Targeted next-generation sequencing identifies the disruption of the SHANK3 and RYR2 genes in a patient carrying a de novo t(1;22)(q43;q13.3) associated with signs of Phelan-McDermid syndrome

Breakpoint analysis for cytogenetically balanced translocation revealed unexpected complex structural abnormalities and suggested the position effect for MEF2C

Many disease-causing genes have been identified by determining the breakpoints of balanced chromosomal translocations. Recent progress in genomic analysis has accelerated the analysis of chromosomal translocation-breakpoints at the nucleotide level. Using a long-read whole-genome sequence, we analyzed the breakpoints of the cytogenetically balanced chromosomal translocation t(5;15)(q21;26.3), which was confirmed to be of de novo origin, in a patient with a neurodevelopmental disorder. The results showed complex rearrangements with seven fragments consisting of five breakpoint-junctions (BJs). Four of the five BJs showed microhomologies of 1-3-bp, and only one BJ displayed a signature of blunt-end ligation, indicating chromothripsis as the underlying mechanism. Although the BJs did not disrupt any disease-causing gene, the clinical features of the patient were compatible with MEF2C haploinsufficiency syndrome. Complex rearrangements were located approximately 2.5-Mb downstream of MEF2C. Therefore, position effects were considered the mechanism of the occurrence of MEF2C haploinsufficiency syndrome.

Dissecting the 22q13 region to explore the genetic and phenotypic diversity of patients with Phelan-McDermid syndrome

SHANK3-related Phelan-McDermid syndrome (PMS) is caused by a loss of the distal part of chromosome 22, including SHANK3, or by a pathological SHANK3 variant. There is an important genetic and phenotypic diversity among patients who can present with developmental delay, language impairments, autism, epilepsy, and other symptoms. SHANK3, encoding a synaptic scaffolding protein, is deleted in the majority of patients with PMS and is considered a major gene involved in the neurological impairments of the patients. However, differences in deletion size can influence clinical features, and in some rare cases, deletions at the 22q13 locus in individuals with SHANK3-unrelated PMS do not encompass SHANK3. These individuals with SHANK3-unrelated PMS still display a PMS-like phenotype. This suggests the participation of other 22q13 genes in the pathogenesis of PMS. Here, we review the biological function and potential implication in PMS symptoms of 110 genes located in the 22q13 region, focusing on 35 genes with evidence for association with neurodevelopmental disorders, including 13 genes for epilepsy and 11 genes for microcephaly and/or macrocephaly. Our review is restricted to the 22q13 region, but future large-scale studies using whole genome sequencing and deep-phenotyping are warranted to develop predictive models of clinical trajectories and to target specific medical and educational care for each individual with PMS.

Detection of a Cryptic 25 bp Deletion and a 269 Kb Microduplication by Nanopore Sequencing in a Seemingly Balanced Translocation Involving the LMLN and LOC105378102 Genes

Preimplantation genetic testing plays a critical role in enabling a balanced translocation carrier to obtain the normal embryo. Identifying the precise breakpoints for the carriers with phenotypic abnormity, allows us to reveal disrupted genes. In this study, a seemingly balanced translocation 46, XX, t (3; 6) (q29; q26) was first detected using conventional karyotype analysis. To locate the precise breakpoints, whole genomes of DNA were sequenced based on the nanopore GridION platform, and bioinformatic analyses were further confirmed by polymerase-chain-reaction (PCR) and copy number variation (CNV). Nanopore sequencing results were consistent with the karyotype analysis. Meanwhile, two breakpoints were successfully validated using polymerase-chain-reaction and Sanger Sequencing. LOC105378102 and LMLN genes were disrupted at the breakpoint junctions. Notably, observations found that seemingly balanced translocation was unbalanced due to a cryptic 269 kilobases (Kb) microduplication and a 25 bp deletion at the breakpoints of chromosome (chr) 6 and chr 3, respectively. Furthermore, 269 Kb microduplication was also confirmed by copy number variation analyses. In summary, nanopore sequencing was a rapid and direct method for identifying the precise breakpoints of a balanced translocation despite low coverage (3.8×). In addition, cryptic deletion and duplication were able to be detected at the single-nucleotide level.

Clinical Findings on Chromosome 1 Copy Number Variations

Copy number variants (CNVs) are a major contribution to genome variability, and the presence of CNVs on chromosome 1 is a known cause of morbidity. The main objective of this study was to contribute to chromosome 1 disease map, through the analysis of patients with chromosome 1 CNVs.A cross-sectional study was performed using the array comparative genomic hybridization database of the Genetic Department of the Faculty of Medicine. Patients with pathogenic (P) or likely pathogenic (LP) CNVs on chromosome 1 were selected for the study. Clinical information was collected for all patients. Databases and related literature were used for genotype-phenotype correlation.From a total of 2,516 patients included in the database we identified 24 patients (0.95%) with P (9 patients) or LP (15 patients) CNVs on chromosome 1. These CNVs account for 6.1% (24/392 CNVs) of the total P/LP CNVs in the database. Most common CNVs found were in the 1q21.1-1q21.2 region.This study reinforces the association between chromosome 1 CNV and neurodevelopmental disorders and craniofacial dysmorphisms. Additionally, it also strengthened the idea that CNVs interpretation is not always a linear task due to the broad spectrum of variants that can be identified between benign and clearly pathogenic CNVs.