Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements

Jobanputra, V., Sebat, J., Troge, J., Chung, W., Anyane-Yeboa, K., Wigler, M. H., Warburton, D. (February 2005) Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements. Genetics in Medicine, 7 (2). pp. 111-118. ISSN 1098-3600

URL: https://www.ncbi.nlm.nih.gov/pubmed/15714078
DOI: 10.1097/01.GIM.0000153661

Abstract

Purpose: To demonstrate the accuracy and sensitivity of Representational Oligonucleotide Microarray Analysis (ROMA) to describe copy number changes in patients with chromosomal abnormalities. Methods: ROMA was performed using Bg/II digested DNA from two cases with cytogenetically detected deletions and one case with an unbalanced terminal rearrangement detected only by subtelomeric FISH. Hybridization was to an 85,000-probe oligonucleotide microarray, providing an average resolution of 35 kb. FISH was used to confirm some of the ROMA findings. Results: By ROMA, a del(13)(q14.3q21.2) was shown to be noncontiguous, with deletions extending from 53.08 to 61.40 Mb and from 72.88 to 74.83 Mb. The 10-Mb deletion contained only six known genes. FISH confirmed L-he noncontiguous nature of the deletion, as well as a small amplification in 6q that was also found in the patient's mother. A del(4)(q12q21.2) was found by ROMA to be 23 Mb in length, from 58.8 to 81.9 Mb on chromosome 4, in agreement with the cytogenetically assigned breakpoints. ROMA showed that an unbalanced "subtelomeric" rearrangement involved a 6-Mb deletion of 22q and an 8-Mb duplication of 16q. Conclusions: ROMA can define cytogenetic aberrations with extraordinary precision. Unexpected findings included the interrupted nature of the deletion in 13q and the large size of the imbalances in the "subtelomeric" rearrangement. Together with the information from the human genome sequence and proteomics, the ability to define rearrangements with "ultra-high" resolution will improve the ability to provide accurate prognosis both prenatally and postnatally to parents of offspring with chromosomal aberrations.

Item Type: Paper
Uncontrolled Keywords: cytogenetics deletion microarray oligonucleotide ROMA human genone parkin gene PARKIN gene representational oligonucleotide microarray analysis deletions
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
Investigative techniques and equipment > ROMA
CSHL Authors:
Communities: CSHL labs > Wigler lab
Depositing User: CSHL Librarian
Date: February 2005
Date Deposited: 10 Jan 2012 17:20
Last Modified: 17 Oct 2016 15:57
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22611

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