Recurrent microdeletion 2q21.1: report on a new patient with neurological disorders

Prenatal Diagnosis of a de novo 2q14.3-q22.1 Deletion with Complex Chromosomal Rearrangement

Introduction

Chromosomal aberrations due to complex chromosomal rearrangements (CCRs) can cause abnormal phenotypes if accompanied by microdeletions or microduplications near the breakpoint, or gene breaks.

Case Presentation

We report a prenatal diagnostic case of 2q14.3-q22.1 deletion with ultrasound suggestive of absent nasal bone accompanied by CCRs involving 6 chromosomes. Cytogenetic analysis revealed a karyotype of 46,XY,der(1)t(1;2)(p13.3;p11.2),der(2)t(1;2)inv(2)(q12q14.2)del(2)(q14.3q22.1),t(12;16)(q21.2;q12.1),t(13;21)(q32;q22.1). Chromosomal microarray analysis identified a 14.90 Mb deletion on 2q14.3q22.1. The copy number variant was de novo, as determined by karyotype analysis of the parents' peripheral blood G-banding.

Conclusion

The region contains haploinsufficient genes that can cause different phenotypes, mainly associated with neurodevelopmental and autism spectrum disorders. However, the genotype-phenotype correlation is limited in prenatal evaluation. Therefore, the combined use of multiple diagnostic techniques has an important role in the assessment of CCRs and genetic counseling.

Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness

Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.

Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders

INTRODUCTION

Aneuploids, copy number variations (CNVs), and single nucleotide variants in specific genes are the main genetic causes of developmental delay (DD) and intellectual disability disorder (IDD). These genetic changes can be detected using chromosome analysis, chromosomal microarray (CMA), and next-generation DNA sequencing techniques. Therefore; In this study, we aimed to investigate the importance of CMA in determining the genomic etiology of unexplained DD and IDD in 123 patients.

METHOD

For 123 patients, chromosome analysis, DNA fragment analysis and microarray were performed. Conventional G-band karyotype analysis from peripheral blood was performed as part of the initial screening tests. FMR1 gene CGG repeat number and methylation analysis were carried out to exclude fragile X syndrome.

RESULTS

CMA analysis was performed in 123 unexplained IDD/DD patients with normal karyotypes and fragile X screening, which were evaluated by conventional cytogenetics. Forty-four CNVs were detected in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients were reported. In 6 patients, one or more pathogenic CNVs were determined. Therefore, the diagnostic efficiency of CMA was found to be 31.7% (39/123).

CONCLUSION

Today, genetic analysis is still not part of the routine in the evaluation of IDD patients who present to psychiatry clinics. A genetic diagnosis from CMA can eliminate genetic question marks and thus alter the clinical management of patients. Approximately one-third of the positive CMA findings are clinically intervenable. However, the emergence of CNVs as important risk factors for multiple disorders increases the need for individuals with comorbid neurodevelopmental conditions to be the priority where the CMA test is recommended.

A novel interstitial deletion of chromosome 2q21.1-q23.3: Case report and literature review

Background

Interstitial deletions of 2q are rare. Those that have been reported show varying clinical manifestations according to the size of the deletion and the genomic region involved.

Method and Results

We describe a preterm male harboring a novel interstitial deletion encompassing the 2q21.2‐q23.3 region of 2q, a deletion that has not been described previously. The patient had multiple congenital anomalies including agenesis of the corpus callosum, congenital cardiac defects, bilateral hydronephrosis, spontaneous intestinal perforation, hypospadias and cryptorchidism, sacral dimple and rocker‐bottom feet. Array comparative genomic hybridization (aCGH) analysis revealed a de novo >18 Mb deletion at 2q21.1–q23.3, a region that included (605802, 611472 and 604593) OMIM genes.

Conclusion

To the best of our knowledge this is the first report of a de novo interstitial deletion at 2q21.1–q23.3 in which haploinsufficiency of dose‐sensitive genes is shown to contribute to the patient's phenotype.