Suspected microdeletion syndromes and molecular cytogenetic techniques: an experience with 330 cases

摘要

BackgroundMicrodeletion syndromes are characterized by small( 5Mb) chromosomal deletion in which one or moregenes are involved. They are frequently associated withmultiple congenital anomalies. The phenotype is the resultof haploin sufficiency of genes in the critical interval. FluorescentIn-Situ Hybridization (FISH), Multiplex LigationdependentProbe Amplification (MLPA), QuantitativeFluorescent Polymerase Chain Reaction (QFPCR) andArray (microarray) Comparative Genomic Hybridization(aCGH) techniques are commonly used for precise geneticdiagnosis of microdeletion syndromes.MethodsThis study comprised of 330 cases of suspected microdeletionsyndromes. There were 184 cases of 22q11.2microdeletion, 52 cases of William, 47 cases of PraderWilli/Angelman, 18 cases of Miller Dieker, 14 cases ofRetinoblastoma (bilateral infantile), 5 cases of Trichorhinophalangeal(TRP) and 10 cases of other microdeletionsyndromes. FISH was carried out on all 330 clinicallysuspected microdeletion syndrome cases using noncommercialFISH probes. Subsequently, we have performedaCGH in 100 cases (77 cases of 22q11.2; 9 casesof William Syndrome, 8 cases of Prader Willi Syndrome,4 cases of Miller Dieker Syndrome and 2 cases of othermicrodeletion syndromes) including one monozygotictwin pairs with discordant phenotype. Another 50 cases,including 22q11.2 microdeletion, aCGH experiment andanalysis are in progress.ResultsFISH was confirmatory in 28 cases only (8.48%; 19 casesof 22q11.2 microdeletion, 5 cases of Prader Willi,3 cases of William and 1 case of TRP syndrome). Therewere 8 cases with mosaicism and 20 cases with puredeletion. Microarray was picked up copy number variation(CNV) with or without copy neutral loss of heterozygosity(LOH) in approximately 70% of cases, mostlyinvolving several chromosome loci. However, aCGH wasfailed to pick up mosaic cases (with even 45% deletedcell lines). Clinically suspected specific locus CNV wasdetectable in approximately 24% cases only by aCGH.Variation in deletion sizes and or break point differences(with genes involvement variations) as well as otherCNVs with or without LOH was evident.ConclusionsWe conclude that FISH in this format should not be themethod of choice for clinically suspected microdeletionsyndromes as cost, labor & time versus benefit is unjust.Microarray seems better technique, in clinically doubtfulcases. However, microarray is likely going to miss mosaiccases, if deleted cell lines concentration is less than 50%.It seems time has come to follow strict clinical criteriafor FISH testing or preferably to follow better methodsviz., DNA microarray (array comparative genomic hybridization).We think that whole genome screening shouldbe adopted as first line of investigation and FISH may beused for detecting mosaicism, screening family membersand prenatal diagnosis. Furthermore, microdeletion syndromebest fitted with genomic disorder as several chromosomalloci are involved in CNV with or without LOHand alteration in deletion size or breakpoint. Our studyhas not found identical deletion profile in any cases, thus explaining reason for phenotypic variability betweendeletion positive cases.