BackgroundThere is a great need for reporting and cataloging of genotypephenotype correlation of clusters of individualssharing similar genomic rearrangements and phenotypes.This will facilitate diagnosis and personalized geneticcounseling and will also improve our understanding ofgene function and disease. Karyotyping and FISH aremicroscopic classical cytogenetic methods of detectinggain, loss or rearrangement of genetic material. ArrayComparative Genomic Hybridisation (CGH) can used formolecular characterization, to size the abnormality andstudy the gene content.Materials and methodsA pilot study was designed: Combined classical cytogenetic,Array CGH and phenotypic findings were correlatedin 20 patients with autism, mental retardation orcongenital malformations.ResultsTen out of 20 patients with autism, mental retardationor congenital malformations had a normal karyotypeand ten had abnormal karyotype. Ten normal subjectswere included as normal controls, of which two hadbalanced translocations, which were not recognized byACGH.ConclusionsCopy number variations detected by ACGH can be novelor extremely rare such that uncertainty may remain as towhether the aberration is pathogenic or simply a benignvariant. Copy number variant (CNV) loci have been listedin the database of genomic variants (DGV). Using thisand the UCSC browser the analysis of the size of theaberration and gene content was done in all individualcases, with normal or abnormal karyotypes. These findingswere correlated with the phenotype to recognizeindividual syndromes.ConclusionsThis pilot study is just the beginning. Identification ofmore patients, who share a region of genomic duplicationor deletion and have phenotypic features in common, willallow greater certainty to be given to the pathogenicnature of the rearrangement and delineation of new syndromes.Most data available is western. Therefore there isa need to document and register Indian data accumulatedto recognize the more common syndromes affecting ourpopulation and the common benign CNVs which can bediscounted in our population, during the CNV analysis.
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