K562 is a cell line with two acrocentric marker chromosomes containing abnormally banded regions (ABRs), derived from a Ph-positive chronic myelogenous leukemia (CML) patient. Using reverse and forward chromosome painting FISH analysis, we found that 9q34, 13q31, and 22q11 regions co-amplified in the ABRs-bearing acrocentric marker chromosomes of K562. Utilizing the ABRs of the cell line as target DNA for cDNA selection, we established a simple procedure for chromosome region-specific cDNA isolation. After first strand cDNA synthesis from fetal brain mRNAs, short fragment cDNAs (sf-cDNAs) were synthesized with a two-step amplification system by use of our modified Degenerate Oligonucleotide Primed Shuttle Polymerase Chain Reaction (DOP-Shuttle-PCR) method. The sf-cDNAs were hybridized onto RNase A treated metaphases from K562, and the ABRs were microdissected and reamplified with DOP-Shuttle-PCR primer-II. The reamplified sf-cDNAs were cloned into a pBluescript vector. Twenty randomly chosen clones were sequenced and classified into 8 groups. Three out of the 8 grouped clones had been mapped to the long arm of chromosome 22 (22q11), whereas the other 5 were novel cDNAs. Quantitative Southern blot analysis indicated that 7 out of the 8 grouped clones (87.5%) were derived from the co-amplified regions.
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