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. 2004 Dec;41(12):908–915. doi: 10.1136/jmg.2004.023184

Detection of aneuploidies by paralogous sequence quantification

S Deutsch 1, U Choudhury 1, G Merla 1, C Howald 1, A Sylvan 1, S Antonarakis 1
PMCID: PMC1735643  PMID: 15591276

Abstract

Background: Chromosomal aneuploidies are a common cause of congenital disorders associated with cognitive impairment and multiple dysmorphic features. Pre-natal diagnosis of aneuploidies is most commonly performed by the karyotyping of fetal cells obtained by amniocentesis or chorionic villus sampling, but this method is labour intensive and requires about 14 days to complete.

Methods: We have developed a PCR based method for the detection of targeted chromosome number abnormalities termed paralogous sequence quantification (PSQ), based on the use of paralogous genes. Paralogous sequences have a high degree of sequence identity, but accumulate nucleotide substitutions in a locus specific manner. These sequence differences, which we term paralogous sequence mismatches (PSMs), can be quantified using pyrosequencing technology, to estimate the relative dosage between different chromosomes. We designed 10 assays for the detection of trisomies of chromosomes 13, 18, and 21 and sex chromosome aneuploidies.

Results: We evaluated the performance of this method on 175 DNAs, highly enriched for abnormal samples. A correct and unambiguous diagnosis was given for 119 out of 120 aneuploid samples as well as for all the controls. One sample which gave an intermediate value for the chromosome 13 assays could not be diagnosed.

Conclusions: Our data suggests that PSQ is a robust, easy to interpret, and easy to set up method for the diagnosis of common aneuploidies, and can be performed in less than 48 h, representing a competitive alternative for widespread use in diagnostic laboratories.

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Selected References

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  1. Adinolfi M., Pertl B., Sherlock J. Rapid detection of aneuploidies by microsatellite and the quantitative fluorescent polymerase chain reaction. Prenat Diagn. 1997 Dec;17(13):1299–1311. [PubMed] [Google Scholar]
  2. Alderborn A., Kristofferson A., Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res. 2000 Aug;10(8):1249–1258. doi: 10.1101/gr.10.8.1249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Armour J. A. L., Barton D. E., Cockburn D. J., Taylor G. R. The detection of large deletions or duplications in genomic DNA. Hum Mutat. 2002 Nov;20(5):325–337. doi: 10.1002/humu.10133. [DOI] [PubMed] [Google Scholar]
  4. Armour J. A., Sismani C., Patsalis P. C., Cross G. Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res. 2000 Jan 15;28(2):605–609. doi: 10.1093/nar/28.2.605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Deutsch Samuel, Rideau Alexandra, Bochaton-Piallat Marie-Luce, Merla Giuseppe, Geinoz Antoine, Gabbiani Giulio, Schwede Torsten, Matthes Thomas, Antonarakis Stylianos E., Beris Photis. Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome. Blood. 2003 Mar 20;102(2):529–534. doi: 10.1182/blood-2002-09-2783. [DOI] [PubMed] [Google Scholar]
  6. Hochberg Ephraim P., Miklos David B., Neuberg Donna, Eichner Daniel A., McLaughlin Stephen F., Mattes-Ritz Alex, Alyea Edwin P., Antin Joseph H., Soiffer Robert J., Ritz Jerome. A novel rapid single nucleotide polymorphism (SNP)-based method for assessment of hematopoietic chimerism after allogeneic stem cell transplantation. Blood. 2002 Aug 29;101(1):363–369. doi: 10.1182/blood-2002-05-1365. [DOI] [PubMed] [Google Scholar]
  7. Hultén Maj A., Dhanjal Seema, Pertl Barbara. Rapid and simple prenatal diagnosis of common chromosome disorders: advantages and disadvantages of the molecular methods FISH and QF-PCR. Reproduction. 2003 Sep;126(3):279–297. doi: 10.1530/rep.0.1260279. [DOI] [PubMed] [Google Scholar]
  8. JACOBS P. A., BAIKIE A. G., COURT BROWN W. M., STRONG J. A. The somatic chromosomes in mongolism. Lancet. 1959 Apr 4;1(7075):710–710. doi: 10.1016/s0140-6736(59)91892-6. [DOI] [PubMed] [Google Scholar]
  9. Kuo W. L., Tenjin H., Segraves R., Pinkel D., Golbus M. S., Gray J. Detection of aneuploidy involving chromosomes 13, 18, or 21, by fluorescence in situ hybridization (FISH) to interphase and metaphase amniocytes. Am J Hum Genet. 1991 Jul;49(1):112–119. [PMC free article] [PubMed] [Google Scholar]
  10. LEJEUNE J., GAUTIER M., TURPIN R. Etude des chromosomes somatiques de neuf enfants mongoliens. C R Hebd Seances Acad Sci. 1959 Mar 16;248(11):1721–1722. [PubMed] [Google Scholar]
  11. Lander E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860–921. doi: 10.1038/35057062. [DOI] [PubMed] [Google Scholar]
  12. Mann K., Fox S. P., Abbs S. J., Yau S. C., Scriven P. N., Docherty Z., Ogilvie C. M. Development and implementation of a new rapid aneuploidy diagnostic service within the UK National Health Service and implications for the future of prenatal diagnosis. Lancet. 2001 Sep 29;358(9287):1057–1061. doi: 10.1016/S0140-6736(01)06183-9. [DOI] [PubMed] [Google Scholar]
  13. Neve B., Froguel P., Corset L., Vaillant E., Vatin V., Boutin P. Rapid SNP allele frequency determination in genomic DNA pools by pyrosequencing. Biotechniques. 2002 May;32(5):1138–1142. doi: 10.2144/02325dd03. [DOI] [PubMed] [Google Scholar]
  14. Pertl B., Kopp S., Kroisel P. M., Tului L., Brambati B., Adinolfi M. Rapid detection of chromosome aneuploidies by quantitative fluorescence PCR: first application on 247 chorionic villus samples. J Med Genet. 1999 Apr;36(4):300–303. [PMC free article] [PubMed] [Google Scholar]
  15. Pertl B., Yau S. C., Sherlock J., Davies A. F., Mathew C. G., Adinolfi M. Rapid molecular method for prenatal detection of Down's syndrome. Lancet. 1994 May 14;343(8907):1197–1198. doi: 10.1016/s0140-6736(94)92404-x. [DOI] [PubMed] [Google Scholar]
  16. Qiu Ping, Soder George J., Sanfiorenzo Vincent J., Wang Luquan, Greene Jonathan R., Fritz Mary Ann, Cai Xiao-Yan. Quantification of single nucleotide polymorphisms by automated DNA sequencing. Biochem Biophys Res Commun. 2003 Sep 19;309(2):331–338. doi: 10.1016/j.bbrc.2003.08.008. [DOI] [PubMed] [Google Scholar]
  17. Slater H. R., Bruno D. L., Ren H., Pertile M., Schouten J. P., Choo K. H. A. Rapid, high throughput prenatal detection of aneuploidy using a novel quantitative method (MLPA). J Med Genet. 2003 Dec;40(12):907–912. doi: 10.1136/jmg.40.12.907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Snijders A. M., Nowak N., Segraves R., Blackwood S., Brown N., Conroy J., Hamilton G., Hindle A. K., Huey B., Kimura K. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001 Nov;29(3):263–264. doi: 10.1038/ng754. [DOI] [PubMed] [Google Scholar]
  19. Veltman Joris A., Schoenmakers Eric F. P. M., Eussen Bert H., Janssen Irene, Merkx Gerard, van Cleef Brigitte, van Ravenswaaij Conny M., Brunner Han G., Smeets Dominique, van Kessel Ad Geurts. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet. 2002 Apr 9;70(5):1269–1276. doi: 10.1086/340426. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Venter J. C., Adams M. D., Myers E. W., Li P. W., Mural R. J., Sutton G. G., Smith H. O., Yandell M., Evans C. A., Holt R. A. The sequence of the human genome. Science. 2001 Feb 16;291(5507):1304–1351. doi: 10.1126/science.1058040. [DOI] [PubMed] [Google Scholar]
  21. Verma L., Macdonald F., Leedham P., McConachie M., Dhanjal S., Hultén M. Rapid and simple prenatal DNA diagnosis of Down's syndrome. Lancet. 1998 Jul 4;352(9121):9–12. doi: 10.1016/S0140-6736(97)11090-X. [DOI] [PubMed] [Google Scholar]

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