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We studied the presence of benign infantile epilepsy (BIE), paroxysmal kinesigenic dyskinesia (PKD), and PKD with infantile convulsions (PKD/IC) in patients with a 16p11.2 deletion including PRRT2 or with a PRRT2 loss-of-function sequence variant. Index patients were recruited from seven Dutch university hospitals. The presence of BIE, PKD and PKD/IC was retrospectively evaluated using questionnaires and medical records. We included 33 patients with a 16p11.2 deletion: three (9%) had BIE, none had PKD or PKD/IC. Twelve patients had a PRRT2 sequence variant: BIE was present in four (p = 0.069), PKD in six (p < 0.001) and PKD/IC in two (p = 0.067). Most patients with a deletion had undergone genetic testing because of developmental problems (87%), whereas all patients with a sequence variant were tested because of a movement disorder (55%) or epilepsy (45%). BIE, PKD and PKD/IC clearly showed incomplete penetrance in patients with 16p11.2 deletions, but were found in all and 95% of patients with a PRRT2 sequence variant in our study and a large literature cohort, respectively. Deletions and sequence variants have the same underlying loss-of-function disease mechanism. Thus, differences in ascertainment have led to overestimating the frequency of BIE, PKD and PKD/IC in patients with a PRRT2 sequence variant. This has important implications for counseling if genome-wide sequencing shows such variants in patients not presenting the PRRT2-related phenotypes., (Copyright © 2018 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

Polymicrogyria (PMG) is a brain malformation due to abnormal cortical organisation. It is a heterogeneous disorder associated with 22q11.2 deletion syndrome (also known as velocardiofacial (VCF) syndrome) amongst others. Since this association was first recognised in 1996, over 30 patients with PMG and 22q11.2 deletion have been described. In 22q11.2 deletion syndrome, PMG is mainly located in the perisylvian areas; it frequently has an asymmetrical presentation with a striking predisposition for the right hemisphere. Neurological features of perisylvian PMG include developmental delay/mental retardation, seizures, microcephaly, spasticity and oromotor dysfunction. Thus in children diagnosed with 22q11.2 deletion syndrome, a finding of PMG has important prognostic value. We present a seven-month old boy with microcephaly, short stature and developmental delay. A cerebral MRI showed slightly enlarged ventricles and symmetrical perisylvian polymicrogyria. A 22q11.2 deletion was revealed by array-based comparative genomic hybridization. Remarkably the boy had no other manifestations of VCF syndrome. Paediatricians, child neurologists and clinical geneticists should be aware that the presence of PMG (especially in the perisylvian areas) needs investigating for 22q11.2 deletion, even if other more common VCF syndrome features are absent., (Copyright © 2010 Elsevier Masson SAS. All rights reserved.)

Postaxial polydactyly type A2 (PAP-A2; OMIM 602085) is a common feature seen in patients with a partial duplication of the long arm of chromosome 13. Dose dependency has been shown for digital malformations in this region, deletions resulting in oligodactyly and duplications in polydactyly. We aimed to narrow down the critical region for PAP-A2 in order to identify candidate genes. We performed chromosomal analysis, FISH and array-CGH in a patient with an interstitial duplication of chromosome 13q31.3q32.1 and a mild phenotype including postaxial polydactyly. The duplicated region spanned 5.59 Mb (89.67-95.25 Mb) and contained eleven known genes, including GPC5 and GPC6. GPC5 and GPC6 show homology with GPC3 and GPC4, genes involved in Simpson-Golabi-Behmel syndrome, an overgrowth syndrome in which also polydactyly can occur. Mouse studies have shown expression of both GPC5 and GPC6 in developing limbs. Therefore, we propose that GPC5 and GPC6 are the most likely candidate genes for PAP-A2., (Copyright (c) 2009 Elsevier Masson SAS. All rights reserved..)

We report on a male patient with intra-uterine growth retardation, microcephaly, coloboma, laryngomalacia and developmental delay. Array CGH analysis revealed a 649 kb duplication on chromosome 1p34.1. Only five patients with overlapping duplications have been reported thus far. Ten known genes are located in the duplicated region, including the POMGNT1 gene encoding for O-mannose beta-1,2-N-acetylglucosaminyltransferase. This gene, mutated in muscle-eye-brain disease, might be causative for the observed phenotype in our patient.

Nablus mask-like facial syndrome (NMFLS) is a rare microdeletion syndrome with a mask-like facial appearance as the most characteristic feature. In 2000, Teebi, was the first to report on a 4 years old boy affected with NMFLS. Since then two additional patients have been reported. Three years later, with the development of the array CGH technology, Shieh et al., elucidated the etiology of NMFLS by showing that the two patients studied share a approximately 4 Mb microdeletion in the long arm of chromosome 8 (q21.3-q22.1). Here we report on two NMFLS patients among which the first patient described by Teebi in 2000, and present newly described clinical findings including the common happy behaviour of the children. Array CGH analysis of these two patients permitted to reveal a deletion in the same region, 8q21.3-q22.1. Combining the available literature and our data, we were able to narrow the common deleted region to 2.78 Mb (93.56-96.34 Mb) in 8q22.1. Direct relations between the clinical findings with (one of) the genes in the critical region have to await further studies on NFMLS patients with overlapping or smaller deletions.

Behavioural differences have been described in patients with type I deletions (between breakpoints 1 and 3 (BP1-BP3)) or type II deletions (between breakpoints 2 and 3) of the 15q11.2 Prader-Willi/Angelman region. The larger type I deletions appear to coincide with more severe behavioural problems (autism, ADHD, obsessive-compulsive disorder). The non-imprinted chromosomal segment between breakpoints 1 and 2 involves four highly conserved genes, TUBGCP5, NIPA1, NIPA2, and CYFIP1; the latter three are widely expressed in the central nervous system, while TUBGCP5 is expressed in the subthalamic nuclei. These genes might explain the more severe behavioural problems seen in type I deletions. We describe nine cases with a microdeletion at 15q11.2 between BP1-BP2, thus having a haploinsufficiency for TUBGCP5, NIPA1, NIPA2, and CYFIP1 without Prader-Willi/Angelman syndrome. The clinical significance of a pure BP1-BP2 microdeletion has been debated, however, our patients shared several clinical features, including delayed motor and speech development, dysmorphisms and behavioural problems (ADHD, autism, obsessive-compulsive behaviour). Although the deletion often appeared to be inherited from a normal or mildly affected parent, it was de novo in two cases and we did not find it in 350 healthy unrelated controls. Our results suggest a pathogenic nature for the BP1-BP2 microdeletion and, although there obviously is an incomplete penetrance, they support the existence of a novel microdeletion syndrome in 15q11.2.

We report on a female patient with XY sex reversal with clitoromegaly, neonatal male testosterone and AMH levels, and a normal urine steroid profile. Array CGH revealed a de novo microdeletion of chromosome 9q33.3, including the NR5A1 gene. NR5A1 encodes for the steroidogenic factor-1 (SF-1) and heterozygous mutations in this gene were recently identified as an important cause of XY sex reversal. However, a deletion of NR5A1 has only been reported once. Patients with a mutation in NR5A1, have severe underandrogenisation with mild testicular dysgenesis. Müllerian structures may be present, while postnatal testosterone levels may be normal. This points towards a predominantly early embryonic effect of low, local, androgen levels, with or without reduced AMH levels. We recommend not only NR5A1 mutation screening, but also copy number analysis in patients with 46,XY sex reversal of unknown cause, even in the absence of dysmorphisms or congenital abnormalities.

In 2-8% of patients with mental retardation, small copy number changes in the subtelomeric region are thought to be the underlying cause. As detection of these genomic rearrangements is labour intensive using FISH, we constructed and validated a high-density BAC/PAC array covering the first 5 Mb of all subtelomeric regions and applied it in our routine screening of patients with idiopathic mental retardation for submicroscopic telomeric rearrangements. The present study shows the efficiency of this comprehensive subtelomere array in detecting terminal deletions and duplications but also small interstitial subtelomeric rearrangements, starting from small amounts of DNA. With our array, the size of the affected segments, at least those smaller than 5 Mb, can be determined simultaneously in the same experiment. In the first 100 patient samples analysed in our diagnostic practice by the use of this comprehensive telomere array, we found three patients with deletions in 3p, 10q and 15q, respectively, four patients with duplications in 9p, 12p, 21q and Xp, respectively, and one patient with a del 6q/dup 16q. The patients with del 3p and 10q and dup 12p had interstitial rearrangements that would have been missed with techniques using one probe per subtelomeric region chosen close to the telomere.