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. 2004 Dec;41(12):916–922. doi: 10.1136/jmg.2004.022855

Molecular karyotyping using an SNP array for genomewide genotyping

A Rauch 1, F Ruschendorf 1, J Huang 1, U Trautmann 1, C Becker 1, C Thiel 1, K Jones 1, A Reis 1, P Nurnberg 1
PMCID: PMC1735639  PMID: 15591277

Abstract

Background: Chromosomal imbalances are a major cause of developmental defects as well as cancer and often constitute the key in identification of novel disease related genes. Classical cytogenetic methods are limited in resolution and dependent on highly skilled labour, while methods with higher resolution, based on molecular cytogenetics approaches such as matrix CGH, are not widely available.

Methods: We have developed and evaluated a method we term "molecular karyotyping", using readily available and easy to handle oligonucleotide arrays originally designed for parallel genomewide analysis of over 10 000 SNPs. We show that we can easily and reliably detect unbalanced chromosomal aberrations of various sizes from as little as 250 ng of DNA on a single microarray, based on fluorescence intensity information from clusters of SNPs.

Results: We determined the resolution of this method through analysis of 20 trios with 21 previously confirmed subtle aberrations sizing between 0.2 and 13 Mb. Duplications and deletions of at least 5 Mb in size were reliably detectable, but detection of smaller aberrations was dependent on the number of SNPs they contained, thus seven of 10 different deletions analysed, with sizes ranging from 0.2 to 3.7 Mb, were not detectable due to insufficient SNP densitiy in the respective region.

Conclusions: Deduction of reliable cut off levels for array peaks in our series of well characterised patients allows the use of the GeneChip Mapping 10K SNP array for performing rapid molecular karyotyping from small amounts of DNA for the detection of even subtle deletions and duplications with high sensitivity and specificity.

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Selected References

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  1. Abecasis G. R., Cherny S. S., Cookson W. O., Cardon L. R. GRR: graphical representation of relationship errors. Bioinformatics. 2001 Aug;17(8):742–743. doi: 10.1093/bioinformatics/17.8.742. [DOI] [PubMed] [Google Scholar]
  2. Bignell Graham R., Huang Jing, Greshock Joel, Watt Stephen, Butler Adam, West Sofie, Grigorova Mira, Jones Keith W., Wei Wen, Stratton Michael R. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 2004 Feb;14(2):287–295. doi: 10.1101/gr.2012304. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Flint Jonathan, Knight Samantha. The use of telomere probes to investigate submicroscopic rearrangements associated with mental retardation. Curr Opin Genet Dev. 2003 Jun;13(3):310–316. doi: 10.1016/s0959-437x(03)00049-2. [DOI] [PubMed] [Google Scholar]
  4. Hollox E. J., Atia T., Cross G., Parkin T., Armour J. A. L. High throughput screening of human subtelomeric DNA for copy number changes using multiplex amplifiable probe hybridisation (MAPH). J Med Genet. 2002 Nov;39(11):790–795. doi: 10.1136/jmg.39.11.790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Huang Jing, Wei Wen, Zhang Jane, Liu Guoying, Bignell Graham R., Stratton Michael R., Futreal P. Andrew, Wooster Richard, Jones Keith W., Shapero Michael H. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics. 2004 May;1(4):287–299. doi: 10.1186/1479-7364-1-4-287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ishkanian Adrian S., Malloff Chad A., Watson Spencer K., DeLeeuw Ronald J., Chi Bryan, Coe Bradley P., Snijders Antoine, Albertson Donna G., Pinkel Daniel, Marra Marco A. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet. 2004 Feb 15;36(3):299–303. doi: 10.1038/ng1307. [DOI] [PubMed] [Google Scholar]
  7. Knight S. J., Horsley S. W., Regan R., Lawrie N. M., Maher E. J., Cardy D. L., Flint J., Kearney L. Development and clinical application of an innovative fluorescence in situ hybridization technique which detects submicroscopic rearrangements involving telomeres. Eur J Hum Genet. 1997 Jan-Feb;5(1):1–8. [PubMed] [Google Scholar]
  8. Knight S. J., Lese C. M., Precht K. S., Kuc J., Ning Y., Lucas S., Regan R., Brenan M., Nicod A., Lawrie N. M. An optimized set of human telomere clones for studying telomere integrity and architecture. Am J Hum Genet. 2000 Jun 22;67(2):320–332. doi: 10.1086/302998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lucito Robert, Healy John, Alexander Joan, Reiner Andrew, Esposito Diane, Chi Maoyen, Rodgers Linda, Brady Amy, Sebat Jonathan, Troge Jennifer. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 2003 Sep 15;13(10):2291–2305. doi: 10.1101/gr.1349003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Matsuzaki Hajime, Loi Halina, Dong Shoulian, Tsai Ya-Yu, Fang Joy, Law Jane, Di Xiaojun, Liu Wei-Min, Yang Geoffrey, Liu Guoying. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res. 2004 Mar;14(3):414–425. doi: 10.1101/gr.2014904. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. O'Connell J. R., Weeks D. E. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet. 1998 Jul;63(1):259–266. doi: 10.1086/301904. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D., Collins C., Kuo W. L., Chen C., Zhai Y. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998 Oct;20(2):207–211. doi: 10.1038/2524. [DOI] [PubMed] [Google Scholar]
  13. Rauch A., Schellmoser S., Kraus C., Dörr H. G., Trautmann U., Altherr M. R., Pfeiffer R. A., Reis A. First known microdeletion within the Wolf-Hirschhorn syndrome critical region refines genotype-phenotype correlation. Am J Med Genet. 2001 Apr 1;99(4):338–342. doi: 10.1002/ajmg.1203. [DOI] [PubMed] [Google Scholar]
  14. Rauch Anita, Beese Maike, Mayatepek Ertan, Dörr Helmut-Günther, Wenzel Dieter, Reis André, Trautmann Udo. A novel 5q35.3 subtelomeric deletion syndrome. Am J Med Genet A. 2003 Aug 15;121A(1):1–8. doi: 10.1002/ajmg.a.20173. [DOI] [PubMed] [Google Scholar]
  15. Rauch Anita, Hofbeck Michael, Cesnjevar Robert, Koch Andreas, Rauch Ralf, Buheitel Gernot, Singer Helmut, Weyand Michael. Search for somatic 22q11.2 deletions in patients with conotruncal heart defects. Am J Med Genet A. 2004 Jan 15;124A(2):165–169. doi: 10.1002/ajmg.a.20323. [DOI] [PubMed] [Google Scholar]
  16. Rooms Liesbeth, Reyniers Edwin, van Luijk Rob, Scheers Stefaan, Wauters Jan, Ceulemans Berten, Van Den Ende Jenneke, Van Bever Yolande, Kooy R. Frank. Subtelomeric deletions detected in patients with idiopathic mental retardation using multiplex ligation-dependent probe amplification (MLPA). Hum Mutat. 2004 Jan;23(1):17–21. doi: 10.1002/humu.10300. [DOI] [PubMed] [Google Scholar]
  17. Schoumans Jacqueline, Nielsen Kate, Jeppesen Iben, Anderlid Britt-Marie, Blennow Elisabeth, Brøndum-Nielsen Karen, Nordenskjöld Magnus. A comparison of different metaphase CGH methods for the detection of cryptic chromosome aberrations of defined size. Eur J Hum Genet. 2004 Jun;12(6):447–454. doi: 10.1038/sj.ejhg.5201175. [DOI] [PubMed] [Google Scholar]
  18. Thiel Christian T., Kraus Cornelia, Rauch Anita, Ekici Arif B., Rautenstrauss Bernd, Reis André. A new quantitative PCR multiplex assay for rapid analysis of chromosome 17p11.2-12 duplications and deletions leading to HMSN/HNPP. Eur J Hum Genet. 2003 Feb;11(2):170–178. doi: 10.1038/sj.ejhg.5200920. [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. Vissers Lisenka E. L. M., de Vries Bert B. A., Osoegawa Kazutoyo, Janssen Irene M., Feuth Ton, Choy Chik On, Straatman Huub, van der Vliet Walter, Huys Erik H. L. P. G., van Rijk Anke. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet. 2003 Nov 18;73(6):1261–1270. doi: 10.1086/379977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Wilkie A. O. Detection of cryptic chromosomal abnormalities in unexplained mental retardation: a general strategy using hypervariable subtelomeric DNA polymorphisms. Am J Hum Genet. 1993 Sep;53(3):688–701. [PMC free article] [PubMed] [Google Scholar]
  22. Zenker M., Rittinger O., Grosse K. P., Speicher M. R., Kraus J., Rauch A., Trautmann U. Monosomy 1p36--a recently delineated, clinically recognizable syndrome. Clin Dysmorphol. 2002 Jan;11(1):43–48. doi: 10.1097/00019605-200201000-00009. [DOI] [PubMed] [Google Scholar]
  23. Zweier C., Temple I. K., Beemer F., Zackai E., Lerman-Sagie T., Weschke B., Anderson C. E., Rauch A. Characterisation of deletions of the ZFHX1B region and genotype-phenotype analysis in Mowat-Wilson syndrome. J Med Genet. 2003 Aug;40(8):601–605. doi: 10.1136/jmg.40.8.601. [DOI] [PMC free article] [PubMed] [Google Scholar]

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