Aims In April 2013 the North West region replaced the standard karyoptype (SK) with the chromosomal microarray (CMA) as the first line investigation for children with developmental delay. The yield of pathologic copy number variations (CNV) is reported to be 15–20% in CMA compared to 3% in SK (excluding Trisomy 21). The aim of this study was to describe the experience of a secondary care paediatrics unit in Blackpool with regards to the diagnostic yield of CMA compared to SK.

Method Using the laboratory database, two study groups were selected: children who had had a SK between 1^st April 2010 and 31^st March 2011 (Group 1, n = 79) and children who had had CMA between 1^st April 2013 and 31^st March 2014 (Group 2, n = 61). Casenotes were requested and data collection was stopped after 12 months for analysis.

Results Data was extracted from 40 patients in Group 1 and 43 patients in Group 2 with a majority of males in both groups. The total yield for all CNVs for CMA was 20.9% compared to 5.0% for SK (excluding Trisomy 21). Pathologic CNVs occurred in 4.7% of CMA patients with none in the SK group. Insignificant findings were reported in 2.3% CMA and 2.5% SK. Variants of unknown significance (VOUS) were found in 13.9% of CMA patients and 2.5% SK patients. Referrals to genetics increased from 27.5% to 39.5% with the implementation of CMA. A final diagnosis was reached for 37.5% and 20.9% of patients in Groups 1 and 2 respectively. Fragile X testing was co-requested in 55% and 62.7% of patients in Groups 1 and 2 respectively with only 1 ‘intermediate’ result in Group 2.

Conclusions Diagnostic yield of CMA for pathologic CNVs in our population was much less than previously described in the published literature. The implementation of CMA as a first line genetic test does appear to have increased VOUS findings and may have increased referrals to Regional Genetics Services. Repeating this study with a larger study population would be beneficial as our results may be limited by a small and incomplete sample.