The Genetic Profile of CML- New Revelations with Matrix CGH.

Samples from 20 CML patients and 12 CML derived cell lines were studied by matrix comparative genomic hybridization (CGH) using 1Mbp BAC micro-arrays with increased density at the telomere regions (Spectral Genomics, Houston). The micro-arrays reproducibly delineated previously characterised gains and losses (Gribble et al., 1999 & 2003). Novel non random imbalances, gains and losses were revealed to affect either single loci or short regions summarised as follows:

i) Cryptic deletions

The cryptic deletions affected either a single BAC clone or a group of several consecutive clones. These losses were seen in chromosome areas with either normal banding or within regions of apparently balanced translocations. These include the BAC clone RP11-259N12 in the short arm of chromosome 1, found as a single BAC loss or as part of a small segment in 1p35 sub-band. Other examples include deletions of up to five consecutive BAC clones within the 9p21 region known to contain tumour suppressor genes, deletions within 14q11.2, 16p13.1 and 20q11.2/12 regions.

ii) Cryptic gain

Gain of extra copy of the BAC clone RP11-130P22 was in patients samples, which did not appear to have abnormalities of the short of chromosome 2; similarly additional copy of the RP11-96F19 clone were detected in 4 patients and 3 cells lines without evidence for aberrations of 12q24 region. Other examples of cryptic gains include regions of 16p11.2, 19p13.1 and 19q13.

iii) High level amplification

Array analysis successfully refined common amplicons within regions of known high level amplifications from the regions of 9q34.1, 22q11.2, and 8q24.13. In the 8q region three separate common amplicons were identified, all of which do not include the cMyc oncogene.

iv) Single locus nullisomy

Heterozygous deletions were found to affect a single locus located within a large chromosome segment present in only one copy. There are two such examples - (i) lack of the RP11-87O1 clone in the cell line K562, where the whole of the short arm of chromosome 9 is present in one copy only and (ii) deletion of both copies of the RP11-79J17 clone seen in the cell like KYO-1, where the short arm of chromosome 6 is monosomic.

v) Deletions of regions as large as 5Mbp adjacent to the chromosome telomeres

These were revealed by the loss of more than one BAC probe and estimated to range in size from 1 to 5 Mbp. The para-telomeric deletions frequently affected the short arms of chromosomes 4 and 12 as well as the long arm of chromosome 3.

vi) Low level imbalances

Low levels of gain or loss, indicated by ratio values more than 0.5 or less than 1.5, for large regions, spanning several chromosome bands, were seen throughout the whole chromosome complement. Most frequently involved areas include the 14q22-qter, 15q22-qter, 20p12-p12 ter as well as 20q12-qter, 19p13.1-c-q13.3 and 10p12-pter. These reflect genetic aberrations in cell clones presented at low levels (20–30%).

vii) Deletions flanking translocation breakpoints

Deletion of single BAC clone covering sequences upstream of the ABL gene was found in the cell line MC3 and 3 patients. The loss of this region on der(9)t(9;22) is well characterised and we have known by FISH that it extends 3 Mbp from ABL exon 1a in MC3 cells (Reid et al., 2003). The micro-arrays faithfully reproduced the mapping data and allowed us to size the deletions in the der(9) chromosome in the patients samples. This demonstrates the ability of the array CGH to detect cryptic deletions accompanying balanced translocations.