Severe congenital microcephaly with AP4M1 mutation, a case report

Background: Autosomal recessive defects of either the B1, E1, M1 or S1 subunit of the Adaptor Protein complex-4 (AP4) are characterized by developmental delay, severe intellectual disability, spasticity, and occasionally mild to moderate microcephaly of essentially postnatal onset. Case presentation: We report on a patient with severe microcephaly of prenatal onset, and progressive spasticity, developmental delay, and severe intellectual deficiency. Exome sequencing showed a homozygous mutation in AP4M1, causing the replacement of an arginine by a stop codon at position 338 of the protein (p.Arg338X). The premature stop codon truncates the Mu homology domain of AP4M1, with predicted loss of function. Exome analysis also showed heterozygous variants in three genes, ATR, MCPH1 and BLM, which are known causes of autosomal recessive primary microcephaly. Conclusions: Our findings expand the AP4M1 phenotype to severe microcephaly of prenatal onset, and more generally suggest that the AP4 defect might share mechanisms of prenatal neuronal depletion with other genetic defects of brain development causing congenital, primary microcephaly

Congenital hydrocephalus : new Mendelian mutations and evidence for oligogenic inheritance

Peer reviewe

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Hérédité monogénique et digénique de la microcéphalie primaire

Primary Microcephalies (PMs) are characterized by a small head since birth, resulting from an insufficient production of mature neurons during neurogenesis. PMs carry a heavy burden of intellectual deficiency, and serve as model diseases for brain volumic development. Known PM genes are ascribed to several cellular pathways such as the centriole duplication pathway, the control of cellcycle checkpoints and the general control of DNA replication licensing, although the exact mechanisms remain unclear. Genes causing monogenic forms of PM can be identified in fewer than 50% of patients. Digenic inheritance has recently been described in the mouse for PM caused by Aspm and Wdr62, but it is not known whether this applies to humans. The genetic dissection of PM will provide interesting clues about the cellular mechanisms involved.In this study, we used two different holistic, in vivo approaches: high throughput DNA sequencing of multiple PM genes in human PM patients, and genome-edited zebrafish modeling of selected PM genes.Analysis of a large mostly outbred PM cohort revealed 15 novel mutations in known PM genes, ASPM and WDR62 being the most frequently mutated. Mutations in AP4M1 and TRAPPC9 were for the first time associated with PM in two families. A mutation in MCPH1 truncating the last BRCT domain was surprisingly not associated with PM. The analysis of the exome cohort also revealed variants in four candidate genes that are not yet associated with human pathologies. Furthermore, exomes of PM patients showed a significant excess of variants in 75 PM genes, that persisted after removing monogenic causes of PM. A PM gene panel showed that the burden was carried by six centrosomal genes. In zebrafish, non-centrosomal gene casc5 biallelic invalidation produced a severe PM phenotype, that was not modified by centrosomal genes aspm or wdr62 invalidation. A digenic, quadriallelic PM phenotype was produced by aspm and wdr62. Digenic analysis of the PM cohort revealed candidates for digenic inheritance, among which heterozygous mutations in CEP135 and WDR62 in one PM patient.In this study, we widened the spectrum of known deleterious mutations in PM genes and provided detailed patients’ clinical information, improving genetic counseling provided to families. We expanded AP4M1 and TRAPPC9 phenotypes to severe microcephaly of prenatal onset, and suggested a bifunctional model of MCPH1 where the centrosomal function is involved in brain volumic development and not the DNA Damage Repair function. We presented four interesting candidate genes for PM that need further investigations. Moreover, our observations provided strong evidence for digenic inheritance of human PM, involving centrosomal genes. Absence of genetic interaction between casc5 and aspm or wdr62 delineated centrosomal and non-centrosomal pathways in PM. Candidate pairs for digenic inheritance in human PM will be worth investigating in the future and will contribute to unravel the complex genetic architecture of PM.Les Microcéphalies Primaires (MPs) sont caractérisées par une tête trop petite dès la naissance, résultant d’une production insuffisante de neurones durant le développement embryonnaire. Les MPs sont responsables d’une lourde charge de déficits intellectuels, et servent de maladies modèles pour le développement volumique cérébral. Les gènes connus de MP appartiennent à des voies cellulaires distinctes, comme la duplication centriolaire, le contrôle du cycle cellulaire et le contrôle général de la réplication de l’ADN, bien que le mécanisme exact responsable des MP ne soit pas clair. Des gènes causant des formes monogéniques de MP sont identifiés dans moins de 50% des patients. Une hérédité digénique a récemment été décrite chez la souris pour la MP causée par Aspm et Wdr62, mais il n’est pas clair que ceci s’applique aussi à l’humain. La dissection génétique de la MP pourra fournir des informations intéressantes concernant les mécanismes cellulaires impliqués.Dans cette étude, nous avons utilisé deux approches holistiques, in vivo :séquençage à haut débit de multiples gènes de MP chez des patients MP humains, et invalidation de gènes sélectionnés de MP chez le poisson-zèbre.L’analyse d’une large cohorte de patients MP a révélé 15 nouvelles mutations dans des gènes MP connus, ASPM et WDR62 étant les gènes les plus fréquemment mutés. Des mutations dans les gènes AP4M1 et TRAPPC9 ont été associées à la MP dans deux familles. Une mutation dans le gène MCPH1 tronquant le dernier domaine BRCT n’a étonnamment pas été associée à la MP. L’analyse de la cohorte a aussi révélé des variants dans quatre gènes candidats n’ayant pas encore été associés à des pathologies humaines. De plus, l’analyse d’exomes de patients MP a montré un excès significatif de variants dans 75 gènes MP, persistant après retrait des causes monogéniques de MP. Un panel de gènes MP a montré que l’excès de variants était porté par six gènes centrosomaux. Chez le poisson-zèbre, l’invalidation biallélique du gène non centrosomal casc5 a induit un phénotype de MP sévère, non modifié par l’invalidation des gènes centrosomaux aspm ou wdr62. Un phénotype de MP digénique, quadriallélique, a été induit par aspm et wdr62. L’analyse digénique de la cohorte MP a révélé des candidats pour une hérédité digénique, parmi lesquels des mutations hétérozygotes dans les gènes CEP135 et WDR62 chez un patient MP.Dans cette étude, nous élargissons le spectre des mutations délétères connues dans les gènes MP et nous fournissons des renseignements cliniques détaillés au sujet des patients, deux éléments aboutissant à l’amélioration du conseil génétique apporté aux familles. Nous étendons les phénotypes AP4M1 et TRAPPC9 à une MP sévère, et suggérons un modèle bifonctionnel de MCPH1 où seule la fonction centrosomale serait impliquée dans le développement volumique cérébral, et pas la fonction de réparation de l’ADN. Nous présentons quatre gènes candidats intéressants pour la MP, qui nécessiteront des investigations supplémentaires. De plus, nos observations apportent des preuves fortes en faveur de l’existence d’une hérédité digénique dans la MP, impliquant des gènes centrosomaux. L’absence d’interaction génétique entre casc5 d’une part, et aspm ou wdr62 d’autre part, distingue des voies centrosomale et non centrosomale dans la MP. Des paires candidates pour une hérédité digénique dans la MP humaine pourront faire l’objet de recherches intéressantes durant les prochaines années, contribuant à éclaircir l’architecture génétique complexe de la MP.Doctorat en Sciences médicales (Médecine)info:eu-repo/semantics/nonPublishe

The genetics of congenitally small brains.

Primary microcephaly (PM) refers to a congenitally small brain, resulting from insufficient prenatal production of neurons, and serves as a model disease for brain volumic development. Known PM genes delineate several cellular pathways, among which the centriole duplication pathway, which provide interesting clues about the cellular mechanisms involved. The general interest of the genetic dissection of PM is illustrated by the convergence of Zika virus infection and PM gene mutations on congenital microcephaly, with CENPJ/CPAP emerging as a key target. Physical (protein-protein) and genetic (digenic inheritance) interactions of Wdr62 and Aspm have been demonstrated in mice, and should now be sought in humans using high throughput parallel sequencing of multiple PM genes in PM patients and control subjects, in order to categorize mutually interacting genes, hence delineating functional pathways in vivo in humans.SCOPUS: re.jinfo:eu-repo/semantics/publishe

Autosomal recessive primary microcephaly due to ASPM mutations: An update

Autosomal recessive microcephaly or microcephaly primary hereditary (MCPH) is a genetically heterogeneous neurodevelopmental disorder characterized by a reduction in brain volume, indirectly measured by an occipitofrontal circumference (OFC) 2 standard deviations or more below the age- and sex-matched mean (−2SD) at birth and −3SD after 6 months, and leading to intellectual disability of variable severity. The abnormal spindle-like microcephaly gene (ASPM), the human ortholog of the Drosophila melanogaster “abnormal spindle” gene (asp), encodes ASPM, a protein localized at the centrosome of apical neuroprogenitor cells and involved in spindle pole positioning during neurogenesis. Loss-of-function mutations in ASPM cause MCPH5, which affects the majority of all MCPH patients worldwide. Here, we report 47 unpublished patients from 39 families carrying 28 new ASPM mutations, and conduct an exhaustive review of the molecular, clinical, neuroradiological, and neuropsychological features of the 282 families previously reported (with 161 distinct ASPM mutations). Furthermore, we show that ASPM-related microcephaly is not systematically associated with intellectual deficiency and discuss the association between the structural brain defects (strong reduction in cortical volume and surface area) that modify the cortical map of these patients and their cognitive abilities.0SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Phenotypes in siblings with homozygous mutations of TRAPPC9 and/or MCPH1 support a bifunctional model of MCPH1.

Autosomal recessive intellectual disability (ARID) is vastly heterogeneous. Truncating mutations of TRAPPC9 were reported in 8 ARID families. Autosomal recessive primary microcephaly (MCPH) represents another subgroup of ARID, itself very heterogeneous, where the size of the brain is very small since birth. MCPH1 plays a role at the centrosome via a BRCT1 domain, and in DNA Damage Repair (DDR) via BRCT2 and BRCT3, and it is not clear which of these two mechanisms causes MCPH in man.SCOPUS: ar.jinfo:eu-repo/semantics/publishe