Diagnostic Yield of Chromosomal Microarray Analysis in a Cohort of 300 Indian Patients

To present authors' experience of chromosome microarray analysis (CMA) as the first-tier test, which contributed to accumulation and annotation of copy number variations (CNVs) and discovery of novel genetic hot spots in Indian pediatric patients.

Karyotyping and CMA (4X180K Agilent) were performed in 300 patients with developmental delay, dysmorphism, autism, intellectual disability or congenital malformations. Various databases such as ClinVar, Clin Gen, OMIM, DECIPHER, etc. were used for interpretation of the results.

The diagnostic yield of clinically significant findings by CMA [16.00% (48/300)] was 9.0% higher than that by karyotyping [7.0% (21/300)]. There were 2.66% (08/300) patients with variations of uncertain significance (VOUS) which were challenging to interpret. Benign variations were considered normal.

CMA allows increased diagnostic yield of known and new microdeletion/duplication syndromes and molecular characterization of marker chromosomes with gene annotations. There is insufficient data published from India. Every such test done on Indian patients contributes to Indian data accumulation of pathogenic CNVs (pCNVs) and VOUS for future resolution. The benefit of CMA as a first-tier test is that it can improve the understanding towards the associated known and new genetic hot spots, thus providing a better genotype-phenotype correlation. Pre-test and post-test genetic counseling is important.