Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: Evidence for differences and commonalities in size distributions and size restrictions

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Schaap, Mireille ^a   Lemmers, Richard J L F ^a   Maassen, Roel ^a   van der Vliet, Patrick J ^a   Hoogerheide, Lennart F ^b   van Dijk, Herman K ^c   Baştürk, Nalan ^c,d   de Knijff, Peter ^a   van der Maarel, Silvère M ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c ERASMUS UNIVERSITY ROTTERDAM   (Netherlands)

^d Rimini Centre for Economic Analysis   (Italy)

Author keywords

Bayes theorem; DNA copy number variations; Population genetics; Tandem repeat sequences

Indexed keywords

AFRICAN AMERICAN; ALLELE; ARTICLE; ASIAN; CAUCASIAN; CHROMOSOME 10Q; CHROMOSOME 13Q; CHROMOSOME 17Q; CHROMOSOME 4P; CHROMOSOME 4Q; CHROMOSOME 5P; CHROMOSOME POLYMORPHISM; CONTROLLED STUDY; COPY NUMBER VARIATION; CT47 GENE; D4Z4 GENE; DXZ4 GENE; ETHNIC DIFFERENCE; FEMALE; FLJ40296 GENE; GENE; GENE LOCATION; GENETIC ASSOCIATION; GENETIC STABILITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMIC INSTABILITY; HUMAN; HUMAN CELL; HUMAN GENOME; MALE; MSR5P GENE; MUTATION RATE; MUTATIONAL ANALYSIS; NUCLEOTIDE SEQUENCE; POPULATION SIZE; RNU2 GENE; RS447 GENE; SHORT TANDEM REPEAT; X CHROMOSOME; COMPARATIVE STUDY; GENETICS; GENOME SIZE; GENOMICS; INTERNATIONAL COOPERATION; MITOSIS; NUCLEOTIDE REPEAT;

ALLELES; DNA COPY NUMBER VARIATIONS; GENOME SIZE; GENOME, HUMAN; GENOMICS; HUMANS; INTERNATIONALITY; MITOSIS; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84874446626     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-143     Document Type: Article

References (46)

1. Warburton PE, Hasson D, Guillem F, Lescale C, Jin X, Abrusan G. Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 2008, 9:533. 10.1186/1471-2164-9-533, 2588610, 18992157.
2. van Deutekom JC, Wijmenga C, van Tienhoven EA, Gruter AM, Hewitt JE, Padberg GW, van Ommen GJ, Hofker MH, Frants RR. FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. Hum Mol Genet 1993, 2:2037-2042. 10.1093/hmg/2.12.2037, 8111371.
3. Wijmenga C, Hewitt JE, Sandkuijl LA, Clark LN, Wright TJ, Dauwerse HG, Gruter AM, Hofker MH, Moerer P, Williamson R, van Ommen GJ, Padberg GW, Frants RR. Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy. Nat Genet 1992, 2:26-30. 10.1038/ng0992-26, 1363881.
4. Lemmers RJ, van der Vliet PJ, Klooster R, Sacconi S, Camano P, Dauwerse JG, Snider L, Straasheijm KR, van Ommen GJ, Padberg GW, Miller DG, Tapscott SJ, Tawil R, Frants RR, van der Maarel SM. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science 2010, 329:1650-1653. 10.1126/science.1189044, 20724583.
5. Bakker E, Wijmenga C, Vossen RH, Padberg GW, Hewitt J, van der Wielen M, Rasmussen K, Frants RR. The FSHD-linked locus D4F104S1 (p13E-11) on 4q35 has a homologue on 10qter. Muscle Nerve 1995, 2:S39-S44.
6. Tremblay DC, Moseley S, Chadwick BP. Variation in Array Size, Monomer Composition and Expression of the Macrosatellite DXZ4. PLoS One 2011, 6:e18969. 10.1371/journal.pone.0018969, 3081327, 21544201.
7. Chadwick BP. DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts. Genome Res 2008, 18:1259-1269. 10.1101/gr.075713.107, 2493436, 18456864.
8. Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R, Tapscott SJ. DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev Cell 2012, 22:38-51. 10.1016/j.devcel.2011.11.013, 3264808, 22209328.
9. Bodega B, Ramirez GD, Grasser F, Cheli S, Brunelli S, Mora M, Meneveri R, Marozzi A, Mueller S, Battaglioli E, Ginelli E. Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation. BMC Biol 2009, 7:41. 10.1186/1741-7007-7-41, 2719609, 19607661.
10. Zeng W, de Greef JC, Chen YY, Chien R, Kong X, Gregson HC, Winokur ST, Pyle A, Robertson KD, Schmiesing JA, Kimonis VE, Balog J, Frants RR, Ball AR, Lock LF, Donovan PJ, van der Maarel SM, Yokomori K. Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet 2009, 5:e1000559. 10.1371/journal.pgen.1000559, 2700282, 19593370.
11. Balog J, Miller D, Sanchez-Curtailles E, Carbo-Marques J, Block G, Potman M, de Knijff P, Lemmers RJ, Tapscott SJ, van der Maarel SM. Epigenetic regulation of the X-chromosomal macrosatellite repeat encoding for the cancer/testis gene CT47. Eur J Hum Genet 2012, 20:185-191. 10.1038/ejhg.2011.150, 3260913, 21811308.
12. Kogi M, Fukushige S, Lefevre C, Hadano S, Ikeda JE. A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization. Genomics 1997, 42:278-283. 10.1006/geno.1997.4746, 9192848.
13. Okada T, Gondo Y, Goto J, Kanazawa I, Hadano S, Ikeda JE. Unstable transmission of the RS447 human megasatellite tandem repetitive sequence that contains the USP17 deubiquitinating enzyme gene. Hum Genet 2002, 110:302-313. 10.1007/s00439-002-0698-2, 11941478.
14. Tremblay DC, Alexander G, Moseley S, Chadwick BP. Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome. BMC Genomics 2010, 11:632. 10.1186/1471-2164-11-632, 3018141, 21078170.
15. Bruce HA, Sachs N, Rudnicki DD, Lin SG, Willour VL, Cowell JK, Conroy J, McQuaid DE, Rossi M, Gaile DP, Nowak NJ, Holmes SE, Sklar P, Ross CA, Delisi LE, Margolis R. Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations. Psychiatr Genet 2009, 19:64-71. 10.1097/YPG.0b013e3283207ff6, 19672138.
16. Pavelitz T, Rusche L, Matera AG, Scharf JM, Weiner AM. Concerted evolution of the tandem array encoding primate U2 snRNA occurs in situ, without changing the cytological context of the RNU2 locus. EMBO J 1995, 14:169-177. 398064, 7828589.
17. Chen YT, Iseli C, Venditti CA, Old LJ, Simpson AJ, Jongeneel CV. Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome. Genes Chromosomes Cancer 2006, 45:392-400. 10.1002/gcc.20298, 16382448.
18. Lemmers RJ, van der Vliet PJ, van der Gaag KJ, Zuniga S, Frants RR, de Knijff P, van der Maarel SM. Worldwide population analysis of the 4q and 10q subtelomeres identifies only four discrete interchromosomal sequence transfers in human evolution. Am J Hum Genet 2010, 86:364-377. 10.1016/j.ajhg.2010.01.035, 2833386, 20206332.
19. van der Maarel SM, Deidda G, Lemmers RJ, Van Overveld PG, van der Wielen M, Hewitt JE, Sandkuijl L, Bakker B, van Ommen GJ, Padberg GW, Frants RR. De novo facioscapulohumeral muscular dystrophy: frequent somatic mosaicism, sex-dependent phenotype, and the role of mitotic transchromosomal repeat interaction between chromosomes 4 and 10. Am J Hum Genet 2000, 66:26-35. 10.1086/302730, 1288331, 10631134.
20. Lemmers RJ, Van Overveld PG, Sandkuijl LA, Vrieling H, Padberg GW, Frants RR, van der Maarel SM. Mechanism and timing of mitotic rearrangements in the subtelomeric D4Z4 repeat involved in facioscapulohumeral muscular dystrophy. Am J Hum Genet 2004, 75:44-53. 10.1086/422175, 1182007, 15154112.
21. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science 2002, 298:2381-2385. 10.1126/science.1078311, 12493913.
22. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008, 319:1100-1104. 10.1126/science.1153717, 18292342.
23. Ellegren H. Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet 2000, 16:551-558. 10.1016/S0168-9525(00)02139-9, 11102705.
24. Levinson G, Gutman GA. High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucleic Acids Res 1987, 15:5323-5338. 10.1093/nar/15.13.5323, 305964, 3299269.
25. Lemmers RJ, Wohlgemuth M, van der Gaag KJ, van der Vliet PJ, van Teijlingen CM, de Knijff P, Padberg GW, Frants RR, van der Maarel SM. Specific sequence variations within the 4q35 region are associated with facioscapulohumeral muscular dystrophy. Am J Hum Genet 2007, 81:884-894. 10.1086/521986, 2265642, 17924332.
26. Van Overveld PG, Lemmers RJ, Deidda G, Sandkuijl L, Padberg GW, Frants RR, van der Maarel SM. Interchromosomal repeat array interactions between chromosomes 4 and 10: a model for subtelomeric plasticity. Hum Mol Genet 2000, 9:2879-2884. 10.1093/hmg/9.19.2879, 11092764.
27. Weber JL, Wong C. Mutation of human short tandem repeats. Hum Mol Genet 1993, 2:1123-1128. 10.1093/hmg/2.8.1123, 8401493.
28. Heyer E, Puymirat J, Dieltjes P, Bakker E, de Knijff P. Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees. Hum Mol Genet 1997, 6:799-803. 10.1093/hmg/6.5.799, 9158156.
29. Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Caceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE, Stone AC, Lee C. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci U S A 2006, 103:8006-8011. 10.1073/pnas.0602318103, 1472420, 16702545.
30. International HapMap Consortium The International HapMap Project. Nature 2003, 426:789-796. 10.1038/nature02168, 14685227, International HapMap Consortium.
31. Coriell Institute for Medical Research. http://www.coriell.org/.
32. UCSC Genome Browser. http://genome.ucsc.edu/.
33. GenBank. http://www.ncbi.nlm.nih.gov/genbank/.
34. RepeatMasker. http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker/.
35. Primer3. http://frodo.wi.mit.edu/primer3/.
36. NCBI Blast. http://www.ncbi.nlm.nih.gov/BLAST/.
37. Lemmers RJL, de Knijff P, van Geel M, van der Wielen MJ, Bakker E, Padberg GW, Frants RR, van der Maarel SM. Complete allele information in the diagnosis of facioscapulohumeral muscular dystrophy by triple DNA analysis. Ann Neurol 2001, 50:816-819. 10.1002/ana.10057, 11761483.
38. Berg D. Copula goodness-of-fit testing: an overview and power comparison. European Journal of Finance 2009, 15:675-701.
39. Genest C, Rémillard B, Beaudoin D. Goodness-of-fit tests for copulas: A review and a power study. Insurance: Mathematics and Economics 2009, 44:199-214.
40. Hoogerheide LF, Kaashoek JF, van Dijk HK. On the shape of posterior densities and credible sets in instrumental variable regression models with reduced rank: an application of flexible sampling methods using neural networks. Journal of Econometrics 2007, 139:154-180.
41. Hoogerheide LF, Opschoor A, van Dijk HK. A class of adaptive importance sampling weighted EM algorithms for efficient and robust posterior and predictive simulation. Journal of Econometrics 2012, 171:101-120.
42. Silverman BW. Using Kernel Density Estimates to Investigate Multimodality. Journal of the Royal Statistical Society - Series B (Methodological) 1981, 43:97-99.
43. Hall P, York M. On the Calibration of Silverman's Test for Multimodality. Statistica Sinica 2001, 11:515-536.
44. Geman S, Geman D. Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans Pattern Anal Mach Intell 1984, PAMI-6:721-741.
45. Tanner MA, Wong WH. The calculation of posterior distributions by data augmentation. J Am Stat Assoc 1987, 82:528-540.
46. Lindgren V, Ares M, Weiner AM, Francke U. Human genes for U2 small nuclear RNA map to a major adenovirus 12 modification site on chromosome 17. Nature 1985, 314:115-116. 10.1038/314115a0, 2579339.