non-recurrent 17p11.2 deletions are generated by homologous and non-homologous mechanisms. Hum Genet 116: 1–7.
31. ChandaB, Asai-CoakwellM, YeM, MungallAJ, BarrowM, et al. (2008) A novel mechanistic spectrum underlies glaucoma-associated chromosome 6p25 copy number variation. Hum Mol Genet 17: 3446–3458.
32. NagamaniSC, ZhangF, ShchelochkovOA, BiW, OuZ, et al. (2009) Microdeletions including YWHAE in the Miller-Dieker syndrome region on chromosome 17p13.3 result in facial dysmorphisms, growth restriction, and cognitive impairment. J Med Genet 46: 825–833.
33. YatsenkoSA, BrundageEK, RoneyEK, CheungSW, ChinaultAC, et al. (2009) Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum Mol Genet 18: 1924–1936.
34. ZhangF, SeemanP, LiuP, WetermanMA, Gonzaga-JaureguiC, et al. (2010) Mechanisms for nonrecurrent genomic rearrangements associated with CMT1A or HNPP: rare CNVs as a cause for missing heritability. Am J Hum Genet 86: 892–903.
35. JennesI, de JongD, MeesK, HogendoornPC, SzuhaiK, et al. (2011) Breakpoint characterization of large deletions in EXT1 or EXT2 in 10 multiple osteochondromas families. BMC Med Genet 12: 85.
36. OleyC, BaraitserM (1988) Blepharophimosis, ptosis, epicanthus inversus syndrome (BPES syndrome). J Med Genet 25: 47–51.
37. ZlotogoraJ, SagiM, CohenT (1983) The blepharophimosis, ptosis, and epicanthus inversus syndrome: delineation of two types. Am J Hum Genet 35: 1020–1027.
38. CrisponiL, DeianaM, LoiA, ChiappeF, UdaM, et al. (2001) The putative forkhead transcription factor FOXL2 is mutated in blepharophimosis/ptosis/epicanthus inversus syndrome. Nat Genet 27: 159–166.
39. De BaereE, DixonMJ, SmallKW, JabsEW, LeroyBP, et al. (2001) Spectrum of FOXL2 gene mutations in blepharophimosis-ptosis-epicanthus inversus (BPES) families demonstrates a genotype–phenotype correlation. Hum Mol Genet 10: 1591–1600.
40. De BaereE, BeysenD, OleyC, LorenzB, CocquetJ, et al. (2003) FOXL2 and BPES: mutational hotspots, phenotypic variability, and revision of the genotype-phenotype correlation. Am J Hum Genet 72: 478–487.
41. BeysenD, De PaepeA, BaereED (2008) FOXL2 mutations and genomic rearrangements in BPES. Hum Mutat
42. BeysenD, RaesJ, LeroyBP, LucassenA, YatesJR, et al. (2005) Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome. Am J Hum Genet 77: 205–218.
43. D'HaeneB, AttanasioC, BeysenD, DostieJ, LemireE, et al. (2009) Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet 5: e1000522 doi:10.1371/journal.pgen.1000522.
44. D'HaeneB, NevadoJ, PugeatM, PierquinG, LowryRB, et al. (2010) FOXL2 copy number changes in the molecular pathogenesis of BPES: unique cohort of 17 deletions. Hum Mutat 31 (5)
45. ConradDF, BirdC, BlackburneB, LindsayS, MamanovaL, et al. (2010) Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet 42: 385–391.
46. VissersLE, BhattSS, JanssenIM, XiaZ, LalaniSR, et al. (2009) Rare pathogenic microdeletions and tandem duplications are microhomology-mediated and stimulated by local genomic architecture. Hum Mol Genet 18: 3579–3593.
47. AbeysingheSS, ChuzhanovaN, KrawczakM, BallEV, CooperDN (2003) Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs. Hum Mutat 22: 229–244.
48. WellsRD (2007) Non-B DNA conformations, mutagenesis and disease. Trends Biochem Sci 32: 271–278.
49. GuW, ZhangF, LupskiJR (2008) Mechanisms for human genomic rearrangements. Pathogenetics 1: 4.
50. MaJL, KimEM, HaberJE, LeeSE (2003) Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double-strand breaks lacking overlapping end sequences. Mol Cell Biol 23: 8820–8828.
51. BoonePM, LiuP, ZhangF, CarvalhoCM, TowneCF, et al. (2011) Alu-specific microhomology-mediated deletion of the final exon of SPAST in three unrelated subjects with hereditary spastic paraplegia. Genet Med 13: 582–592.
52. PavlovYI, ShcherbakovaPV, RogozinIB (2006) Roles of DNA polymerases in replication, repair, and recombination in eukaryotes. Int Rev Cytol 255: 41–132.
53. RattrayAJ, StrathernJN (2003) Error-prone DNA polymerases: when making a mistake is the only way to get ahead. Annu Rev Genet 37: 31–66.
54. DeS, BabuMM (2010) A time-invariant principle of genome evolution. Proc Natl Acad Sci U S A 107: 13004–13009.
55. LiuP, CarvalhoCM, HastingsPJ, LupskiJR (2012) Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 22: 211–220.
56. BallifBC, RosenfeldJA, TraylorR, TheisenA, BaderPI, et al. (2012) High-resolution array CGH defines critical regions and candidate genes for microcephaly, abnormalities of the corpus callosum, and seizure phenotypes in patients with microdeletions of 1q43q44. Hum Genet 131: 145–156.
57. KuechlerA, BuysseK, Clayton-SmithJ, Le CaignecC, DavidA, et al. (2011) Five patients with novel overlapping interstitial deletions in 8q22.2q22.3. Am J Med Genet A 155A: 1857–1864.
58. PalomaresM, DelicadoA, MansillaE, de TorresML, VallespinE, et al. (2011) Characterization of a 8q21.11 microdeletion syndrome associated with intellectual disability and a recognizable phenotype. Am J Hum Genet 89: 295–301.
59. TalkowskiME, MullegamaSV, RosenfeldJA, van BonBW, ShenY, et al. (2011) Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder. Am J Hum Genet 89: 551–563.
60. VergultS, DauberA, Delle ChiaieB, Van OudenhoveE, SimonM, et al. (2012) 17q24.2 microdeletions: a new syndromal entity with intellectual disability, truncal obesity, mood swings and hallucinations. Eur J Hum Genet 20: 534–539.
61. ArguesoJL, WestmorelandJ, MieczkowskiPA, GawelM, PetesTD, et al. (2008) Double-strand breaks associated with repetitive DNA can reshape the genome. Proc Natl Acad Sci U S A 105: 11845–11850.
62. VoineaguI, NarayananV, LobachevKS, MirkinSM (2008) Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc Natl Acad Sci U S A 105: 9936–9941.
63. WangG, VasquezKM (2006) Non-B DNA structure-induced genetic instability. Mutation research 598: 103–119.
64. BacollaA, WellsRD (2004) Non-B DNA conformations, genomic rearrangements, and human disease. J Biol Chem 279: 47411–47414.
65. LanderES, LintonLM, BirrenB, NusbaumC, ZodyMC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.
66. BuysseK, Delle ChiaieB, Van CosterR, LoeysB, De PaepeA, et al. (2009) Challenges for CNV interpretation in clinical molecular karyotyping: lessons learned from a 1001 sample experience. Eur J Med Genet 52: 398–403.
67. MentenB, PattynF, De PreterK, RobbrechtP, MichelsE, et al. (2005) arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics 6: 124.
68. D'HaeneB, VandesompeleJ, HellemansJ (2010) Accurate and objective copy number profiling using real-time quantitative PCR. Methods 50: 262–270.
69. HellemansJ, MortierG, De PaepeA, SpelemanF, VandesompeleJ (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8: R19.
70. KentWJ (2002) BLAT–the BLAST-like alignment tool. Genome Res 12: 656–664.
71. LarkinMA, BlackshieldsG, BrownNP, ChennaR, McGettiganPA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948.
72. JurkaJ, KapitonovVV, PavlicekA, KlonowskiP, KohanyO, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462–467.
73. AltschulSF, GishW, MillerW, MyersEW, LipmanDJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410.
74. ChampPC, MauriceS, VargasonJM, CampT, HoPS (2004) Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Res 32: 6501–6510.
75. GoiosA, MeirinhosJ, RochaR, LopesR, AmorimA, et al. (2006) RepeatAround: a software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database. Mitochondrion 6: 218–224.
76. KikinO, D'AntonioL, BaggaPS (2006) QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res 34: W676–682.
77. RiceP, LongdenI, BleasbyA (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276–277.
78. HannesF, Van HoudtJ, QuarrellOW, PootM, HochstenbachR, et al. (2010) Telomere healing following DNA polymerase arrest-induced breakages is likely the main mechanism generating chromosome 4p terminal deletions. Hum Mutat 31: 1343–1351.