Mosaic 22q13 deletions: evidence for concurrent mosaic segmental isodisomy and gene conversion

Head Size in Phelan-McDermid Syndrome: A Literature Review and Pooled Analysis of 198 Patients Identifies Candidate Genes on 22q13

Phelan-McDermid syndrome (PMS) is a multisystem disorder that is associated with deletions of the 22q13 genomic region or pathogenic variants in the SHANK3 gene. Notable features include developmental issues, absent or delayed speech, neonatal hypotonia, seizures, autism or autistic traits, gastrointestinal problems, renal abnormalities, dolichocephaly, and both macro- and microcephaly. Assessment of the genetic factors that are responsible for abnormal head size in PMS has been hampered by small sample sizes as well as a lack of attention to these features. Therefore, this study was conducted to investigate the relationship between head size and genes on chromosome 22q13. A review of the literature was conducted to identify published cases of 22q13 deletions with information on head size to conduct a pooled association analysis. Across 56 studies, we identified 198 cases of PMS with defined deletion sizes and head size information. A total of 33 subjects (17%) had macrocephaly, 26 (13%) had microcephaly, and 139 (70%) were normocephalic. Individuals with macrocephaly had significantly larger genomic deletions than those with microcephaly or normocephaly (p < 0.0001). A genomic region on 22q13.31 was found to be significantly associated with macrocephaly with CELSR1, GRAMD4, and TBCD122 suggested as candidate genes. Investigation of these genes will aid the understanding of head and brain development.

Clinical significance and mechanisms associated with segmental UPD

Whole chromosome uniparental disomy (UPD) has been well documented with mechanisms largely understood. However, the etiology of segmental limited UPD (segUPD) is not as clear. In a 10-year period of confirming (> 300) cases of whole chromosome UPD, we identified 86 segmental cases in both prenatal and postnatal samples. Thirty-two of these cases showed mosaic segmental UPD at 11p due to somatic selection associated with Beckwith–Wiedemann syndrome. This study focuses on apparent mechanisms associated with the remaining cases, many of which appear to represent corrections of genomic imbalance such as deletions and derivative chromosomes. In some cases, segmental UPD was associated with the generation of additional genomic imbalance while in others it apparently resulted in restoration of euploidy. Multiple tests utilizing noninvasive prenatal testing (NIPT), chorionic villus sampling (CVS) and amniotic fluid samples from the same pregnancy revealed temporal evidence of correction and a “hotspot” at 1p. Although in many cases the genomic imbalance was dosage “repaired” in the analyzed tissue, clinical effects could be sustained due to early developmental effects of the original imbalance or due to its continued existence in other tissues. In addition, if correction did not occur in the gametes there would be recurrence risks for the offspring of those individuals. Familial microarray allele patterns are presented that differentiate lack of gamete correction from somatic derived gonadal mosaicism. These results suggest that the incidence of segUPD mediated correction is underestimated and may explain the etiology of some clinical phenotypes which are undetected by routine microarray analysis and many exome sequencing studies.

Mosaic Segmental and Whole-Chromosome Upd(11)mat in Silver-Russell Syndrome

Molecular defects altering the expression of the imprinted genes of the 11p15.5 cluster are responsible for the etiology of two congenital disorders characterized by opposite growth disturbances, Silver-Russell syndrome (SRS), associated with growth restriction, and Beckwith-Wiedemann syndrome (BWS), associated with overgrowth. At the molecular level, SRS and BWS are characterized by defects of opposite sign, including loss (LoM) or gain (GoM) of methylation at the H19/IGF2:intergenic differentially methylated region (H19/IGF2:IG-DMR), maternal or paternal duplication (dup) of 11p15.5, maternal (mat) or paternal (pat) uniparental disomy (upd), and gain or loss of function mutations of CDKN1C. However, while upd(11)pat is found in 20% of BWS cases and in the majority of them it is segmental, upd(11)mat is extremely rare, being reported in only two SRS cases to date, and in both of them is extended to the whole chromosome. Here, we report on two novel cases of mosaic upd(11)mat with SRS phenotype. The upd is mosaic and isodisomic in both cases but covers the entire chromosome in one case and is restricted to 11p14.1-pter in the other case. The segmental upd(11)mat adds further to the list of molecular defects of opposite sign in SRS and BWS, making these two imprinting disorders even more specular than previously described.

Two siblings with 11qter deletion syndrome that had been rescued in their mother by uniparental disomy

Jacobsen syndrome refers to a congenital anomaly caused by deletion at 11q23.3-qter. We here describe two siblings with the same 11q23.3-qter deletion. Both parents were healthy with a normal karyotype. Cytogenetic microarray analysis revealed no mosaicism in either parent but the mother showed uniparental disomy encompassing the deleted region found in the two siblings. The pattern of X chromosome inactivation was almost completely skewed in the mother. These data suggested that the mother was a carrier of the 11q23.3-qter deletion but that this had been rescued by disomy formation during early embryogenesis except for her germinal cells.

Mosaicism for structural non-centromeric autosomal rearrangements in disease-defined carriers: sex differences in the rearrangements profile and maternal age distributions

Background

Mosaicism for an autosomal structural rearrangement (Rea) associated with clinical manifestation of chromosomal imbalance is rare. Consequently, there is a lack of basic epidemiological characterization of this kind of mosaicism, such as population rate, cytogenetic profile of Reas involved, maternal age distribution, and sex (male to female) ratio among Rea carriers. The objectives of the present study were: (i) determination of the Rea profile in clinically affected individuals, (ii) comparative analysis of the cytogenetic profile and involvement of single chromosomes to rearrangements in affected and previously reported asymptomatic carriers, (iii) analysis of the male/female ratio in carriers of various types of Rea, and, (iv) examination of parental ages distributions according to carriers’ sex.

Results

Two hundred and forty six disease-defined cases of mosaicism for autosomal non-centromeric Rea with a normal cell line of known sex were identified from the literature. There was a significant difference in single chromosome involvements compared to structural rearrangements between affected and asymptomatic carriers of unbalanced Rea, p =0.0030. In affected carriers, chromosome 18 was most frequently involved in structural rearrangements (12.6% of 246 instances). The least frequently rearranged were chromosomes 16 and 21 (0.8% and 1.2%, respectively). In asymptomatic carriers, the most frequently rearranged were chromosomes 5 and 21 (13% of 51 instances each). Among carriers of “loss” or “gain/loss” of genomic material, a female predominance was observed (50 M/89 F, different from population ratio of 1.06 at p = 0.0002). Carriers of either “gain” or balanced Rea demonstrated typical male predominance (41 M/30 F and 18 M/16 F), not different from 1.06. Maternal and paternal ages were reported in 129 and in 109 cases, respectively. There was a significant difference in maternal age distribution between male and female carriers, with mean maternal age of 25.2 years vs 28.3 years (p = 0.032). However, there was no difference in paternal age, with mean paternal age of 29.4 in both groups.

Conclusion

The data suggested that structural rearrangements of certain chromosomes involved in mosaicism may not be tolerated by the embryo, while others have higher survival prospects. Maternal age appears to be a risk factor for somatic mosaicism of structural Rea in female offspring or might cause an adverse effect on male embryo viability.

Electronic supplementary material

The online version of this article (doi:10.1186/s13039-017-0321-9) contains supplementary material, which is available to authorized users.

Phelan McDermid Syndrome: From Genetic Discoveries to Animal Models and Treatment

Phelan-McDermid syndrome or 22q13.3 deletion syndrome is a rare neurodevelopmental disorder characterized by generalized developmental delay, intellectual disability, absent or delayed speech, seizures, autism spectrum disorder, neonatal hypotonia, physical dysmorphic features, and recurrent medical comorbidities. Individuals with Phelan-McDermid syndrome have terminal deletions of the chromosomal region 22q13.3 encompassing SHANK3, a gene encoding a structural component of excitatory synapses indispensable for proper synaptogenesis and neuronal physiology, or point mutations within the gene. Here, we review the clinical aspects of the syndrome and the genetic findings shedding light onto the underlying etiology. We also provide an overview on the evidence from genetic studies and mouse models that supports SHANK3 haploinsufficiency as a major contributor of the neurobehavioral manifestations of Phelan-McDermid syndrome. Finally, we discuss how all these discoveries are uncovering the pathophysiology of Phelan-McDermid syndrome and are being translated into clinical trials for novel therapeutics ameliorating the core symptoms of the disorder.

A child with mosaicism for deletion (14)(q11.2q13)

In this case report we describe a child with a de novo deletion in the (q11.2q13) region of chromosome 14. The child presented with dysmorphic features - anophthalmia, microcephaly, and growth retardation. Cytogenetic studies showed mosaicism. The karyotype was 46,XX,del(14)(q11.2;q13) [16] /46,XX [9]. We compared the features observed in this child with that of others with the same deletion reported in scientific literature and found that this is the first report of a child mosaic for this deletion. It is also the first time it has been reported in association with anophthalmia.

Molecular mechanisms generating and stabilizing terminal 22q13 deletions in 44 subjects with Phelan/McDermid syndrome

In this study, we used deletions at 22q13, which represent a substantial source of human pathology (Phelan/McDermid syndrome), as a model for investigating the molecular mechanisms of terminal deletions that are currently poorly understood. We characterized at the molecular level the genomic rearrangement in 44 unrelated patients with 22q13 monosomy resulting from simple terminal deletions (72%), ring chromosomes (14%), and unbalanced translocations (7%). We also discovered interstitial deletions between 17-74 kb in 9% of the patients. Haploinsufficiency of the SHANK3 gene, confirmed in all rearrangements, is very likely the cause of the major neurological features associated with PMS. SHANK3 mutations can also result in language and/or social interaction disabilities. We determined the breakpoint junctions in 29 cases, providing a realistic snapshot of the variety of mechanisms driving non-recurrent deletion and repair at chromosome ends. De novo telomere synthesis and telomere capture are used to repair terminal deletions; non-homologous end-joining or microhomology-mediated break-induced replication is probably involved in ring 22 formation and translocations; non-homologous end-joining and fork stalling and template switching prevail in cases with interstitial 22q13.3. For the first time, we also demonstrated that distinct stabilizing events of the same terminal deletion can occur in different early embryonic cells, proving that terminal deletions can be repaired by multistep healing events and supporting the recent hypothesis that rare pathogenic germline rearrangements may have mitotic origin. Finally, the progressive clinical deterioration observed throughout the longitudinal medical history of three subjects over forty years supports the hypothesis of a role for SHANK3 haploinsufficiency in neurological deterioration, in addition to its involvement in the neurobehavioral phenotype of PMS.

Familial Kleefstra syndrome due to maternal somatic mosaicism for interstitial 9q34.3 microdeletions

The Kleefstra syndrome (Online Mendelian Inheritance in Man 607001) is caused by a submicroscopic 9q34.3 deletion or by intragenic euchromatin histone methyl transferase 1 (EHMT1) mutations. So far only de novo occurrence of mutations has been reported, whereas 9q34.3 deletions can be either de novo or caused by complex chromosomal rearrangements or translocations. Here we give the first descriptions of affected parent-to-child transmission of Kleefstra syndrome caused by small interstitial deletions, approximately 200 kb, involving part of the EHMT1 gene. Additional genome-wide array studies in the parents showed the presence of similar deletions in both mothers who only had mild learning difficulties and minor facial characteristics suggesting either variable clinical expression or somatic mosaicism for these deletions. Further studies showed only one of the maternal deletions resulted in significantly quantitative differences in signal intensity on the array between the mother and her child. But by investigating different tissues with additional fluorescent in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA) analyses, we confirmed somatic mosaicism in both mothers. Careful clinical and cytogenetic assessments of parents of an affected proband with an (interstitial) 9q34.3 microdeletion are merited for accurate estimation of recurrence risk.

Analysis of relative gene dosage and expression differences of the paralogs RABL2A and RABL2B by Pyrosequencing

The paralogous genes RABL2A (chr2) and RABL2B (chr22) emerged by duplication of a single gene in the human-chimpanzee ancestor and share a high degree of sequence similarity. In Phelan-McDermid-Syndrome microdeletions of 22q13 often also affecting RABL2B are of clinical importance but their incidence is still unknown. We analyzed a German population (190 individuals) for such aneuploidies and the paralogs' expression in cell lines by RABL2 paralogous sequence quantification. For determination of the genomic and transcriptional ratios of RABL2A and RABL2B a Pyrosequencing protocol was introduced as a high-throughput method. During PCR the 3' end of the biotinylated strand is engineered by a backfolding oligonucleotide to hybridize in the Pyrosequencing reaction to an internal site near the sequence to be analyzed. In human samples no deviations of the euploid genomic state could be detected indicating that 22q13 microdeletions involving RABL2B are rare. However, despite equal gene dosage a preferential expression of RABL2B in human tissues and lymphoblastoid cell lines was detected which is most pronounced in brain and placenta. This renders a complete functional complementation of one paralog by the respective other unlikely and hints to a functional and clinical importance, in particular with respect to the 22q13 chromosomal deletion syndrome. Remarkably and in contrast to human, expression levels of the two paralogs in a chimpanzee cell line are equal. This finding is discussed in view of the relocation of RABL2A from its ancestral telomeric to its pericentromeric location in human.