Abstract
The development of the bacterial artificial chromosome (BAC) system was driven in part by the human genome project in order to construct genomic DNA libraries and physical maps for genomic sequencing. The availability of BAC clones has become a valuable tool for identifying cancer genes. We report here our experience in identifying genes located at breakpoints of chromosomal rearrangements and in defining the size and boundaries of deletions in hematological diseases. The methodology used in our laboratory consists of a three-step approach using conventional cytogenetics followed by FISH with commercial probes, then BAC clones. One limitation to the BAC system is that it can only accommodate inserts of up to 300 kb. As a consequence, analyzing the extent of deletions requires a large amount of material. Array comparative genomic hybridization (array-CGH) using a BAC/PAC system can be an alternative. However, this technique has limitations also, and it cannot be used to identify candidate genes at breakpoints of chromosomal rearrangements such as translocations, insertions, and inversions.
Highlights
Since chromosome banding techniques have been applied to the analysis of chromosomal aberrations in leukemia and cancer, several hundreds of recurring chromosomal breakpoints have been identified
The methodology used in our laboratory consists of a three-step approach using conventional cytogenetics followed by FISH with commercial probes, bacterial artificial chromosome (BAC) clones
A three-step methodology consisting in conventional cytogenetics followed by FISH with commercial probes, BAC clones is currently used in the laboratory
Summary
Since chromosome banding techniques have been applied to the analysis of chromosomal aberrations in leukemia and cancer, several hundreds of recurring chromosomal breakpoints have been identified. They allowed the recognition of regions of nonrandom copy number changes such as deletions. The availability of large-insert genomic librairies such as bacterial artificial chromosomes (BACs) is a valuable tool for identifying cancer genes. It is widely used in sequencing efforts and in studies of genomics and functional genomics [1,2,3]. We illustrate here by several examples our experience at the University Cytogenetics Laboratory in Brest (France) using BAC clones to identify genes at chromosomal breakpoints and define commonly deleted regions in myelodysplastic syndromes, myeloproliferative neoplasms and leukemia
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