Chromosomal Microarray Analysis Uncovers Pathogenic Copy Number Variations in Unexplained Neurodevelopmental Disorders and Congenital Anomalies
Background: Neurodevelopmental disorders represent a broad spectrum of cognitive, neurological, and/or psychiatric dysfunction caused by impairment of the brain during development. The present deals with the chromosomal rearrangements in patients with neurodevelopmental disorders, Developmental Delay/ Intellectual Disability (DD/ID) and/or congenital anomalies employing Chromosomal Microarray (CMA).
Methods: We used the CytoScan_750k array platform (Affymetrix) to analyze 102 patients with unexplained neurodevelopmental disorders and congenital anomalies. In this process, we have identified several deleted or duplicated genes possibly underlying the DD/ID phenotype to correlate the genetics with the clinical data.
Results: Of all the 102 patients identified with DD/ID, 48 patients had a normal profile (46XX/XY), 53 showed pathogenic CNVs along with an exceptional case (case 199), encompassing high levels of homozygosity (approx. 17.5%). The size of the CNVs in affected patients ranged from 36 kb to 15.5 MB. The most common variant in cases with ASD and developmental delay was duplication 22q11.2 of ~400Kb region, which was validated using karyotyping and FISH. Five out of 53 sporadic patients had known microdeletion syndromes. Case 66 showed 17p11.2 deletion; Smith-Magenis syndrome coupled with mosaic loss of chromosome 17p13.2, case 79 had a loss of Xp22.13 region overlapping with Rett syndrome, case 99 had 1q21.1 micro deletion syndrome along with Turner Syndrome, case 118 showed 4p16.3 terminal deletion; Wolf-Hirschhorn syndrome and case 122 had 7q11.23 deletion; William syndrome.
Conclusion: It is envisaged that the application of microarray will expand the spectrum of cytogenomic abnormalities by including complex and cryptic structural variants. Further, delineation of molecular mechanisms of these cytogenomic abnormalities coupled with the development of novel therapeutic approaches will ultimately lead to disease-specific personalized management and precision treatment.
This study is an attempt towards deconvoluting the effect of copy number variants in genetic diseases and more broadly in the clinical evaluation of patients with unexplained DD/ID, congenital anomalies and dysmorphic features. Further, enhancements in genomic microarray analysis will soon allow the reliable analysis of all copy number variations throughout the chromosome at the kilobase or single exon resolution. Also, clarification of the genetic profile generated by CMA coupled with knowledge-based genetic counseling, rational clinical action and follow up familial studies may aid in directing medical management.
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Journal of Biomolecules and Biochemistry
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