Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements.
OBJECTIVE
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 BglII 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 the 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.
Jobanputra
Vaidehi
V
Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA.
Sebat
Jonathan
J
Troge
Jennifer
J
Chung
Wendy
W
Anyane-Yeboa
Kwame
K
Wigler
Michael
M
Warburton
Dorothy
D
D002675:Child, Preschool; D002869:Chromosome Aberrations; D003582:Cytogenetics; D018628:Gene Dosage; D020869:Gene Expression Profiling; D005820:Genetic Testing; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007223:Infant; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D012680:Sensitivity and Specificity