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American Journal of Human Genetics logoLink to American Journal of Human Genetics
. 1993 Sep;53(3):688–701.

Detection of cryptic chromosomal abnormalities in unexplained mental retardation: a general strategy using hypervariable subtelomeric DNA polymorphisms.

A O Wilkie 1
PMCID: PMC1682421  PMID: 8352277

Abstract

Given the availability of DNA from both parents, unusual segregation of hypervariable DNA polymorphisms (HVPs) in the offspring may be attributable to deletion, unbalanced chromosomal translocation, or uniparental disomy. The telomeric regions of chromosomes are rich in both genes and hypervariable minisatellite sequences and may also be particularly prone to cryptic breakage events. Here I describe and analyze a general approach to the detection of subtelomeric abnormalities and uniparental disomy in patients with unexplained mental retardation. With 29 available polymorphic systems, approximately 50%-70% of these abnormalities could currently be detected. Development of subtelomeric HVPs physically localized with respect to their telomeres should provide a valuable resource in routine diagnostics.

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Selected References

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  1. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991 Jun 21;252(5013):1651–1656. doi: 10.1126/science.2047873. [DOI] [PubMed] [Google Scholar]
  2. Altherr M. R., Bengtsson U., Elder F. F., Ledbetter D. H., Wasmuth J. J., McDonald M. E., Gusella J. F., Greenberg F. Molecular confirmation of Wolf-Hirschhorn syndrome with a subtle translocation of chromosome 4. Am J Hum Genet. 1991 Dec;49(6):1235–1242. [PMC free article] [PubMed] [Google Scholar]
  3. Antonarakis S. E., Avramopoulos D., Blouin J. L., Talbot C. C., Jr, Schinzel A. A. Mitotic errors in somatic cells cause trisomy 21 in about 4.5% of cases and are not associated with advanced maternal age. Nat Genet. 1993 Feb;3(2):146–150. doi: 10.1038/ng0293-146. [DOI] [PubMed] [Google Scholar]
  4. Bates G. P., MacDonald M. E., Baxendale S., Youngman S., Lin C., Whaley W. L., Wasmuth J. J., Gusella J. F., Lehrach H. Defined physical limits of the Huntington disease gene candidate region. Am J Hum Genet. 1991 Jul;49(1):7–16. [PMC free article] [PubMed] [Google Scholar]
  5. Beldjord C., Henry I., Bennani C., Vanhaeke D., Labie D. Uniparental disomy: a novel mechanism for thalassemia major. Blood. 1992 Jul 1;80(1):287–289. [PubMed] [Google Scholar]
  6. Bennett P., Vaughan J., Henderson D., Loughna S., Moore G. Association between confined placental trisomy, fetal uniparental disomy, and early intrauterine growth retardation. Lancet. 1992 Nov 21;340(8830):1284–1285. doi: 10.1016/0140-6736(92)92980-t. [DOI] [PubMed] [Google Scholar]
  7. Botstein D., White R. L., Skolnick M., Davis R. W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980 May;32(3):314–331. [PMC free article] [PubMed] [Google Scholar]
  8. Bowcock A. M., van Tonder S., Jenkins T. The haemoglobin H disease mental retardation syndrome: molecular studies on the South African case. Br J Haematol. 1984 Jan;56(1):69–78. doi: 10.1111/j.1365-2141.1984.tb01272.x. [DOI] [PubMed] [Google Scholar]
  9. Cassidy S. B., Lai L. W., Erickson R. P., Magnuson L., Thomas E., Gendron R., Herrmann J. Trisomy 15 with loss of the paternal 15 as a cause of Prader-Willi syndrome due to maternal disomy. Am J Hum Genet. 1992 Oct;51(4):701–708. [PMC free article] [PubMed] [Google Scholar]
  10. Cattanach B. M., Beechey C. V. Autosomal and X-chromosome imprinting. Dev Suppl. 1990:63–72. [PubMed] [Google Scholar]
  11. Chakravarti A., Slaugenhaupt S. A. Methods for studying recombination on chromosomes that undergo nondisjunction. Genomics. 1987 Sep;1(1):35–42. doi: 10.1016/0888-7543(87)90102-9. [DOI] [PubMed] [Google Scholar]
  12. Chakravarti A. The probability of detecting the origin of nondisjunction of autosomal trisomies. Am J Hum Genet. 1989 May;44(5):639–645. [PMC free article] [PubMed] [Google Scholar]
  13. Chao L. Y., Huff V., Tomlinson G., Riccardi V. M., Strong L. C., Saunders G. F. Genetic mosaicism in normal tissues of Wilms' tumour patients. Nat Genet. 1993 Feb;3(2):127–131. doi: 10.1038/ng0293-127. [DOI] [PubMed] [Google Scholar]
  14. Daiger S. P., Chakravarti A. Deletion mapping of polymorphic loci by apparent parental exclusion. Am J Med Genet. 1983 Jan;14(1):43–48. doi: 10.1002/ajmg.1320140108. [DOI] [PubMed] [Google Scholar]
  15. Daniel A. The size of prometaphase chromosome segments. Tables using percentages of haploid autosome length (750 band stage). Clin Genet. 1985 Sep;28(3):216–224. doi: 10.1111/j.1399-0004.1985.tb00389.x. [DOI] [PubMed] [Google Scholar]
  16. Dauwerse J. G., Wiegant J., Raap A. K., Breuning M. H., van Ommen G. J. Multiple colors by fluorescence in situ hybridization using ratio-labelled DNA probes create a molecular karyotype. Hum Mol Genet. 1992 Nov;1(8):593–598. doi: 10.1093/hmg/1.8.593. [DOI] [PubMed] [Google Scholar]
  17. Deka R., Chakravarti A., Surti U., Hauselman E., Reefer J., Majumder P. P., Ferrell R. E. Genetics and biology of human ovarian teratomas. II. Molecular analysis of origin of nondisjunction and gene-centromere mapping of chromosome I markers. Am J Hum Genet. 1990 Oct;47(4):644–655. [PMC free article] [PubMed] [Google Scholar]
  18. Donis-Keller H., Green P., Helms C., Cartinhour S., Weiffenbach B., Stephens K., Keith T. P., Bowden D. W., Smith D. R., Lander E. S. A genetic linkage map of the human genome. Cell. 1987 Oct 23;51(2):319–337. doi: 10.1016/0092-8674(87)90158-9. [DOI] [PubMed] [Google Scholar]
  19. Dworniczak B., Koppers B., Kurlemann G., Holzgreve W., Horst J., Miny P. Uniparental disomy with normal phenotype. Lancet. 1992 Nov 21;340(8830):1285–1285. doi: 10.1016/0140-6736(92)92981-k. [DOI] [PubMed] [Google Scholar]
  20. Engel E., DeLozier-Blanchet C. D. Uniparental disomy, isodisomy, and imprinting: probable effects in man and strategies for their detection. Am J Med Genet. 1991 Sep 15;40(4):432–439. doi: 10.1002/ajmg.1320400411. [DOI] [PubMed] [Google Scholar]
  21. Goodship J., Curtis A., Cross I., Brown J., Emslie J., Wolstenholme J., Bhattacharya S., Burn J. A submicroscopic translocation, t(4;10), responsible for recurrent Wolf-Hirschhorn syndrome identified by allele loss and fluorescent in situ hybridisation. J Med Genet. 1992 Jul;29(7):451–454. [PMC free article] [PubMed] [Google Scholar]
  22. Grundy P., Telzerow P., Paterson M. C., Haber D., Berman B., Li F., Garber J. Chromosome 11 uniparental isodisomy predisposing to embryonal neoplasms. Lancet. 1991 Oct 26;338(8774):1079–1080. doi: 10.1016/0140-6736(91)91937-p. [DOI] [PubMed] [Google Scholar]
  23. Hassold T. J., Pettay D., Freeman S. B., Grantham M., Takaesu N. Molecular studies of non-disjunction in trisomy 16. J Med Genet. 1991 Mar;28(3):159–162. doi: 10.1136/jmg.28.3.159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Helms C., Mishra S. K., Riethman H., Burgess A. K., Ramachandra S., Tierney C., Dorsey D., Donis-Keller H. Closure of a genetic linkage map of human chromosome 7q with centromere and telomere polymorphisms. Genomics. 1992 Dec;14(4):1041–1054. doi: 10.1016/s0888-7543(05)80128-4. [DOI] [PubMed] [Google Scholar]
  25. Henry I., Bonaiti-Pellié C., Chehensse V., Beldjord C., Schwartz C., Utermann G., Junien C. Uniparental paternal disomy in a genetic cancer-predisposing syndrome. Nature. 1991 Jun 20;351(6328):665–667. doi: 10.1038/351665a0. [DOI] [PubMed] [Google Scholar]
  26. Henry I., Puech A., Riesewijk A., Ahnine L., Mannens M., Beldjord C., Bitoun P., Tournade M. F., Landrieu P., Junien C. Somatic mosaicism for partial paternal isodisomy in Wiedemann-Beckwith syndrome: a post-fertilization event. Eur J Hum Genet. 1993;1(1):19–29. doi: 10.1159/000472384. [DOI] [PubMed] [Google Scholar]
  27. Higgs D. R., Vickers M. A., Wilkie A. O., Pretorius I. M., Jarman A. P., Weatherall D. J. A review of the molecular genetics of the human alpha-globin gene cluster. Blood. 1989 Apr;73(5):1081–1104. [PubMed] [Google Scholar]
  28. Kalousek D. K., Langlois S., Barrett I., Yam I., Wilson D. R., Howard-Peebles P. N., Johnson M. P., Giorgiutti E. Uniparental disomy for chromosome 16 in humans. Am J Hum Genet. 1993 Jan;52(1):8–16. [PMC free article] [PubMed] [Google Scholar]
  29. Kidd K. K., Bowcock A. M., Schmidtke J., Track R. K., Ricciuti F., Hutchings G., Bale A., Pearson P., Willard H. F., Gelernter J. Report of the DNA committee and catalogs of cloned and mapped genes and DNA polymorphisms. Cytogenet Cell Genet. 1989;51(1-4):622–947. doi: 10.1159/000132810. [DOI] [PubMed] [Google Scholar]
  30. Kuwano A., Ledbetter S. A., Dobyns W. B., Emanuel B. S., Ledbetter D. H. Detection of deletions and cryptic translocations in Miller-Dieker syndrome by in situ hybridization. Am J Hum Genet. 1991 Oct;49(4):707–714. [PMC free article] [PubMed] [Google Scholar]
  31. Lamb J., Harris P. C., Wilkie A. O., Wood W. G., Dauwerse J. G., Higgs D. R. De novo truncation of chromosome 16p and healing with (TTAGGG)n in the alpha-thalassemia/mental retardation syndrome (ATR-16). Am J Hum Genet. 1993 Apr;52(4):668–676. [PMC free article] [PubMed] [Google Scholar]
  32. Lamb J., Wilkie A. O., Harris P. C., Buckle V. J., Lindenbaum R. H., Barton N. J., Reeders S. T., Weatherall D. J., Higgs D. R. Detection of breakpoints in submicroscopic chromosomal translocation, illustrating an important mechanism for genetic disease. Lancet. 1989 Oct 7;2(8667):819–824. doi: 10.1016/s0140-6736(89)92995-4. [DOI] [PubMed] [Google Scholar]
  33. Laurie D. A., Hultén M. A. Further studies on chiasma distribution and interference in the human male. Ann Hum Genet. 1985 Jul;49(Pt 3):203–214. doi: 10.1111/j.1469-1809.1985.tb01694.x. [DOI] [PubMed] [Google Scholar]
  34. Ledbetter D. H. Minireview: cryptic translocations and telomere integrity. Am J Hum Genet. 1992 Sep;51(3):451–456. [PMC free article] [PubMed] [Google Scholar]
  35. Malcolm S., Clayton-Smith J., Nichols M., Robb S., Webb T., Armour J. A., Jeffreys A. J., Pembrey M. E. Uniparental paternal disomy in Angelman's syndrome. Lancet. 1991 Mar 23;337(8743):694–697. doi: 10.1016/0140-6736(91)90278-w. [DOI] [PubMed] [Google Scholar]
  36. Mascari M. J., Gottlieb W., Rogan P. K., Butler M. G., Waller D. A., Armour J. A., Jeffreys A. J., Ladda R. L., Nicholls R. D. The frequency of uniparental disomy in Prader-Willi syndrome. Implications for molecular diagnosis. N Engl J Med. 1992 Jun 11;326(24):1599–1607. doi: 10.1056/NEJM199206113262404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Mutirangura A., Greenberg F., Butler M. G., Malcolm S., Nicholls R. D., Chakravarti A., Ledbetter D. H. Multiplex PCR of three dinucleotide repeats in the Prader-Willi/Angelman critical region (15q11-q13): molecular diagnosis and mechanism of uniparental disomy. Hum Mol Genet. 1993 Feb;2(2):143–151. doi: 10.1093/hmg/2.2.143. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Nicholls R. D., Knoll J. H., Butler M. G., Karam S., Lalande M. Genetic imprinting suggested by maternal heterodisomy in nondeletion Prader-Willi syndrome. Nature. 1989 Nov 16;342(6247):281–285. doi: 10.1038/342281a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Overhauser J., Bengtsson U., McMahon J., Ulm J., Butler M. G., Santiago L., Wasmuth J. J. Prenatal diagnosis and carrier detection of a cryptic translocation by using DNA markers from the short arm of chromosome 5. Am J Hum Genet. 1989 Aug;45(2):296–303. [PMC free article] [PubMed] [Google Scholar]
  40. Pentao L., Lewis R. A., Ledbetter D. H., Patel P. I., Lupski J. R. Maternal uniparental isodisomy of chromosome 14: association with autosomal recessive rod monochromacy. Am J Hum Genet. 1992 Apr;50(4):690–699. [PMC free article] [PubMed] [Google Scholar]
  41. Petersen M. B., Bartsch O., Adelsberger P. A., Mikkelsen M., Schwinger E., Antonarakis S. E. Uniparental isodisomy due to duplication of chromosome 21 occurring in somatic cells monosomic for chromosome 21. Genomics. 1992 Jun;13(2):269–274. doi: 10.1016/0888-7543(92)90242-k. [DOI] [PubMed] [Google Scholar]
  42. Pinkel D., Landegent J., Collins C., Fuscoe J., Segraves R., Lucas J., Gray J. Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4. Proc Natl Acad Sci U S A. 1988 Dec;85(23):9138–9142. doi: 10.1073/pnas.85.23.9138. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Purvis-Smith S. G., Saville T., Manass S., Yip M. Y., Lam-Po-Tang P. R., Duffy B., Johnston H., Leigh D., McDonald B. Uniparental disomy 15 resulting from "correction" of an initial trisomy 15. Am J Hum Genet. 1992 Jun;50(6):1348–1350. [PMC free article] [PubMed] [Google Scholar]
  44. Ried T., Baldini A., Rand T. C., Ward D. C. Simultaneous visualization of seven different DNA probes by in situ hybridization using combinatorial fluorescence and digital imaging microscopy. Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1388–1392. doi: 10.1073/pnas.89.4.1388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Robinson W. P., Bottani A., Xie Y. G., Balakrishman J., Binkert F., Mächler M., Prader A., Schinzel A. Molecular, cytogenetic, and clinical investigations of Prader-Willi syndrome patients. Am J Hum Genet. 1991 Dec;49(6):1219–1234. [PMC free article] [PubMed] [Google Scholar]
  46. Rosenberg C., Blakemore K. J., Kearns W. G., Giraldez R. A., Escallon C. S., Pearson P. L., Stetten G. Analysis of reciprocal translocations by chromosome painting: applications and limitations of the technique. Am J Hum Genet. 1992 Apr;50(4):700–705. [PMC free article] [PubMed] [Google Scholar]
  47. Royle N. J., Clarkson R. E., Wong Z., Jeffreys A. J. Clustering of hypervariable minisatellites in the proterminal regions of human autosomes. Genomics. 1988 Nov;3(4):352–360. doi: 10.1016/0888-7543(88)90127-9. [DOI] [PubMed] [Google Scholar]
  48. Saccone S., De Sario A., Della Valle G., Bernardi G. The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4913–4917. doi: 10.1073/pnas.89.11.4913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Sherman S. L., Takaesu N., Freeman S. B., Grantham M., Phillips C., Blackston R. D., Jacobs P. A., Cockwell A. E., Freeman V., Uchida I. Trisomy 21: association between reduced recombination and nondisjunction. Am J Hum Genet. 1991 Sep;49(3):608–620. [PMC free article] [PubMed] [Google Scholar]
  50. Spence J. E., Perciaccante R. G., Greig G. M., Willard H. F., Ledbetter D. H., Hejtmancik J. F., Pollack M. S., O'Brien W. E., Beaudet A. L. Uniparental disomy as a mechanism for human genetic disease. Am J Hum Genet. 1988 Feb;42(2):217–226. [PMC free article] [PubMed] [Google Scholar]
  51. Spotila L. D., Sereda L., Prockop D. J. Partial isodisomy for maternal chromosome 7 and short stature in an individual with a mutation at the COL1A2 locus. Am J Hum Genet. 1992 Dec;51(6):1396–1405. [PMC free article] [PubMed] [Google Scholar]
  52. Stallings R. L., Ford A. F., Nelson D., Torney D. C., Hildebrand C. E., Moyzis R. K. Evolution and distribution of (GT)n repetitive sequences in mammalian genomes. Genomics. 1991 Jul;10(3):807–815. doi: 10.1016/0888-7543(91)90467-s. [DOI] [PubMed] [Google Scholar]
  53. Stallings R. L., Torney D. C., Hildebrand C. E., Longmire J. L., Deaven L. L., Jett J. H., Doggett N. A., Moyzis R. K. Physical mapping of human chromosomes by repetitive sequence fingerprinting. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6218–6222. doi: 10.1073/pnas.87.16.6218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Stoll C. Nonrandom distribution of exchange points in patients with reciprocal translocations. Hum Genet. 1980;56(1):89–93. doi: 10.1007/BF00281575. [DOI] [PubMed] [Google Scholar]
  55. Sutcliffe J. G. mRNA in the mammalian central nervous system. Annu Rev Neurosci. 1988;11:157–198. doi: 10.1146/annurev.ne.11.030188.001105. [DOI] [PubMed] [Google Scholar]
  56. Vasarhelyi K., Friedman J. M. Analysing rearrangement breakpoint distributions by means of binomial confidence intervals. Ann Hum Genet. 1989 Oct;53(Pt 4):375–380. doi: 10.1111/j.1469-1809.1989.tb01805.x. [DOI] [PubMed] [Google Scholar]
  57. Voss R., Ben-Simon E., Avital A., Godfrey S., Zlotogora J., Dagan J., Tikochinski Y., Hillel J. Isodisomy of chromosome 7 in a patient with cystic fibrosis: could uniparental disomy be common in humans? Am J Hum Genet. 1989 Sep;45(3):373–380. [PMC free article] [PubMed] [Google Scholar]
  58. Wahlström J. Gene map of mental retardation. J Ment Defic Res. 1990 Feb;34(Pt 1):11–27. doi: 10.1111/j.1365-2788.1990.tb01511.x. [DOI] [PubMed] [Google Scholar]
  59. Wang D., Fang H., Cantor C. R., Smith C. L. A contiguous Not I restriction map of band q22.3 of human chromosome 21. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3222–3226. doi: 10.1073/pnas.89.8.3222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Wang J. C., Passage M. B., Yen P. H., Shapiro L. J., Mohandas T. K. Uniparental heterodisomy for chromosome 14 in a phenotypically abnormal familial balanced 13/14 Robertsonian translocation carrier. Am J Hum Genet. 1991 Jun;48(6):1069–1074. [PMC free article] [PubMed] [Google Scholar]
  61. Wapenaar M. C., Petit C., Basler E., Ballabio A., Henke A., Rappold G. A., van Paassen H. M., Blonden L. A., van Ommen G. J. Physical mapping of 14 new DNA markers isolated from the human distal Xp region. Genomics. 1992 May;13(1):167–175. doi: 10.1016/0888-7543(92)90217-g. [DOI] [PubMed] [Google Scholar]
  62. Warren A. C., Chakravarti A., Wong C., Slaugenhaupt S. A., Halloran S. L., Watkins P. C., Metaxotou C., Antonarakis S. E. Evidence for reduced recombination on the nondisjoined chromosomes 21 in Down syndrome. Science. 1987 Aug 7;237(4815):652–654. doi: 10.1126/science.2955519. [DOI] [PubMed] [Google Scholar]
  63. Weissenbach J., Gyapay G., Dib C., Vignal A., Morissette J., Millasseau P., Vaysseix G., Lathrop M. A second-generation linkage map of the human genome. Nature. 1992 Oct 29;359(6398):794–801. doi: 10.1038/359794a0. [DOI] [PubMed] [Google Scholar]
  64. Welch T. R., Beischel L. S., Choi E., Balakrishnan K., Bishof N. A. Uniparental isodisomy 6 associated with deficiency of the fourth component of complement. J Clin Invest. 1990 Aug;86(2):675–678. doi: 10.1172/JCI114760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Wilkie A. O., Buckle V. J., Harris P. C., Lamb J., Barton N. J., Reeders S. T., Lindenbaum R. H., Nicholls R. D., Barrow M., Bethlenfalvay N. C. Clinical features and molecular analysis of the alpha thalassemia/mental retardation syndromes. I. Cases due to deletions involving chromosome band 16p13.3. Am J Hum Genet. 1990 Jun;46(6):1112–1126. [PMC free article] [PubMed] [Google Scholar]
  66. Wilkie A. O., Higgs D. R., Rack K. A., Buckle V. J., Spurr N. K., Fischel-Ghodsian N., Ceccherini I., Brown W. R., Harris P. C. Stable length polymorphism of up to 260 kb at the tip of the short arm of human chromosome 16. Cell. 1991 Feb 8;64(3):595–606. doi: 10.1016/0092-8674(91)90243-r. [DOI] [PubMed] [Google Scholar]
  67. Wilkie A. O., Malcolm S., Pembrey M. E. Isodisomy in BWS chromosomes. Nature. 1991 Oct 31;353(6347):802–802. doi: 10.1038/353802b0. [DOI] [PubMed] [Google Scholar]
  68. Williamson R., Bowcock A., Kidd K., Pearson P., Schmidtke J., Chan H. S., Chipperfield M., Cooper D. N., Hewitt J., Lewitter F. Report of the DNA committee and catalogues of cloned and mapped genes and DNA polymorphisms. Cytogenet Cell Genet. 1990;55(1-4):457–778. doi: 10.1159/000133027. [DOI] [PubMed] [Google Scholar]

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