Characterization of 23 small supernumerary marker chromosomes detected at pre-natal diagnosis: The value of fluorescence in situ hybridization

Abstract

Abstract. Small supernumerary marker chromosomes (sSMCs) cannot be identified or characterized unambiguously by conventional cytogenetic banding techniques. Until recently, the large variety of marker chromosomes, as well as the limitations in their identification, have presented a diagnostic problem. In order to determine the origin of sSMCs, we used a variety of fluorescence in situ hybridization (FISH) methods, including centromere-specific multicolor FISH, acrocentric specific multicolor FISH, subcentromere-specific multicolor FISH and multicolor FISH with whole chromosome paint probes. Moreover, uniparental disomy testing was in all cases attempted. From a total of 28,000 pre-natal samples from four diagnostic genetics laboratories in Greece, 23 (0.082%) supernumerary marker chromosomes were detected. The mean maternal age was 36.2 years (range 27-43) and the mean gestational age at which amniocentesis was performed was 18.5 weeks (range 16-23). Eighteen markers were de novo and 5 markers were inherited. Molecular cytogenetic methods were applied to determine the chromosomal origin and composition of the sSMC. In total, 17 markers were derived from acrocentric chromosomes (14, 15, 21 and 22) and 6 markers were non-acrocentric, derived from chromosomes 9, 16, 18, 20 and Y. Uniparental disomy was not detected in any of the cases studied. With regard to pregnancy outcome, 13 pregnancies resulted in normal healthy neonates, while 10 pregnancies were terminated due to ultrasound abnormalities. A total of 23 marker chromosomes from 28,000 pre-natal samples (0.082%) were identified. Molecular cytogenetic techniques provided valuable information on the chromosomal origin and composition of all the sSMCs. Especially in cases with normal ultrasound, the FISH results rendered genetic counseling possible in a category of cases previously considered a diagnostic problem. Abnormal outcome was observed in 10 cases (43,5%), 7 of which showed abnormal ultrasound findings. New technologies, such as array-comparative genomic hybridization, should be used in future genotype-phenotype correlation studies, although the high mosaicism rate poses a problem. IntroductionSmall supernumerary marker chromosomes (sSMcs) are structurally abnormal chromosomes, equal in size or smaller than chromosome 20, which cannot be identified or characterized unambiguously by conventional cytogenetic banding techniques (1). These chromosomes are detected in 0.04% of newborn children, whereas in developmentally retarded patients the rate is 0.22% (1-3). sSMCs are also present in 0.08% of unselected pre-natal cases and in 0.20% of pre-natal cases with ultrasound abnormalities (2). The large variety of sSMCs, as well as the limitations in their cytogenetic identification, have presented a diagnostic problem in their interpretation. In general, the risk for an abnormal phenotype is approximately 13%, varying from 7% when de novo sSMCs derived from chromosomes 13, 14, 21 and 22 are encountered, to 28% for non-acrocentric

Design and validation of a pericentromeric BAC clone set aimed at improving diagnosis and phenotype prediction of supernumerary marker chromosomes

“…Among the non-acrocentric marker chromosomes collected in our series, the SMC characterization revealed breakpoints within pericentromeric noncritical regions in two cases [4,14-16,20,22,33,34], consistent with the observation that the corresponding patients (3 and 15) had normal phenotypes (Figures 2A–C and 3A–D, Additional file 2: Table S2). Notably, the association of sSMC(2) and sSMC(18) observed in patient 15 has not been previously reported.…”

“…Accordingly, we declare no clinical signs reported in association with acrocentric sSMCs that have breakpoints localized in predicted pericentromeric noncritical regions [4,14,16,22,31] (patients 6–9, 12, and 13), with the exception of patient 7, who exhibited a growth delay likely not associated with the sSMC (Additional file 2: Table S2). Furthermore, in siblings 10 and 11, the 14q breakpoint characterization was useful in linking the reported clinical findings specifically to trisomy of 6pter-p25 (Additional file 2: Table S2).…”

“…However, array CGH may fail to identify the origins of very small SMCs in up to 50% of cases because its pericentromeric coverage is limited to the presence of segmental duplications, and it may also be unable to detect low-level and cryptic mosaicism [13,19-21]. Consequently, it is necessary to complement array CGH using FISH approaches [13,22]. In addition, to allow rapid discrimination between sSMCs that are positive or negative for unique sequences, an alternative approach using multiplex ligation-dependent probe amplification (MLPA) analysis has recently been developed for use in the context of prenatal diagnosis [23].…”

Molecular characterization of 39 de novosSMC: contribution to prognosis and genetic counselling, a prospective study

“…However, there have been no large series reporting the application of this technology to sSMC in a postnatal (14)(15)(16)(17)(18)(19)(20)(21)(22) or prenatal context (23)(24)(25)(26)(27)(28)(29), or both (30,31). Genotype-phenotype correlations should be extended, and SNP array also offers the possibility to detect uniparental disomy (UPD), in particular, for sSMC derived from chromosome 6, 7, 11 and 20 (32,33). However, one limitation of the application of this technology is the percentage of mosaicism.…”

Patient with three euchromatic supernumerary marker chromosomes derived from chromosomes 1, 12, and 18: Characterization and evaluation of the aberrations

“…sSMCs are detected in 0.04% of live births [Liehr and Weise, 2007; for review Hu et al, 2011]. The probability for an abnormal phenotype is approximately 13%, and depends on its chromosomal origin and its formation (de novo or inherited) [Liehr and Weise, 2007;Manolakos et al, 2010].…”