#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence


Inversions have been an evolutionary biology model for almost a century, and recently the discovery of a high amount of structural variation in multiple organisms, including humans, has renewed the interest in them. Since early on, it was shown that they were adaptive and that they were involved in human diseases. However, in humans, the study of inversions has lagged behind due to important limitations in the experimental methods to analyze them. Here, we have optimized a technique for high-throughput validation and genotyping of inversions mediated by inverted repeats. By genotyping 17 of these inversions in a diverse sample of human individuals, including many of European origin and several non-human primates, we have carried out the most complete genotyping effort of human inversions to date. The results of our study indicate that a high proportion of these inversions are recurrent and have occurred multiple times during evolution. This represents an example of the plasticity of the genome and opens a new paradigm in the study of inversions, challenging the common view that inversions have a unique origin.


Vyšlo v časopise: Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence. PLoS Genet 10(3): e32767. doi:10.1371/journal.pgen.1004208
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004208

Souhrn

Inversions have been an evolutionary biology model for almost a century, and recently the discovery of a high amount of structural variation in multiple organisms, including humans, has renewed the interest in them. Since early on, it was shown that they were adaptive and that they were involved in human diseases. However, in humans, the study of inversions has lagged behind due to important limitations in the experimental methods to analyze them. Here, we have optimized a technique for high-throughput validation and genotyping of inversions mediated by inverted repeats. By genotyping 17 of these inversions in a diverse sample of human individuals, including many of European origin and several non-human primates, we have carried out the most complete genotyping effort of human inversions to date. The results of our study indicate that a high proportion of these inversions are recurrent and have occurred multiple times during evolution. This represents an example of the plasticity of the genome and opens a new paradigm in the study of inversions, challenging the common view that inversions have a unique origin.


Zdroje

1. ConradDF, PintoD, RedonR, FeukL, GokcumenO, et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704–712.

2. CooperGM, CoeBP, GirirajanS, RosenfeldJA, VuTH, et al. (2011) A copy number variation morbidity map of developmental delay. Nat Genet 43: 838–846.

3. CraddockN, HurlesME, CardinN, PearsonRD, PlagnolV, et al. (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464: 713–720.

4. FeukL (2010) Inversion variants in the human genome: role in disease and genome architecture. Genome Med 2: 11.

5. HoffmannAA, RiesebergLH (2008) Revisiting the impact of inversions in evolution: From population genetic markers to drivers of adaptive shifts and speciation? Annu Rev Ecol Evol Syst 39: 21–42.

6. KirkpatrickM (2012) How and why chromosome inversions evolve. PLoS Biol 8: e1000501.

7. LakichD, KazazianHHJr, AntonarakisSE, GitschierJ (1993) Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nat Genet 5: 236–241.

8. TantisiraKG, LazarusR, LitonjuaAA, KlandermanB, WeissST (2008) Chromosome 17: association of a large inversion polymorphism with corticosteroid response in asthma. Pharmacogenet Genomics 18: 733–737.

9. SmallK, IberJ, WarrenST (1997) Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Nat Genet 16: 96–99.

10. SmallK, WarrenST (1998) Emerin deletions occurring on both Xq28 inversion backgrounds. Hum Mol Genet 7: 135–139.

11. GiglioS, CalvariV, GregatoG, GimelliG, CamaniniS, et al. (2002) Heterozygous submicroscopic inversions involving olfactory receptor-gene clusters mediate the recurrent t(4;8)(p16;p23) translocation. Am J Hum Genet 71: 276–285.

12. AntonacciF, KiddJM, Marques-BonetT, VenturaM, SiswaraP, et al. (2009) Characterization of six human disease-associated inversion polymorphisms. Hum Mol Genet 18: 2555–2566.

13. KoolenDA, VissersLE, PfundtR, de LeeuwN, KnightSJ, et al. (2006) A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat Genet 38: 999–1001.

14. StefanssonH, HelgasonA, ThorleifssonG, SteinthorsdottirV, MassonG, et al. (2005) A common inversion under selection in Europeans. Nat Genet 37: 129–137.

15. EntesarianM, CarlssonB, MansouriMR, StattinEL, HolmbergE, et al. (2009) A chromosome 10 variant with a 12 Mb inversion [inv(10)(q11.22q21.1)] identical by descent and frequent in the Swedish population. Am J Med Genet A 149A: 380–386.

16. GillingM, DullingerJS, GeskS, Metzke-HeidemannS, SiebertR, et al. (2006) Breakpoint cloning and haplotype analysis indicate a single origin of the common Inv(10)(p11.2q21.2) mutation among northern Europeans. Am J Hum Genet 78: 878–883.

17. GimelliG, PujanaMA, PatricelliMG, RussoS, GiardinoD, et al. (2003) Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet 12: 849–858.

18. MartinJ, HanC, GordonLA, TerryA, PrabhakarS, et al. (2004) The sequence and analysis of duplication-rich human chromosome 16. Nature 432: 988–994.

19. OsborneLR, LiM, PoberB, ChitayatD, BodurthaJ, et al. (2001) A 1.5 million-base pair inversion polymorphism in families with Williams-Beuren syndrome. Nat Genet 29: 321–325.

20. PangAW, MigitaO, MacdonaldJR, FeukL, SchererSW (2013) Mechanisms of formation of structural variation in a fully sequenced human genome. Hum Mutat 34: 345–354.

21. SalmMP, HorswellSD, HutchisonCE, SpeedyHE, YangX, et al. (2012) The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism. Genome Res 22: 1144–1153.

22. StarkeH, SeidelJ, HennW, ReichardtS, VollethM, et al. (2002) Homologous sequences at human chromosome 9 bands p12 and q13–21.1 are involved in different patterns of pericentric rearrangements. Eur J Hum Genet 10: 790–800.

23. KiddJM, CooperGM, DonahueWF, HaydenHS, SampasN, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56–64.

24. KiddJM, GravesT, NewmanTL, FultonR, HaydenHS, et al. (2010) A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143: 837–847.

25. KorbelJO, UrbanAE, AffourtitJP, GodwinB, GrubertF, et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420–426.

26. ThomasNS, BryantV, MaloneyV, CockwellAE, JacobsPA (2008) Investigation of the origins of human autosomal inversions. Hum Genet 123: 607–616.

27. FeukL, MacDonaldJR, TangT, CarsonAR, LiM, et al. (2005) Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLoS Genet 1: e56.

28. LevyS, SuttonG, NgPC, FeukL, HalpernAL, et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5: e254.

29. AhnSM, KimTH, LeeS, KimD, GhangH, et al. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res 19: 1622–1629.

30. McKernanKJ, PeckhamHE, CostaGL, McLaughlinSF, FuY, et al. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19: 1527–1541.

31. TuzunE, SharpAJ, BaileyJA, KaulR, MorrisonVA, et al. (2005) Fine-scale structural variation of the human genome. Nat Genet 37: 727–732.

32. WangJ, WangW, LiR, LiY, TianG, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60–65.

33. Lucas-LledóJI, CáceresM (2013) On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing. PLoS One 8: e61292.

34. Onishi-SeebacherM, KorbelJO (2011) Challenges in studying genomic structural variant formation mechanisms: the short-read dilemma and beyond. Bioessays 33: 840–850.

35. BansalV, BashirA, BafnaV (2007) Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res 17: 219–230.

36. MaJ, AmosCI (2012) Investigation of inversion polymorphisms in the human genome using principal components analysis. PLoS One 7: e40224.

37. CáceresA, SindiSS, RaphaelBJ, CáceresM, GonzálezJR (2012) Identification of polymorphic inversions from genotypes. BMC Bioinformatics 13: 28.

38. LiuQ, NozariG, SommerSS (1998) Single-tube polymerase chain reaction for rapid diagnosis of the inversion hotspot of mutation in hemophilia A. Blood 92: 1458–1459.

39. RossettiLC, RadicCP, AbelleyroMM, LarripaIB, De BrasiCD (2011) Eighteen years of molecular genotyping the hemophilia inversion hotspot: From southern blot to inverse shifting-PCR. Int J Mol Sci 12: 7271–7285.

40. TurnerDJ, ShendureJ, PorrecaG, ChurchG, GreenP, et al. (2006) Assaying chromosomal inversions by single-molecule haplotyping. Nat Methods 3: 439–445.

41. TurnerDJ, Tyler-SmithC, HurlesME (2008) Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping. Nucleic Acids Res 36: e82.

42. OchmanH, GerberAS, HartlDL (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120: 621–623.

43. PavlopoulosA (2011) Identification of DNA sequences that flank a known region by inverse PCR. Methods Mol Biol 772: 267–275.

44. SaitsuH, OsakaH, SugiyamaS, KurosawaK, MizuguchiT, et al. (2012) Early infantile epileptic encephalopathy associated with the disrupted gene encoding Slit-Robo Rho GTPase activating protein 2 (SRGAP2). Am J Med Genet A 158A: 199–205.

45. ThorsenJ, MicciF, HeimS (2011) Identification of chromosomal breakpoints of cancer-specific translocations by rolling circle amplification and long-distance inverse PCR. Cancer Genet 204: 458–461.

46. PengZ, ZhaoZ, NathN, FroulaJL, ClumA, et al. (2012) Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. PLoS One 7: e29437.

47. RossettiLC, RadicCP, LarripaIB, De BrasiCD (2005) Genotyping the hemophilia inversion hotspot by use of inverse PCR. Clin Chem 51: 1154–1158.

48. RossettiLC, RadicCP, LarripaIB, De BrasiCD (2008) Developing a new generation of tests for genotyping hemophilia-causative rearrangements involving int22h and int1h hotspots in the factor VIII gene. J Thromb Haemost 6: 830–836.

49. Abou-ElewH, AhmedH, RaslanH, AbdelwahabM, HammoudR, et al. (2011) Genotyping of intron 22-related rearrangements of F8 by inverse-shifting PCR in Egyptian hemophilia A patients. Ann Hematol 90: 579–584.

50. FujitaJ, MiyawakiY, SuzukiA, MakiA, OkuyamaE, et al. (2012) A possible mechanism for Inv22-related F8 large deletions in severe hemophilia A patients with high responding factor VIII inhibitors. J Thromb Haemost 10: 2099–2107.

51. HeZH, ChenSF, ChenJ, JiangWY (2012) A modified I-PCR to detect the factor VIII Inv22 for genetic diagnosis and prenatal diagnosis in haemophilia A. Haemophilia 18: 452–456.

52. AltshulerDM, GibbsRA, PeltonenL, DermitzakisE, SchaffnerSF, et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52–58.

53. AbecasisGR, AutonA, BrooksLD, DePristoMA, DurbinRM, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56–65.

54. Martínez-FundichelyA, CasillasS, EgeaR, RamiaM, BarbadillaA, et al. (2013) InvFEST, a database integrating information of polymorphic inversions in the human genome. Nucleic Acids Res 42: D1027–D1032.

55. ChurchDM, SchneiderVA, GravesT, AugerK, CunninghamF, et al. (2011) Modernizing reference genome assemblies. PLoS Biol 9: e1001091.

56. WoYY, PengSH, PanFM (2006) Enrichment of circularized target DNA by inverse polymerase chain reaction. Anal Biochem 358: 149–151.

57. StephensM, DonnellyP (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73: 1162–1169.

58. StephensM, SmithNJ, DonnellyP (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978–989.

59. CáceresM (2007) National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program (2007) SullivanRT, ThomasJW (2007) A recurrent inversion on the eutherian X chromosome. Proc Natl Acad Sci U S A 104: 18571–18576.

60. Krimbas CB, Powell JR, editors(1992) Drosophila Inversion Polymorphism. Boca Raton, FL.: CRC Press. 576 p.

61. WangJ, FanHC, BehrB, QuakeSR (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150: 402–412.

62. BerchowitzLE, CopenhaverGP (2010) Genetic interference: don't stand so close to me. Curr Genomics 11: 91–102.

63. ChenJM, CooperDN, ChuzhanovaN, FerecC, PatrinosGP (2007) Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet 8: 762–775.

64. DengL, TangX, HaoX, ChenW, LinJ, et al. (2011) Genetic flux between h1 and h2 haplotypes of the 17q21.31 inversion in European population. Genomics Proteomics Bioinformatics 9: 113–118.

65. ComeronJM, RatnappanR, BailinS (2012) The many landscapes of recombination in Drosophila melanogaster. PLoS Genet 8: e1002905.

66. BagnallRD, WaseemN, GreenPM, GiannelliF (2002) Recurrent inversion breaking intron 1 of the factor VIII gene is a frequent cause of severe hemophilia A. Blood 99: 168–174.

67. ZodyMC, JiangZ, FungHC, AntonacciF, HillierLW, et al. (2008) Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat Genet 40: 1076–1083.

68. FickelscherI, LiehrT, WattsK, BryantV, BarberJC, et al. (2007) The variant inv(2)(p11.2q13) is a genuinely recurrent rearrangement but displays some breakpoint heterogeneity. Am J Hum Genet 81: 847–856.

69. FloresM, MoralesL, Gonzaga-JaureguiC, Dominguez-VidanaR, ZepedaC, et al. (2007) Recurrent DNA inversion rearrangements in the human genome. Proc Natl Acad Sci U S A 104: 6099–6106.

70. MolinaO, AntonE, VidalF, BlancoJ (2012) High rates of de novo 15q11q13 inversions in human spermatozoa. Mol Cytogenet 5: 11.

71. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. 1626 p.

72. NCBI Resource Coordinators (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 41: D8–D20.

73. VinczeT, PosfaiJ, RobertsRJ (2003) NEBcutter: A program to cleave DNA with restriction enzymes. Nucleic Acids Res 31: 3688–3691.

74. UntergasserA, NijveenH, RaoX, BisselingT, GeurtsR, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71–74.

75. PfafflMW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45.

76. ExcoffierL, LavalG, SchneiderS (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47–50.

77. BarrettJC, FryB, MallerJ, DalyMJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263–265.

78. BandeltHJ, ForsterP, RohlA (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37–48.

79. FelsensteinJ (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164–166.

80. MeyerM, KircherM, GansaugeMT, LiH, RacimoF, et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222–226.

81. LibradoP, RozasJ (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2014 Číslo 3
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#