The laboratory currently uses one megabase (1Mb) BAC arrays for clinical screening, however the low probe density of this system limits the detection of small chromosomal variations. This low resolution makes detection of small copy number variations (CNVs) difficult, particularly in chromosomal regions with a very low probe density, such as subtelomeric regions. In comparison, OGT’s CytoSure arrays offer very high resolution to improve not only detection rates of known aberrations, but also the discovery of novel aberrations.

Paul Brady, from the constitutional cytogenetics laboratory, explained: “Since acquiring our CytoSure array we have tested over 100 selected samples in parallel on the oligo arrays and our 1Mb BAC arrays. For initial validation studies we have specifically selected patients whose parents are also available for testing, as this provides additional insight into the origin of any aberrations detected. The oligo array analysis of samples has been in concordance with results obtained from our
BAC arrays. Samples require no more preparation than for BAC array analysis, and this validation is helping us to develop expertise in OGT’s technology before we begin high throughput screening.”

“The major limitation of the current 1Mb BAC array is the lower resolution. The increased genome-wide resolution of the OGT CytoSure array can detect previously unidentified aberrations, and we expect this type of oligonucleotide array to replace BAC arrays in both clinical diagnostic and research applications in the future. The high density of probes in over 400 clinically relevant genes is of particular importance, allowing much better mapping of breakpoints and improved detection of
partial gene and intragenic deletions. The superior analysis of this type of array will benefit patients by facilitating clinical diagnosis and genetic counselling, and ultimately improving patient care.”

“The CytoSure array is a sensitive and robust platform using either manual or automated protocols. We have tried several different sample purification methods, and the arrays have always given accurate and reproducible results. The technology is also very cost effective, as two arrays are mounted on a single slide, allowing us to perform either a dye swap or run two patients’ samples in a single experiment. Interpretation of data is aided by OGT’s user-friendly software, and the built-in CBS
algorithm assists with automated calling of aberrant copy number regions. Annotation tracks provide relevant information including details of syndromes, genes and regions of known variation or segmental duplications, as well as links to Ensembl and UCSC.”

“We have worked closely with OGT and have a good working relationship. The team is very supportive, and regular updates to the software have added a lot of useful functionality, such as additional data within the annotation tracks and direct links to various databases. We are continually consulting with OGT about future enhancements to our array, but we are very happy with the way the array is currently performing.”