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1.
Am J Med Genet A ; 188(12): 3550-3554, 2022 12.
Article in English | MEDLINE | ID: mdl-36129367

ABSTRACT

Deleterious variants in the vascular endothelial growth factor C (VEGFC) gene have been recently associated with Milroy-like primary lymphedema, an autosomal dominant disorder, characterized mainly by swelling of the lower limbs due to functional impairment of the lymphatic vessels. To date, only 26 patients with congenital lymphedema harboring VEGFC pathogenic variants were documented. Here, we describe the first prenatal case of a fetus with Milroy-like disease. Fetal ultrasound showed bilateral foot swelling. Chromosomal microarray analysis revealed a 137-kb copy number loss in 4q34.3 including only VEGFC gene in the propositus fetus. Segregation analysis showed that the deletion was inherited from the affected mother and grandmother. Taken together, our study highlights the important role of microarray analysis to detect subtle chromosomal imbalances in the prenatal setting and contributes to delineate the fetal phenotype of VEGFC-related primary congenital lymphedema.


Subject(s)
Lymphedema , Vascular Endothelial Growth Factor C , Pregnancy , Female , Humans , Vascular Endothelial Growth Factor C/genetics , Vascular Endothelial Growth Factor C/metabolism , Lymphedema/diagnostic imaging , Lymphedema/genetics , Phenotype , Heterozygote
2.
J Med Genet ; 59(6): 559-567, 2022 06.
Article in English | MEDLINE | ID: mdl-33820833

ABSTRACT

BACKGROUND: Arthrogryposis multiplex congenita (AMC) is characterised by congenital joint contractures in two or more body areas. AMC exhibits wide phenotypic and genetic heterogeneity. Our goals were to improve the genetic diagnosis rates of AMC, to evaluate the added value of whole exome sequencing (WES) compared with targeted exome sequencing (TES) and to identify new genes in 315 unrelated undiagnosed AMC families. METHODS: Several genomic approaches were used including genetic mapping of disease loci in multiplex or consanguineous families, TES then WES. Sanger sequencing was performed to identify or validate variants. RESULTS: We achieved disease gene identification in 52.7% of AMC index patients including nine recently identified genes (CNTNAP1, MAGEL2, ADGRG6, ADCY6, GLDN, LGI4, LMOD3, UNC50 and SCN1A). Moreover, we identified pathogenic variants in ASXL3 and STAC3 expanding the phenotypes associated with these genes. The most frequent cause of AMC was a primary involvement of skeletal muscle (40%) followed by brain (22%). The most frequent mode of inheritance is autosomal recessive (66.3% of patients). In sporadic patients born to non-consanguineous parents (n=60), de novo dominant autosomal or X linked variants were observed in 30 of them (50%). CONCLUSION: New genes recently identified in AMC represent 21% of causing genes in our cohort. A high proportion of de novo variants were observed indicating that this mechanism plays a prominent part in this developmental disease. Our data showed the added value of WES when compared with TES due to the larger clinical spectrum of some disease genes than initially described and the identification of novel genes.


Subject(s)
Arthrogryposis , Arthrogryposis/diagnosis , Arthrogryposis/genetics , Arthrogryposis/pathology , Genomics , Humans , Pedigree , Phenotype , Proteins/genetics , Transcription Factors/genetics , Exome Sequencing
3.
Brain ; 144(9): 2616-2624, 2021 10 22.
Article in English | MEDLINE | ID: mdl-34270682

ABSTRACT

Heterozygous missense HTRA1 mutations have been associated with an autosomal dominant cerebral small vessel disease (CSVD) whereas the pathogenicity of heterozygous HTRA1 stop codon variants is unclear. We performed a targeted high throughput sequencing of all known CSVD genes, including HTRA1, in 3853 unrelated consecutive CSVD patients referred for molecular diagnosis. The frequency of heterozygous HTRA1 mutations leading to a premature stop codon in this patient cohort was compared with their frequency in large control databases. An analysis of HTRA1 mRNA was performed in several stop codon carrier patients. Clinical and neuroimaging features were characterized in all probands. Twenty unrelated patients carrying a heterozygous HTRA1 variant leading to a premature stop codon were identified. A highly significant difference was observed when comparing our patient cohort with control databases: gnomAD v3.1.1 [P = 3.12 × 10-17, odds ratio (OR) = 21.9], TOPMed freeze 5 (P = 7.6 × 10-18, OR = 27.1) and 1000 Genomes (P = 1.5 × 10-5). Messenger RNA analysis performed in eight patients showed a degradation of the mutated allele strongly suggesting a haploinsufficiency. Clinical and neuroimaging features are similar to those previously reported in heterozygous missense mutation carriers, except for penetrance, which seems lower. Altogether, our findings strongly suggest that heterozygous HTRA1 stop codons are pathogenic through a haploinsufficiency mechanism. Future work will help to estimate their penetrance, an important information for genetic counselling.


Subject(s)
Brain/diagnostic imaging , Codon, Nonsense/genetics , Frameshift Mutation/genetics , Heterozygote , High-Temperature Requirement A Serine Peptidase 1/genetics , Aged , Female , Humans , Male , Middle Aged , Pedigree
4.
Cancers (Basel) ; 13(12)2021 Jun 13.
Article in English | MEDLINE | ID: mdl-34199217

ABSTRACT

Complete deletion of the NF1 gene is identified in 5-10% of patients with neurofibromatosis type 1 (NF1). Several studies have previously described particularly severe forms of the disease in NF1 patients with deletion of the NF1 locus, but comprehensive descriptions of large cohorts are still missing to fully characterize this contiguous gene syndrome. NF1-deleted patients were enrolled and phenotypically characterized with a standardized questionnaire between 2005 and 2020 from a large French NF1 cohort. Statistical analyses for main NF1-associated symptoms were performed versus an NF1 reference population. A deletion of the NF1 gene was detected in 4% (139/3479) of molecularly confirmed NF1 index cases. The median age of the group at clinical investigations was 21 years old. A comprehensive clinical assessment showed that 93% (116/126) of NF1-deleted patients fulfilled the NIH criteria for NF1. More than half had café-au-lait spots, skinfold freckling, Lisch nodules, neurofibromas, neurological abnormalities, and cognitive impairment or learning disabilities. Comparison with previously described "classic" NF1 cohorts showed a significantly higher proportion of symptomatic spinal neurofibromas, dysmorphism, learning disabilities, malignancies, and skeletal and cardiovascular abnormalities in the NF1-deleted group. We described the largest NF1-deleted cohort to date and clarified the more severe phenotype observed in these patients.

6.
Clin Genet ; 98(3): 261-273, 2020 09.
Article in English | MEDLINE | ID: mdl-32621347

ABSTRACT

Megacystis-microcolon-intestinal-hypoperistalsis syndrome (MMIHS) is a severe congenital visceral myopathy characterized by an abdominal distension due to a large non-obstructed urinary bladder, a microcolon and intestinal hypo- or aperistalsis. Most of the patients described to date carry a sporadic heterozygous variant in ACTG2. More recently, recessive forms have been reported and mutations in MYH11, LMOD1, MYLK and MYL9 have been described at the molecular level. In the present report, we describe five patients carrying a recurrent heterozygous variant in ACTG2. Exome sequencing performed in four families allowed us to identify the genetic cause in three. In two families, we identified variants in MMIHS causal genes, respectively a nonsense homozygous variant in MYH11 and a previously described homozygous deletion in MYL9. Finally, we identified compound heterozygous variants in a novel candidate gene, PDCL3, c.[143_144del];[380G>A], p.[(Tyr48Ter)];[(Cys127Tyr)]. After cDNA analysis, a complete absence of PDLC3 expression was observed in affected individuals, indicating that both mutated transcripts were unstable and prone to mediated mRNA decay. PDCL3 encodes a protein involved in the folding of actin, a key step in thin filament formation. Presumably, loss-of-function of this protein affects the contractility of smooth muscle tissues, making PDCL3 an excellent candidate gene for autosomal recessive forms of MMIHS.


Subject(s)
Abnormalities, Multiple/genetics , Carrier Proteins/genetics , Colon/abnormalities , Genetic Predisposition to Disease , Intestinal Pseudo-Obstruction/genetics , Nerve Tissue Proteins/genetics , Urinary Bladder/abnormalities , Abnormalities, Multiple/pathology , Aborted Fetus , Actins/genetics , Colon/pathology , Female , Homozygote , Humans , Infant, Newborn , Intestinal Pseudo-Obstruction/pathology , Male , Mutation/genetics , Myosin Heavy Chains/genetics , Myosin Light Chains/genetics , Pedigree , Urinary Bladder/pathology , Exome Sequencing
7.
Genet Med ; 22(11): 1887-1891, 2020 11.
Article in English | MEDLINE | ID: mdl-32565546

ABSTRACT

PURPOSE: Abnormality of the corpus callosum (AbnCC) is etiologically a heterogeneous condition and the prognosis in prenatally diagnosed cases is difficult to predict. The purpose of our research was to establish the diagnostic yield using chromosomal microarray (CMA) and exome sequencing (ES) in cases with prenatally diagnosed isolated (iAbnCC) and nonisolated AbnCC (niAbnCC). METHODS: CMA and prenatal trio ES (pES) were done on 65 fetuses with iAbnCC and niAbnCC. Only pathogenic gene variants known to be associated with AbnCC and/or intellectual disability were considered. RESULTS: pES results were available within a median of 21.5 days (9-53 days). A pathogenic single-nucleotide variant (SNV) was identified in 12 cases (18%) and a pathogenic CNV was identified in 3 cases (4.5%). Thus, the genetic etiology was determined in 23% of cases. In all diagnosed cases, the results provided sufficient information regarding the neurodevelopmental prognosis and helped the parents to make an informed decision regarding the outcome of the pregnancy. CONCLUSION: Our results show the significant diagnostic and prognostic contribution of CMA and pES in cases with prenatally diagnosed AbnCC. Further prospective cohort studies with long-term follow-up of the born children will be needed to provide accurate prenatal counseling after a negative pES result.


Subject(s)
Corpus Callosum , Exome , Child , Corpus Callosum/diagnostic imaging , Exome/genetics , Female , Fetus/diagnostic imaging , Humans , Pregnancy , Prospective Studies , Ultrasonography, Prenatal
8.
Epilepsia ; 61(6): 1142-1155, 2020 06.
Article in English | MEDLINE | ID: mdl-32452540

ABSTRACT

OBJECTIVE: To define the phenotypic spectrum of phosphatidylinositol glycan class A protein (PIGA)-related congenital disorder of glycosylation (PIGA-CDG) and evaluate genotype-phenotype correlations. METHODS: Our cohort encompasses 40 affected males with a pathogenic PIGA variant. We performed a detailed phenotypic assessment, and in addition, we reviewed the available clinical data of 36 previously published cases and assessed the variant pathogenicity using bioinformatical approaches. RESULTS: Most individuals had hypotonia, moderate to profound global developmental delay, and intractable seizures. We found that PIGA-CDG spans from a pure neurological phenotype at the mild end to a Fryns syndrome-like phenotype. We found a high frequency of cardiac anomalies including structural anomalies and cardiomyopathy, and a high frequency of spontaneous death, especially in childhood. Comparative bioinformatical analysis of common variants, found in the healthy population, and pathogenic variants, identified in affected individuals, revealed a profound physiochemical dissimilarity of the substituted amino acids in variant constrained regions of the protein. SIGNIFICANCE: Our comprehensive analysis of the largest cohort of published and novel PIGA patients broadens the spectrum of PIGA-CDG. Our genotype-phenotype correlation facilitates the estimation on pathogenicity of variants with unknown clinical significance and prognosis for individuals with pathogenic variants in PIGA.


Subject(s)
Genetic Variation/genetics , Hernia, Diaphragmatic/diagnostic imaging , Hernia, Diaphragmatic/genetics , Limb Deformities, Congenital/diagnostic imaging , Limb Deformities, Congenital/genetics , Membrane Proteins/genetics , Adult , Amino Acid Sequence , Child , Cohort Studies , Electroencephalography/methods , Facies , Hernia, Diaphragmatic/physiopathology , Humans , Infant, Newborn , Limb Deformities, Congenital/physiopathology , Magnetic Resonance Imaging/methods , Male
9.
Hum Mutat ; 41(5): 926-933, 2020 05.
Article in English | MEDLINE | ID: mdl-32058622

ABSTRACT

Sirenomelia is a rare severe malformation sequence of unknown cause characterized by fused legs and severe visceral abnormalities. We present a series of nine families including two rare familial aggregations of sirenomelia investigated by a trio-based exome sequencing strategy. This approach identified CDX2 variants in the two familial aggregations, both fitting an autosomal dominant pattern of inheritance with variable expressivity. CDX2 is a major regulator of caudal development in vertebrate and mouse heterozygotes are a previously described model of sirenomelia. Remarkably, the p.(Arg237His) variant has already been reported in a patient with persistent cloaca. Analysis of the sporadic cases revealed six additional candidate variants including a de novo frameshift variant in the genetically constrained NKD1 gene, encoding a known interactor of CDX2. We provide the first insights for a genetic contribution in human sirenomelia and highlight the role of Cdx and Wnt signaling pathways in the development of this disorder.


Subject(s)
Ectromelia/diagnosis , Ectromelia/genetics , Exome Sequencing , Genetic Association Studies , Genetic Predisposition to Disease , Adaptor Proteins, Signal Transducing/genetics , Alleles , Amino Acid Substitution , CDX2 Transcription Factor/genetics , Calcium-Binding Proteins/genetics , Female , Genetic Association Studies/methods , Genotype , Humans , Male , Pedigree , Phenotype
10.
Eur J Hum Genet ; 28(6): 770-782, 2020 06.
Article in English | MEDLINE | ID: mdl-32005960

ABSTRACT

TBR1, a T-box transcription factor expressed in the cerebral cortex, regulates the expression of several candidate genes for autism spectrum disorders (ASD). Although TBR1 has been reported as a high-confidence risk gene for ASD and intellectual disability (ID) in functional and clinical reports since 2011, TBR1 has only recently been recorded as a human disease gene in the OMIM database. Currently, the neurodevelopmental disorders and structural brain anomalies associated with TBR1 variants are not well characterized. Through international data sharing, we collected data from 25 unreported individuals and compared them with data from the literature. We evaluated structural brain anomalies in seven individuals by analysis of MRI images, and compared these with anomalies observed in TBR1 mutant mice. The phenotype included ID in all individuals, associated to autistic traits in 76% of them. No recognizable facial phenotype could be identified. MRI analysis revealed a reduction of the anterior commissure and suggested new features including dysplastic hippocampus and subtle neocortical dysgenesis. This report supports the role of TBR1 in ID associated with autistic traits and suggests new structural brain malformations in humans. We hope this work will help geneticists to interpret TBR1 variants and diagnose ASD probands.


Subject(s)
Autistic Disorder/genetics , Craniofacial Abnormalities/genetics , Intellectual Disability/genetics , Phenotype , T-Box Domain Proteins/genetics , Adolescent , Adult , Animals , Autistic Disorder/pathology , Child , Child, Preschool , Cognition , Craniofacial Abnormalities/pathology , Female , Hippocampus/diagnostic imaging , Hippocampus/pathology , Humans , Intellectual Disability/pathology , Male , Mice , Mutation , Neocortex/diagnostic imaging , Neocortex/pathology , Syndrome , T-Box Domain Proteins/metabolism
11.
Orphanet J Rare Dis ; 14(1): 288, 2019 12 11.
Article in English | MEDLINE | ID: mdl-31829210

ABSTRACT

BACKGROUND: Segmental progeroid syndromes are a heterogeneous group of rare and often severe genetic disorders that have been studied since the twentieth century. These progeroid syndromes are defined as segmental because only some of the features observed during natural aging are accelerated. METHODS: Since 2015, the Molecular Genetics Laboratory in Marseille La Timone Hospital proposes molecular diagnosis of premature aging syndromes including laminopathies and related disorders upon NGS sequencing of a panel of 82 genes involved in these syndromes. We analyzed the results obtained in 4 years on 66 patients issued from France and abroad. RESULTS: Globally, pathogenic or likely pathogenic variants (ACMG class 5 or 4) were identified in about 1/4 of the cases; among these, 9 pathogenic variants were novel. On the other hand, the diagnostic yield of our panel was over 60% when the patients were addressed upon a nosologically specific clinical suspicion, excepted for connective tissue disorders, for which clinical diagnosis may be more challenging. Prenatal testing was proposed to 3 families. We additionally detected 16 variants of uncertain significance and reclassified 3 of them as benign upon segregation analysis in first degree relatives. CONCLUSIONS: High throughput sequencing using the Laminopathies/ Premature Aging disorders panel allowed molecular diagnosis of rare disorders associated with premature aging features and genetic counseling for families, representing an interesting first-level analysis before whole genome sequencing may be proposed, as a future second step, by the National high throughput sequencing platforms ("Medicine France Genomics 2025" Plan), in families without molecular diagnosis.


Subject(s)
Aging, Premature/genetics , Adolescent , Adult , Aged , Child , Child, Preschool , Female , Genetic Counseling , Genetic Testing , Genetic Variation/genetics , Genomics/methods , High-Throughput Nucleotide Sequencing , Humans , Infant , Male , Middle Aged , Mutation/genetics , Sequence Analysis, DNA/methods , Whole Genome Sequencing/methods , Young Adult
12.
Eur J Med Genet ; 62(2): 144-148, 2019 Feb.
Article in English | MEDLINE | ID: mdl-29981851

ABSTRACT

Congenital analbuminemia (OMIM # 616000) is an extremely rare autosomal recessive disorder, caused by variations in the albumin gene (ALB), which is generally thought to be a relatively benign condition in adulthood, but seems to be potentially life threatening in the pre- and peri-natal period. The subject of our study was a consanguineous family, in which we identified two analbuminemic individuals. Mutation analysis of ALB revealed that both are homozygous for a previously unreported insertion in exon 9 (c.1098dupT), causing a subsequent frame-shift with the generation of a premature stop codon, and an aberrant truncated putative protein product, p.Val367fsTer12. This variation is present in heterozygous condition in several other members of the family. The phenotype and the molecular genetics of CAA are discussed.


Subject(s)
Hypoalbuminemia/genetics , Mutation , Serum Albumin, Human/genetics , Adult , Aged , Codon, Terminator , Consanguinity , Female , Humans , Hypoalbuminemia/pathology , Male , Pedigree , Phenotype
13.
Brain ; 141(3): 698-712, 2018 03 01.
Article in English | MEDLINE | ID: mdl-29365063

ABSTRACT

Polymicrogyria is a malformation of cortical development. The aetiology of polymicrogyria remains poorly understood. Using whole-exome sequencing we found de novo heterozygous missense GRIN1 mutations in 2 of 57 parent-offspring trios with polymicrogyria. We found nine further de novo missense GRIN1 mutations in additional cortical malformation patients. Shared features in the patients were extensive bilateral polymicrogyria associated with severe developmental delay, postnatal microcephaly, cortical visual impairment and intractable epilepsy. GRIN1 encodes GluN1, the essential subunit of the N-methyl-d-aspartate receptor. The polymicrogyria-associated GRIN1 mutations tended to cluster in the S2 region (part of the ligand-binding domain of GluN1) or the adjacent M3 helix. These regions are rarely mutated in the normal population or in GRIN1 patients without polymicrogyria. Using two-electrode and whole-cell voltage-clamp analysis, we showed that the polymicrogyria-associated GRIN1 mutations significantly alter the in vitro activity of the receptor. Three of the mutations increased agonist potency while one reduced proton inhibition of the receptor. These results are striking because previous GRIN1 mutations have generally caused loss of function, and because N-methyl-d-aspartate receptor agonists have been used for many years to generate animal models of polymicrogyria. Overall, our results expand the phenotypic spectrum associated with GRIN1 mutations and highlight the important role of N-methyl-d-aspartate receptor signalling in the pathogenesis of polymicrogyria.


Subject(s)
Mutation/genetics , Nerve Tissue Proteins/genetics , Polymicrogyria/genetics , Receptors, N-Methyl-D-Aspartate/genetics , Animals , Child , Child, Preschool , DNA Mutational Analysis , Excitatory Amino Acid Agonists/pharmacology , Family Health , Female , Glutamic Acid/pharmacology , Glycine/metabolism , Glycine/pharmacology , HEK293 Cells , Humans , Infant , Magnetic Resonance Imaging , Male , Membrane Potentials/genetics , Models, Molecular , Mutagenesis/genetics , N-Methylaspartate/pharmacology , Patch-Clamp Techniques , Polymicrogyria/diagnostic imaging , Rats , Transfection
14.
Am J Med Genet C Semin Med Genet ; 175(4): 417-430, 2017 12.
Article in English | MEDLINE | ID: mdl-29178447

ABSTRACT

CHARGE syndrome (CS) is a genetic disorder whose first description included Coloboma, Heart disease, Atresia of choanae, Retarded growth and development, Genital hypoplasia, and Ear anomalies and deafness, most often caused by a genetic mutation in the CHD7 gene. Two features were then added: semicircular canal anomalies and arhinencephaly/olfactory bulb agenesis, with classification of typical, partial, or atypical forms on the basis of major and minor clinical criteria. The detection rate of a pathogenic variant in the CHD7 gene varies from 67% to 90%. To try to have an overview of this heterogenous clinical condition and specify a genotype-phenotype relation, we conducted a national study of phenotype and genotype in 119 patients with CS. Selected clinical diagnostic criteria were from Verloes (2005), updated by Blake & Prasad (). Besides obtaining a detailed clinical description, when possible, patients underwent a full ophthalmologic examination, audiometry, temporal bone CT scan, gonadotropin analysis, and olfactory-bulb MRI. All patients underwent CHD7 sequencing and MLPA analysis. We found a pathogenic CHD7 variant in 83% of typical CS cases and 58% of atypical cases. Pathogenic variants in the CHD7 gene were classified by the expected impact on the protein. In all, 90% of patients had a typical form of CS and 10% an atypical form. The most frequent features were deafness/semicircular canal hypoplasia (94%), pituitary defect/hypogonadism (89%), external ear anomalies (87%), square-shaped face (81%), and arhinencephaly/anosmia (80%). Coloboma (73%), heart defects (65%), and choanal atresia (43%) were less frequent.


Subject(s)
CHARGE Syndrome/diagnosis , CHARGE Syndrome/genetics , Genetic Association Studies , Genotype , Phenotype , Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , Adolescent , Adult , Alleles , Amino Acid Substitution , Central Nervous System/abnormalities , Child , Child, Preschool , Cohort Studies , Cranial Nerves/abnormalities , DNA Helicases/genetics , DNA-Binding Proteins/genetics , Female , France , Genetic Testing , Humans , Infant , Male , Molecular Diagnostic Techniques , Young Adult
15.
Acta Neuropathol Commun ; 5(1): 36, 2017 05 01.
Article in English | MEDLINE | ID: mdl-28460636

ABSTRACT

Congenital hydrocephalus is considered as either acquired due to haemorrhage, infection or neoplasia or as of developmental nature and is divided into two subgroups, communicating and obstructive. Congenital hydrocephalus is either syndromic or non-syndromic, and in the latter no cause is found in more than half of the patients. In patients with isolated hydrocephalus, L1CAM mutations represent the most common aetiology. More recently, a founder mutation has also been reported in the MPDZ gene in foetuses presenting massive hydrocephalus, but the neuropathology remains unknown. We describe here three novel homozygous null mutations in the MPDZ gene in foetuses whose post-mortem examination has revealed a homogeneous phenotype characterized by multiple ependymal malformations along the aqueduct of Sylvius, the third and fourth ventricles as well as the central canal of the medulla, consisting in multifocal rosettes with immature cell accumulation in the vicinity of ependymal lining early detached from the ventricular zone. MPDZ also named MUPP1 is an essential component of tight junctions which are expressed from early brain development in the choroid plexuses and ependyma. Alterations in the formation of tight junctions within the ependyma very likely account for the lesions observed and highlight for the first time that primary multifocal ependymal malformations of the ventricular system is genetically determined in humans. Therefore, MPDZ sequencing should be performed when neuropathological examination reveals multifocal ependymal rosette formation within the aqueduct of Sylvius, of the third and fourth ventricles and of the central canal of the medulla.


Subject(s)
Carrier Proteins/genetics , Ependyma/abnormalities , Fetal Diseases/genetics , Hydrocephalus/genetics , Loss of Function Mutation , Adult , Ependyma/diagnostic imaging , Family , Female , Fetal Diseases/diagnostic imaging , Fetal Diseases/etiology , Fetal Diseases/pathology , Homozygote , Humans , Hydrocephalus/diagnostic imaging , Hydrocephalus/etiology , Hydrocephalus/pathology , Membrane Proteins
16.
Fam Cancer ; 16(2): 167-171, 2017 04.
Article in English | MEDLINE | ID: mdl-27783335

ABSTRACT

Germline allele specific expression (ASE), resulting in a lowered expression of one of the BRCA1 alleles, has been described as a possible predisposition marker in Hereditary Breast or Ovarian Cancer (HBOC), usable for molecular diagnosis in HBOC. The main objective of this prospective case-control study was to compare the proportion of ASE between controls without familial history of breast or ovarian cancer, and HBOC cases without BRCA1 or BRCA2 deleterious mutation. BRCA1 ASE evaluated on three SNPs among controls and HBOC patients without deleterious mutation were assessed by pyrosequencing. The allelic ratios and the proportion of ASE were compared between controls and cases using a Student's t test and a Fisher exact test, respectively. The linearity and reproducibility of the ASE dosage was demonstrated with R2 > 0.99 and a coefficient of variation below 10 %, and ASE was detected in two positive controls harbouring BRCA1 truncated mutations. In the heterozygote population, composed of 99/264 controls (37.5 %) and 96/227 patients (42.3 %), we detected a 5 % ASE without truncated mutations, in each population. We failed to detect any significant difference of ASE between controls and patients. So far, BRCA1 Allelic specific expression is not usable in routine diagnosis as a possible predisposition marker in HBOC patients except for the detection of truncated mutations.


Subject(s)
Allelic Imbalance/genetics , BRCA1 Protein/genetics , Genes, BRCA1 , Genetic Predisposition to Disease/genetics , Germ-Line Mutation/genetics , Hereditary Breast and Ovarian Cancer Syndrome/genetics , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/genetics , Case-Control Studies , Female , Heterozygote , Humans , Middle Aged , Polymorphism, Single Nucleotide , Prospective Studies , Young Adult
17.
Hum Mutat ; 38(1): 43-47, 2017 01.
Article in English | MEDLINE | ID: mdl-27667122

ABSTRACT

Wagner disease is a rare nonsyndromic autosomal-dominant vitreoretinopathy, associated with splice mutations specifically targeting VCAN exon 8. We report the extensive genetic analysis of two Wagner probands, previously found negative for disease-associated splice mutations. Next-generation sequencing (NGS), quantitative real-time PCR, and long-range PCR identified two deletions (3.4 and 10.5 kb) removing at least one exon-intron boundary of exon 8, and both correlating with an imbalance of VCAN mRNA isoforms. We showed that the 10.5-kb deletion occurred de novo, causing somatic mosaicism in the proband's mother who had an unusually mild asymmetrical phenotype. Therefore, exon 8 deletions are novel VCAN genetic defects responsible for Wagner disease, and VCAN mosaic mutations may be involved in the pathogenesis of Wagner disease with attenuated phenotype. NGS is then an effective screening tool for genetic diagnosis of Wagner disease, improving the chance of identifying all disease-causative variants as well as mosaic mutations in VCAN.


Subject(s)
Exons , Retinal Degeneration/diagnosis , Retinal Degeneration/genetics , Sequence Deletion , Versicans/deficiency , Chromosome Breakpoints , DNA Mutational Analysis , Female , High-Throughput Nucleotide Sequencing , Humans , Male , Pedigree , Real-Time Polymerase Chain Reaction , Translocation, Genetic , Versicans/genetics
18.
Genet Med ; 18(1): 49-56, 2016 Jan.
Article in English | MEDLINE | ID: mdl-25790162

ABSTRACT

PURPOSE: Treacher Collins/Franceschetti syndrome (TCS; OMIM 154500) is a disorder of craniofacial development belonging to the heterogeneous group of mandibulofacial dysostoses. TCS is classically characterized by bilateral mandibular and malar hypoplasia, downward-slanting palpebral fissures, and microtia. To date, three genes have been identified in TCS:,TCOF1, POLR1D, and POLR1C. METHODS: We report a clinical and extensive molecular study, including TCOF1, POLR1D, POLR1C, and EFTUD2 genes, in a series of 146 patients with TCS. Phenotype-genotype correlations were investigated for 19 clinical features, between TCOF1 and POLR1D, and the type of mutation or its localization in the TCOF1 gene. RESULTS: We identified 92/146 patients (63%) with a molecular anomaly within TCOF1, 9/146 (6%) within POLR1D, and none within POLR1C. Among the atypical negative patients (with intellectual disability and/or microcephaly), we identified four patients carrying a mutation in EFTUD2 and two patients with 5q32 deletion encompassing TCOF1 and CAMK2A in particular. Congenital cardiac defects occurred more frequently among patients with TCOF1 mutation (7/92, 8%) than reported in the literature. CONCLUSION: Even though TCOF1 and POLR1D were associated with extreme clinical variability, we found no phenotype-genotype correlation. In cases with a typical phenotype of TCS, 6/146 (4%) remained with an unidentified molecular defect.


Subject(s)
DNA-Directed RNA Polymerases/genetics , Mandibulofacial Dysostosis/genetics , Nuclear Proteins/genetics , Phosphoproteins/genetics , Adolescent , Adult , Amino Acid Sequence , Base Sequence , Child , Female , Genetic Association Studies , Humans , Male , Mandibulofacial Dysostosis/diagnosis , Microcephaly/genetics , Middle Aged , Molecular Sequence Data , Mutation , Peptide Elongation Factors/genetics , Ribonucleoprotein, U5 Small Nuclear/genetics , Sequence Deletion , Young Adult
19.
Orphanet J Rare Dis ; 9: 74, 2014 May 10.
Article in English | MEDLINE | ID: mdl-24884629

ABSTRACT

BACKGROUND: Oral-facial-digital type 1 syndrome (OFD1; OMIM 311200) belongs to the expanding group of disorders ascribed to ciliary dysfunction. With the aim of contributing to the understanding of the role of primary cilia in the central nervous system (CNS), we performed a thorough characterization of CNS involvement observed in this disorder. METHODS: A cohort of 117 molecularly diagnosed OFD type I patients was screened for the presence of neurological symptoms and/or cognitive/behavioral abnormalities on the basis of the available information supplied by the collaborating clinicians. Seventy-one cases showing CNS involvement were further investigated through neuroimaging studies and neuropsychological testing. RESULTS: Seventeen patients were molecularly diagnosed in the course of this study and five of these represent new mutations never reported before. Among patients displaying neurological symptoms and/or cognitive/behavioral abnormalities, we identified brain structural anomalies in 88.7%, cognitive impairment in 68%, and associated neurological disorders and signs in 53% of cases. The most frequently observed brain structural anomalies included agenesis of the corpus callosum and neuronal migration/organisation disorders as well as intracerebral cysts, porencephaly and cerebellar malformations. CONCLUSIONS: Our results support recent published findings indicating that CNS involvement in this condition is found in more than 60% of cases. Our findings correlate well with the kind of brain developmental anomalies described in other ciliopathies. Interestingly, we also described specific neuropsychological aspects such as reduced ability in processing verbal information, slow thought process, difficulties in attention and concentration, and notably, long-term memory deficits which may indicate a specific role of OFD1 and/or primary cilia in higher brain functions.


Subject(s)
Central Nervous System Diseases/physiopathology , Orofaciodigital Syndromes/physiopathology , Central Nervous System Diseases/genetics , Central Nervous System Diseases/psychology , Cohort Studies , Female , Humans , Magnetic Resonance Imaging , Mutation , Neuropsychological Tests , Orofaciodigital Syndromes/genetics , Orofaciodigital Syndromes/psychology
20.
Eur J Hum Genet ; 22(11): 1305-13, 2014 Nov.
Article in English | MEDLINE | ID: mdl-24549055

ABSTRACT

To optimize the molecular diagnosis of hereditary breast and ovarian cancer (HBOC), we developed a next-generation sequencing (NGS)-based screening based on the capture of a panel of genes involved, or suspected to be involved in HBOC, on pooling of indexed DNA and on paired-end sequencing in an Illumina GAIIx platform, followed by confirmation by Sanger sequencing or MLPA/QMPSF. The bioinformatic pipeline included CASAVA, NextGENe, CNVseq and Alamut-HT. We validated this procedure by the analysis of 59 patients' DNAs harbouring SNVs, indels or large genomic rearrangements of BRCA1 or BRCA2. We also conducted a blind study in 168 patients comparing NGS versus Sanger sequencing or MLPA analyses of BRCA1 and BRCA2. All mutations detected by conventional procedures were detected by NGS. We then screened, using three different versions of the capture set, a large series of 708 consecutive patients. We detected in these patients 69 germline deleterious alterations within BRCA1 and BRCA2, and 4 TP53 mutations in 468 patients also tested for this gene. We also found 36 variations inducing either a premature codon stop or a splicing defect among other genes: 5/708 in CHEK2, 3/708 in RAD51C, 1/708 in RAD50, 7/708 in PALB2, 3/708 in MRE11A, 5/708 in ATM, 3/708 in NBS1, 1/708 in CDH1, 3/468 in MSH2, 2/468 in PMS2, 1/708 in BARD1, 1/468 in PMS1 and 1/468 in MLH3. These results demonstrate the efficiency of NGS in performing molecular diagnosis of HBOC. Detection of mutations within other genes than BRCA1 and BRCA2 highlights the genetic heterogeneity of HBOC.


Subject(s)
Breast Neoplasms, Male/genetics , Genomics/methods , High-Throughput Nucleotide Sequencing/methods , Ovarian Neoplasms/genetics , Adult , Aged , BRCA1 Protein/genetics , BRCA1 Protein/metabolism , BRCA2 Protein/genetics , BRCA2 Protein/metabolism , Breast Neoplasms/diagnosis , Breast Neoplasms/genetics , Breast Neoplasms, Male/diagnosis , Case-Control Studies , Computational Biology , Female , Gene Rearrangement , Genetic Predisposition to Disease , Genetic Testing , Humans , Male , Middle Aged , Mutation , Ovarian Neoplasms/diagnosis , Reproducibility of Results , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
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