Logo of jmedgeneJournal of Medical GeneticsVisit this articleSubmit a manuscriptReceive email alertsContact usBMJ
J Med Genet. 2004 Dec; 41(12): 916–922.
PMCID: PMC1735639

Molecular karyotyping using an SNP array for genomewide genotyping

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.

Full Text

The Full Text of this article is available as a PDF (363K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Knight SJ, Horsley SW, Regan R, Lawrie NM, Maher EJ, Cardy DL, 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]
  • Wilkie AO. 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]
  • Hollox EJ, Atia T, Cross G, Parkin T, Armour JAL. 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. [PMC free article] [PubMed]
  • 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. [PubMed]
  • 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 May;70(5):1269–1276. [PMC free article] [PubMed]
  • Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998 Oct;20(2):207–211. [PubMed]
  • 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, et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet. 2004 Mar;36(3):299–303. [PubMed]
  • 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, et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet. 2003 Dec;73(6):1261–1270. [PMC free article] [PubMed]
  • Lucito Robert, Healy John, Alexander Joan, Reiner Andrew, Esposito Diane, Chi Maoyen, Rodgers Linda, Brady Amy, Sebat Jonathan, Troge Jennifer, et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 2003 Oct;13(10):2291–2305. [PMC free article] [PubMed]
  • Bignell Graham R, Huang Jing, Greshock Joel, Watt Stephen, Butler Adam, West Sofie, Grigorova Mira, Jones Keith W, Wei Wen, Stratton Michael R, et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 2004 Feb;14(2):287–295. [PMC free article] [PubMed]
  • Knight SJ, Lese CM, Precht KS, Kuc J, Ning Y, Lucas S, Regan R, Brenan M, Nicod A, Lawrie NM, et al. An optimized set of human telomere clones for studying telomere integrity and architecture. Am J Hum Genet. 2000 Aug;67(2):320–332. [PMC free article] [PubMed]
  • Zenker M, Rittinger O, Grosse KP, Speicher MR, Kraus J, Rauch A, Trautmann U. Monosomy 1p36--a recently delineated, clinically recognizable syndrome. Clin Dysmorphol. 2002 Jan;11(1):43–48. [PubMed]
  • Zweier C, Temple IK, Beemer F, Zackai E, Lerman-Sagie T, Weschke B, Anderson CE, 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. [PMC free article] [PubMed]
  • Rauch A, Schellmoser S, Kraus C, Dörr HG, Trautmann U, Altherr MR, Pfeiffer RA, 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • Matsuzaki Hajime, Loi Halina, Dong Shoulian, Tsai Ya-Yu, Fang Joy, Law Jane, Di Xiaojun, Liu Wei-Min, Yang Geoffrey, Liu Guoying, et al. 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. [PMC free article] [PubMed]
  • Abecasis GR, Cherny SS, Cookson WO, Cardon LR. GRR: graphical representation of relationship errors. Bioinformatics. 2001 Aug;17(8):742–743. [PubMed]
  • O'Connell JR, Weeks DE. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet. 1998 Jul;63(1):259–266. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]

Articles from Journal of Medical Genetics are provided here courtesy of BMJ Group

Formats:

Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Compound
    Compound
    PubChem Compound links
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...