Publications by authors named "Jacques Puechberty"

40 Publications

Genetic analyses of a large cohort of infertile patients with globozoospermia, DPY19L2 still the main actor, GGN confirmed as a guest player.

Hum Genet 2021 Jan 27;140(1):43-57. Epub 2020 Oct 27.

Service de Biologie de la Reproduction-CECOS, Hôpital Tenon, AP-HP, 75020, Paris, France.

Globozoospermia is a rare phenotype of primary male infertility inducing the production of round-headed spermatozoa without acrosome. Anomalies of DPY19L2 account for 50-70% of all cases and the entire deletion of the gene is by far the most frequent defect identified. Here, we present a large cohort of 69 patients with 20-100% of globozoospermia. Genetic analyses including multiplex ligation-dependent probe amplification, Sanger sequencing and whole-exome sequencing identified 25 subjects with a homozygous DPY19L2 deletion (36%) and 14 carrying other DPY19L2 defects (20%). Overall, 11 deleterious single-nucleotide variants were identified including eight novel and three already published mutations. Patients with a higher rate of round-headed spermatozoa were more often diagnosed and had a higher proportion of loss of function anomalies, highlighting a good genotype phenotype correlation. No gene defects were identified in patients carrying < 50% of globozoospermia while diagnosis efficiency rose to 77% for patients with > 50% of globozoospermia. In addition, results from whole-exome sequencing were scrutinized for 23 patients with a DPY19L2 negative diagnosis, searching for deleterious variants in the nine other genes described to be associated with globozoospermia in human (C2CD6, C7orf61, CCDC62, CCIN, DNAH17, GGN, PICK1, SPATA16, and ZPBP1). Only one homozygous novel truncating variant was identified in the GGN gene in one patient, confirming the association of GGN with globozoospermia. In view of these results, we propose a novel diagnostic strategy focusing on patients with at least 50% of globozoospermia and based on a classical qualitative PCR to detect DPY19L2 homozygous deletions. In the absence of the latter, we recommend to perform whole-exome sequencing to search for defects in DPY19L2 as well as in the other previously described candidate genes.
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http://dx.doi.org/10.1007/s00439-020-02229-0DOI Listing
January 2021

A 4.6 Mb Inversion Leading to - and - Fusion Transcripts as a New Pathogenic Mechanism Implicated in Usher Syndrome Type 1.

Front Genet 2020 2;11:623. Epub 2020 Jul 2.

Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France.

Usher type 1 syndrome is a rare autosomal recessive disorder involving congenital severe-to-profound hearing loss, development of vision impairment in the first decade, and severe balance difficulties. The gene, one of the five genes implicated in this disease, is involved in 8-20% of cases. In this study, we aimed to identify and characterize the two causal variants in a French patient with typical Usher syndrome clinical features. Massively parallel sequencing-based gene panel and screening for large rearrangements were used, which detected a single multi-exon deletion in the gene. As the second pathogenic event was likely localized in the unscreened regions of the gene, transcripts from cultured nasal cells were analyzed and revealed a loss of junction between exon 13 and exon 14. This aberration could be explained by the identification of two fusion transcripts, - and -, originating from a 4.6 Mb inversion. This complex chromosomal rearrangement could not be detected by our diagnostic approach but was instead characterized by long-read sequencing, which offers the possibility of detecting balanced structural variants (SVs). This finding extends our knowledge of the mutational spectrum of the gene with the first ever identification of a large causal paracentric inversion of chromosome 10 and illustrates the utility of screening balanced SVs in an exhaustive molecular diagnostic approach.
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http://dx.doi.org/10.3389/fgene.2020.00623DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343966PMC
July 2020

Single Circulating Fetal Trophoblastic Cells Eligible for Non Invasive Prenatal Diagnosis: the Exception Rather than the Rule.

Sci Rep 2020 06 17;10(1):9861. Epub 2020 Jun 17.

Laboratoire de Génétique de Maladies Rares, Institut Universitaire de Recherche Clinique, EA7402 Université de Montpellier, CHU Montpellier, Montpellier, France.

Non-Invasive Prenatal Diagnosis (NIPD), based on the analysis of circulating cell-free fetal DNA (cff-DNA), is successfully implemented for an increasing number of monogenic diseases. However, technical issues related to cff-DNA characteristics remain, and not all mutations can be screened with this method, particularly triplet expansion mutations that frequently concern prenatal diagnosis requests. The objective of this study was to develop an approach to isolate and analyze Circulating Trophoblastic Fetal Cells (CFTCs) for NIPD of monogenic diseases caused by triplet repeat expansion or point mutations. We developed a method for CFTC isolation based on DEPArray sorting and used Huntington's disease as the clinical model for CFTC-based NIPD. Then, we investigated whether CFTC isolation and Whole Genome Amplification (WGA) could be used for NIPD in couples at risk of transmitting different monogenic diseases. Our data show that the allele drop-out rate was 3-fold higher in CFTCs than in maternal cells processed in the same way. Moreover, we give new insights into CFTCs by compiling data obtained by extensive molecular testing by microsatellite multiplex PCR genotyping and by WGA followed by mini-exome sequencing. CFTCs appear to be often characterized by a random state of genomic degradation.
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http://dx.doi.org/10.1038/s41598-020-66923-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7300110PMC
June 2020

A Novel Chromosomal Translocation Identified due to Complex Genetic Instability in iPSC Generated for Choroideremia.

Cells 2019 09 11;8(9). Epub 2019 Sep 11.

Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France.

Induced pluripotent stem cells (iPSCs) have revolutionized the study of human diseases as they can renew indefinitely, undergo multi-lineage differentiation, and generate disease-specific models. However, the difficulty of working with iPSCs is that they are prone to genetic instability. Furthermore, genetically unstable iPSCs are often discarded, as they can have unforeseen consequences on pathophysiological or therapeutic read-outs. We generated iPSCs from two brothers of a previously unstudied family affected with the inherited retinal dystrophy choroideremia. We detected complex rearrangements involving chromosomes 12, 20 and/or 5 in the generated iPSCs. Suspecting an underlying chromosomal aberration, we performed karyotype analysis of the original fibroblasts, and of blood cells from additional family members. We identified a novel chromosomal translocation t(12;20)(q24.3;q11.2) segregating in this family. We determined that the translocation was balanced and did not impact subsequent retinal differentiation. We show for the first time that an undetected genetic instability in somatic cells can breed further instability upon reprogramming. Therefore, the detection of chromosomal aberrations in iPSCs should not be disregarded, as they may reveal rearrangements segregating in families. Furthermore, as such rearrangements are often associated with reproductive failure or birth defects, this in turn has important consequences for genetic counseling of family members.
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http://dx.doi.org/10.3390/cells8091068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770680PMC
September 2019

Mosaic complete tetrasomy 21 in a fetus with complete atrioventricular septal defect and minor morphological variations.

Mol Genet Genomic Med 2019 11 7;7(11):e00895. Epub 2019 Sep 7.

Service de Génétique Clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France.

Background: Tetrasomy 21 is a very rare aneuploidy which could clinically resemble a Down syndrome. It was most often described in its partial form than complete. We report the prenatal, pathological and genetic characteristics of a fetus with mosaic complete tetrasomy 21. This is the second well-documented description of a complete tetrasomy 21 in the literature.

Methods: Prenatal and fetal pathological examinations, cytogenetic and molecular analyses were performed to characterize fetal features with tetrasomy 21.

Results: Prenatal ultrasound examination revealed an isolated complete atrioventricular septal defect with normal karyotype on amniotic fluid. After termination of pregnancy, clinical examination of the fetus evoked trisomy 21 or Down syndrome. Chromosomal microarray analysis and FISH on lung tissue showed a mosaicism with four copies of chromosome 21 (tetrasomy 21).

Conclusion: Our observation and the review of the literature reported the possibility of very weak mosaicism and disease-causing confined tissue-specific mosaicism in fetus or alive patients with chromosome 21 aneuploidy, mainly Down syndrome. In case of clinical diagnosis suggestive of Down syndrome, attention must be paid to the risk of false-negative test due to chromosomal mosaicism (very weak percentage, different tissue distribution). To overcome this risk, it is necessary to privilege the diagnostic techniques without culture step and to increase the number of cells and tissues analyzed, if possible. This study highlights the limits of microarray as the unique diagnostic approach in case of weak mosaic and French cytogenetics guidelines recommend to check anomalies seen in microarray by another technique on the same tissue.
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http://dx.doi.org/10.1002/mgg3.895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825868PMC
November 2019

Estimating the effect size of the 15Q11.2 BP1-BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice.

J Med Genet 2019 10 26;56(10):701-710. Epub 2019 Aug 26.

Department of Pediatrics, University of Montreal, Montreal, Québec, Canada

Background: The 15q11.2 deletion is frequently identified in the neurodevelopmental clinic. Case-control studies have associated the 15q11.2 deletion with neurodevelopmental disorders, and clinical case series have attempted to delineate a microdeletion syndrome with considerable phenotypic variability. The literature on this deletion is extensive and confusing, which is a challenge for genetic counselling. The aim of this study was to estimate the effect size of the 15q11.2 deletion and quantify its contribution to neurodevelopmental disorders.

Methods: We performed meta-analyses on new and previously published case-control studies and used statistical models trained in unselected populations with cognitive assessments. We used new (n=241) and previously published (n=150) data from a clinically referred group of deletion carriers. 15q11.2 duplications (new n=179 and previously published n=35) were used as a neutral control variant.

Results: The deletion decreases IQ by 4.3 points. The estimated ORs and respective frequencies in deletion carriers for intellectual disabilities, schizophrenia and epilepsy are 1.7 (3.4%), 1.5 (2%) and 3.1 (2.1%), respectively. There is no increased risk for heart malformations and autism. In the clinically referred group, the frequency and nature of symptoms in deletions are not different from those observed in carriers of the 15q11.2 duplication suggesting that most of the reported symptoms are due to ascertainment bias.

Conclusions: We recommend that the deletion should be classified as 'pathogenic of mild effect size'. Since it explains only a small proportion of the phenotypic variance in carriers, it is not worth discussing in the developmental clinic or in a prenatal setting.
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http://dx.doi.org/10.1136/jmedgenet-2018-105879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6817694PMC
October 2019

Disruption of chromatin organisation causes MEF2C gene overexpression in intellectual disability: a case report.

BMC Med Genomics 2019 08 2;12(1):116. Epub 2019 Aug 2.

Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France.

Background: Balanced structural variants are mostly described in disease with gene disruption or subtle rearrangement at breakpoints.

Case Presentation: Here we report a patient with mild intellectual deficiency who carries a de novo balanced translocation t(3;5). Breakpoints were fully explored by microarray, Array Painting and Sanger sequencing. No gene disruption was found but the chromosome 5 breakpoint was localized 228-kb upstream of the MEF2C gene. The predicted Topologically Associated Domains analysis shows that it contains only the MEF2C gene and a long non-coding RNA LINC01226. RNA studies looking for MEF2C gene expression revealed an overexpression of MEF2C in the lymphoblastoid cell line of the patient.

Conclusions: Pathogenicity of MEF2C overexpression is still unclear as only four patients with mild intellectual deficiency carrying 5q14.3 microduplications containing MEF2C are described in the literature. The microduplications in these individuals also contain other genes expressed in the brain. The patient presented the same phenotype as 5q14.3 microduplication patients. We report the first case of a balanced translocation leading to an overexpression of MEF2C similar to a functional duplication.
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http://dx.doi.org/10.1186/s12920-019-0558-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6679470PMC
August 2019

Risk estimation of uniparental disomy of chromosome 14 or 15 in a fetus with a parent carrying a non-homologous Robertsonian translocation. Should we still perform prenatal diagnosis?

Prenat Diagn 2019 10 19;39(11):986-992. Epub 2019 Aug 19.

Centre de Génétique Chromosomique, GH de l'Institut Catholique de Lille-Hopital Saint Vincent de Paul, Lille, France.

Objective: Uniparental disomy (UPD) testing is currently recommended during pregnancy in fetuses carrying a balanced Robertsonian translocation (ROB) involving chromosome 14 or 15, both chromosomes containing imprinted genes. The overall risk that such a fetus presents a UPD has been previously estimated to be around ~0.6-0.8%. However, because UPD are rare events and this estimate has been calculated from a number of studies of limited size, we have reevaluated the risk of UPD in fetuses for whom one of the parents was known to carry a nonhomologous ROB (NHROB).

Method: We focused our multicentric study on NHROB involving chromosome 14 and/or 15. A total of 1747 UPD testing were performed in fetuses during pregnancy for the presence of UPD(14) and/or UPD(15).

Result: All fetuses were negative except one with a UPD(14) associated with a maternally inherited rob(13;14).

Conclusion: Considering these data, the risk of UPD following prenatal diagnosis of an inherited ROB involving chromosome 14 and/or 15 could be estimated to be around 0.06%, far less than the previous estimation. Importantly, the risk of miscarriage following an invasive prenatal sampling is higher than the risk of UPD. Therefore, we do not recommend prenatal testing for UPD for these pregnancies and parents should be reassured.
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http://dx.doi.org/10.1002/pd.5518DOI Listing
October 2019

Whole genome paired-end sequencing elucidates functional and phenotypic consequences of balanced chromosomal rearrangement in patients with developmental disorders.

J Med Genet 2019 08 28;56(8):526-535. Epub 2019 Mar 28.

Laboratoire de Cytogénétique, CHU Strasbourg, Strasbourg, France.

Background: Balanced chromosomal rearrangements associated with abnormal phenotype are rare events, but may be challenging for genetic counselling, since molecular characterisation of breakpoints is not performed routinely. We used next-generation sequencing to characterise breakpoints of balanced chromosomal rearrangements at the molecular level in patients with intellectual disability and/or congenital anomalies.

Methods: Breakpoints were characterised by a paired-end low depth whole genome sequencing (WGS) strategy and validated by Sanger sequencing. Expression study of disrupted and neighbouring genes was performed by RT-qPCR from blood or lymphoblastoid cell line RNA.

Results: Among the 55 patients included (41 reciprocal translocations, 4 inversions, 2 insertions and 8 complex chromosomal rearrangements), we were able to detect 89% of chromosomal rearrangements (49/55). Molecular signatures at the breakpoints suggested that DNA breaks arose randomly and that there was no major influence of repeated elements. Non-homologous end-joining appeared as the main mechanism of repair (55% of rearrangements). A diagnosis could be established in 22/49 patients (44.8%), 15 by gene disruption (, , , , , , , , , , , ) and 7 by position effect (, , , ). In addition, 16 new candidate genes were identified. Systematic gene expression studies further supported these results. We also showed the contribution of topologically associated domain maps to WGS data interpretation.

Conclusion: Paired-end WGS is a valid strategy and may be used for structural variation characterisation in a clinical setting.
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http://dx.doi.org/10.1136/jmedgenet-2018-105778DOI Listing
August 2019

Chromosomal microarray analysis in fetuses with an isolated congenital heart defect: A retrospective, nationwide, multicenter study in France.

Prenat Diagn 2019 05 29;39(6):464-470. Epub 2019 Apr 29.

EA7404-GIG, UFR des sciences de la Santé Simone Veil, UVSQ, Montigny le Bretonneux, France.

Objectives: Congenital heart defects (CHDs) may be isolated or associated with other malformations. The use of chromosome microarray (CMA) can increase the genetic diagnostic yield for CHDs by between 4% and 10%. The objective of this study was to evaluate the value of CMA after the prenatal diagnosis of an isolated CHD.

Methods: In a retrospective, nationwide study performed in France, we collected data on all cases of isolated CHD that had been explored using CMAs in 2015.

Results: A total of 239 fetuses were included and 33 copy number variations (CNVs) were reported; 19 were considered to be pathogenic, six were variants of unknown significance, and eight were benign variants. The anomaly detection rate was 10.4% overall but ranged from 0% to 16.7% as a function of the isolated CHD in question. The known CNVs were 22q11.21 deletions (n = 10), 22q11.21 duplications (n = 2), 8p23 deletions (n = 2), an Alagille syndrome (n = 1), and a Kleefstra syndrome (n = 1).

Conclusion: The additional diagnostic yield was clinically significant (3.1%), even when anomalies in the 22q11.21 region were not taken into account. Hence, patients with a suspected isolated CHD and a normal karyotype must be screened for chromosome anomalies other than 22q11.21 duplications and deletions.
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http://dx.doi.org/10.1002/pd.5449DOI Listing
May 2019

NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly.

Am J Hum Genet 2018 11;103(5):752-768

Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA.

The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly.
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http://dx.doi.org/10.1016/j.ajhg.2018.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218805PMC
November 2018

A Broad Test Based on Fluorescent-Multiplex PCR for Noninvasive Prenatal Diagnosis of Cystic Fibrosis.

Fetal Diagn Ther 2019 17;45(6):403-412. Epub 2018 Aug 17.

Laboratoire de Génétique Moléculaire, IURC, CHRU de Montpellier, Montpellier, France,

Background: Analysis of cell-free fetal DNA in maternal plasma is very promising for early diagnosis of monogenic diseases. However, it has been limited by the need to set up patient- or disease-specific custom-made approaches. Here we propose a universal test based on fluorescent multiplex PCR and size fragment analysis for an indirect diagnosis of cystic fibrosis (CF).

Methods: The test, based on haplotyping, includes nine intra- and extragenic short tandem repeats of the CFTR locus, the coamplification of p.Phe508del (the most frequent mutation in CF patients worldwide), and a specific SRY sequence. The assay is able to determine the inherited paternal allele.

Results: Our simple approach was successfully applied to 30 couples and provided clear results from the maternal plasma. The mean rate of informative markers was sufficient to propose it for use in indirect diagnosis.

Conclusions: This noninvasive prenatal diagnosis test, focused on indirect diagnosis of CF, offers many advantages over current methods: it is simple, rapid, and cost-effective. It allows for the testing of a large number of couples with high risk of CF, whatever the familial mutation of the CFTR gene. It provides an alternative method to reduce the number of invasive tests.
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http://dx.doi.org/10.1159/000489776DOI Listing
January 2020

Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Change Analysis in Complex Chromosomal Rearrangements and Chromothripsis.

Methods Mol Biol 2018 ;1769:353-361

Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, CHU Montpellier, Montpellier Cedex 5, France.

Apparition of next-generation sequencing (NGS) was a breakthrough on knowledge of genome structure. Bioinformatic tools are a key point to analyze this huge amount of data from NGS and characterize the three-dimensional organization of chromosomes. This chapter describes usage of different browsers to explore publicly available online data and to search for possible 3D chromatin changes involved during complex chromosomal rearrangements as chromothripsis. Their pathogenic impact on clinical phenotype and gene misexpression can also be evaluated with annotated databases.
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http://dx.doi.org/10.1007/978-1-4939-7780-2_22DOI Listing
February 2019

The genetics of recurrent hydatidiform moles: new insights and lessons from a comprehensive analysis of 113 patients.

Mod Pathol 2018 07 20;31(7):1116-1130. Epub 2018 Feb 20.

Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, 371 avenue du Doyen Gaston Giraud, 34295, Montpellier cedex 5, France.

Hydatidiform mole is an aberrant human pregnancy characterized by early embryonic arrest and excessive trophoblastic proliferation. Recurrent hydatidiform moles are defined by the occurrence of at least two hydatidiform moles in the same patient. Fifty to eighty percent of patients with recurrent hydatidiform moles have biallelic pathogenic variants in NLRP7 or KHDC3L. However, in the remaining patients, the genotypic types of the moles are unknown. We characterized 80 new hydatidiform mole tissues, 57 of which were from patients with no mutations in the known genes, and we reviewed the genotypes of a total of 123 molar tissues. We also reviewed mutation analysis in 113 patients with recurrent hydatidiform moles. While all hydatidiform moles from patients with biallelic NLRP7 or KHDC3L mutations are diploid biparental, we demonstrate that those from patients without mutations are highly heterogeneous and only a small minority of them are diploid biparental (8%). The other mechanisms that were found to recur in patients without mutations are diploid androgenetic monospermic (24%) and triploid dispermic (32%); the remaining hydatidiform moles were misdiagnosed as moles due to errors in the analyses and/or their unusual mechanisms. We compared three parameters of genetic susceptibility in patients with and without mutations and show that patients without mutations are mostly from non-familial cases, have fewer reproductive losses, and more live births. Our data demonstrate that patients with recurrent hydatidiform moles and no mutations in the known genes are, in general, different from those with mutations; they have a milder genetic susceptibility and/or a multifactorial etiology underlying their recurrent hydatidiform moles. Categorizing these patients according to the genotypic types of their recurrent hydatidiform moles may facilitate the identification of novel genes for this entity.
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http://dx.doi.org/10.1038/s41379-018-0031-9DOI Listing
July 2018

A framework to identify contributing genes in patients with Phelan-McDermid syndrome.

NPJ Genom Med 2017 23;2:32. Epub 2017 Oct 23.

Genetics Unit, CHU Estaing, Clermont-Ferrand, France.

Phelan-McDermid syndrome (PMS) is characterized by a variety of clinical symptoms with heterogeneous degrees of severity, including intellectual disability (ID), absent or delayed speech, and autism spectrum disorders (ASD). It results from a deletion of the distal part of chromosome 22q13 that in most cases includes the gene. is considered a major gene for PMS, but the factors that modulate the severity of the syndrome remain largely unknown. In this study, we investigated 85 patients with different 22q13 rearrangements (78 deletions and 7 duplications). We first explored the clinical features associated with PMS, and provide evidence for frequent corpus callosum abnormalities in 28% of 35 patients with brain imaging data. We then mapped several candidate genomic regions at the 22q13 region associated with high risk of clinical features, and suggest a second locus at 22q13 associated with absence of speech. Finally, in some cases, we identified additional clinically relevant copy-number variants (CNVs) at loci associated with ASD, such as 16p11.2 and 15q11q13, which could modulate the severity of the syndrome. We also report an inherited deletion transmitted to five affected daughters by a mother without ID nor ASD, suggesting that some individuals could compensate for such mutations. In summary, we shed light on the genotype-phenotype relationship of patients with PMS, a step towards the identification of compensatory mechanisms for a better prognosis and possibly treatments of patients with neurodevelopmental disorders.
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http://dx.doi.org/10.1038/s41525-017-0035-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677962PMC
October 2017

The role of CNVs in the etiology of rare autosomal recessive disorders: the example of TRAPPC9-associated intellectual disability.

Eur J Hum Genet 2018 01 29;26(1):143-148. Epub 2017 Nov 29.

Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France.

Introduction: A large number of genes involved in autosomal recessive forms of intellectual disability (ID) were identified over the past few years through whole-exome sequencing (WES) or whole-genome sequencing in consanguineous families. Disease-associated variants in TRAPPC9 were reported in eight multiplex consanguineous sibships from different ethnic backgrounds, and led to the delineation of the phenotype. Affected patients have microcephaly, obesity, normal motor development, severe ID, and language impairment and brain anomalies.

Patients: We report six new patients recruited through a national collaborative network.

Results: In the two patients heterozygous for a copy-number variation (CNV), the phenotype was clinically relevant with regard to the literature, which prompted to sequence the second allele, leading to identification of disease-associated variants in both. The third patient was homozygote for an intragenic TRAPPC9 CNV. The phenotype of the patients reported was concordant with the literature. Recent reports emphasized the role of CNVs in the etiology of rare recessive disorders.

Conclusion: This study demonstrates that CNVs significantly contribute to the mutational spectrum of TRAPPC9 gene, and also confirms the interest of combining WES with CNV analysis to provide a molecular diagnosis to patients with rare Mendelian disorders.
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http://dx.doi.org/10.1038/s41431-017-0018-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838970PMC
January 2018

A new autoinflammatory and autoimmune syndrome associated with NLRP1 mutations: NAIAD (associated autoinflammation with arthritis and dyskeratosis).

Ann Rheum Dis 2017 Jul 13;76(7):1191-1198. Epub 2016 Dec 13.

INSERM, U1183, IRMB, Hôpital Saint Eloi, CHU Montpellier, Montpellier, France.

Objectives: Inflammasomes are multiprotein complexes that sense pathogens and trigger biological mechanisms to control infection. Nucleotide-binding oligomerisation domain-like receptor (NLR) containing a PYRIN domain 1 (NLRP1), NLRP3 and NLRC4 plays a key role in this innate immune system by directly assembling in inflammasomes and regulating inflammation. Mutations in and are linked to hereditary autoinflammatory diseases, whereas polymorphisms in are associated with autoimmune disorders such as vitiligo and rheumatoid arthritis. Whether human mutation is associated with autoinflammation remains to be determined.

Methods: To search for novel genes involved in systemic juvenile idiopathic arthritis, we performed homozygosity mapping and exome sequencing to identify causative genes. Immunoassays were performed with blood samples from patients.

Results: We identified a novel disease in three patients from two unrelated families presenting diffuse skin dyskeratosis, autoinflammation, autoimmunity, arthritis and high transitional B-cell level. Molecular screening revealed a non-synonymous homozygous mutation in (c.2176C>T; p.Arg726Trp) in two cousins born of related parents originating from Algeria and a de novo heterozygous mutation (c.3641C>G, p.Pro1214Arg) in a girl of Dutch origin. The three patients showed elevated systemic levels of caspase-1 and interleukin 18, which suggested involvement of NLRP1 inflammasome.

Conclusions: We demonstrate the responsibility of human in a novel autoinflammatory disorder that we propose to call NAIAD for associated autoinflammation with arthritis and dyskeratosis. This disease could be a novel autoimmuno-inflammatory disease combining autoinflammatory and autoimmune features. Our data, combined with that in the literature, highlight the pleomorphic role of in inflammation and immunity.

Trial Registration Number: NCT02067962; Results.
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http://dx.doi.org/10.1136/annrheumdis-2016-210021DOI Listing
July 2017

Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder.

Am J Med Genet A 2015 Dec 3;167A(12):3031-7. Epub 2015 Sep 3.

Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France.

Intellectual disability (ID) is a frequent feature but is highly clinically and genetically heterogeneous. The establishment of the precise diagnosis in patients with ID is challenging due to this heterogeneity but crucial for genetic counseling and appropriate care for the patients. Among the etiologies of patients with ID, apparently balanced de novo rearrangements represent 0.6%. Several mechanisms explain the ID in patients with apparently balanced de novo rearrangement. Among them, disruption of a disease gene at the breakpoint, is frequently evoked. In this context, technologies recently developed are used to characterize precisely such chromosomal rearrangements. Here, we report the case of a boy with ID, facial features and autistic behavior who is carrying a de novo balanced reciprocal translocation t(3;7)(q11.2;q11.22)dn. Using microarray analysis, array painting (AP) technology combined with molecular study, we have identified the interruption of the autism susceptibility candidate 2 gene (AUTS2) and EPH receptor A6 gene (EPHA6). We consider that the disruption of AUTS2 explains the phenotype of the patient; the exact role of EPHA6 in human pathology is not well defined. Based on the observation of recurrent germinal and somatic translocations involving AUTS2 and the molecular environment content, we put forward the hypothesis that the likely chromosomal mechanism responsible for the translocation could be due either to replicative stress or to recombination-based mechanisms.
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http://dx.doi.org/10.1002/ajmg.a.37350DOI Listing
December 2015

Treacher Collins syndrome: a clinical and molecular study based on a large series of patients.

Genet Med 2016 Jan 19;18(1):49-56. Epub 2015 Mar 19.

Service de Génétique Médicale, CHU Strasbourg, Strasbourg, France.

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.
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http://dx.doi.org/10.1038/gim.2015.29DOI Listing
January 2016

15q11.2 microdeletion (BP1-BP2) and developmental delay, behaviour issues, epilepsy and congenital heart disease: a series of 52 patients.

Eur J Med Genet 2015 Mar 14;58(3):140-7. Epub 2015 Jan 14.

Service de génétique médicale, CHRU Montpellier, France.

Proximal region of chromosome 15 long arm is rich in duplicons that, define five breakpoints (BP) for 15q rearrangements. 15q11.2 microdeletion between BP1 and BP2 has been previously associated with developmental delay and atypical psychological patterns. This region contains four highly-conserved and non-imprinted genes: NIPA1, NIPA2, CYFIP1, TUBGCP5. Our goal was to investigate the phenotypes associated with this microdeletion in a cohort of 52 patients. This copy number variation (CNV) was prevalent in 0.8% patients presenting with developmental delay, psychological pattern issues and/or multiple congenital malformations. This was studied by array-CGH at six different French Genetic laboratories. We collected data from 52 unrelated patients (including 3 foetuses) after excluding patients with an associated genetic alteration (known CNV, aneuploidy or known monogenic disease). Out of 52 patients, mild or moderate developmental delay was observed in 68.3%, 85.4% had speech impairment and 63.4% had psychological issues such as Attention Deficit and Hyperactivity Disorder, Autistic Spectrum Disorder or Obsessive-Compulsive Disorder. Seizures were noted in 18.7% patients and associated congenital heart disease in 17.3%. Parents were analysed for abnormalities in the region in 65.4% families. Amongst these families, 'de novo' microdeletions were observed in 18.8% and 81.2% were inherited from one of the parents. Incomplete penetrance and variable expressivity were observed amongst the patients. Our results support the hypothesis that 15q11.2 (BP1-BP2) microdeletion is associated with developmental delay, abnormal behaviour, generalized epilepsy and congenital heart disease. The later feature has been rarely described. Incomplete penetrance and variability of expression demands further assessment and studies.
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http://dx.doi.org/10.1016/j.ejmg.2015.01.002DOI Listing
March 2015

Chromothripsis: potential origin in gametogenesis and preimplantation cell divisions. A review.

Fertil Steril 2014 Dec 18;102(6):1785-96. Epub 2014 Oct 18.

Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France.

Objective: To review the discovery of chromothripsis and analyze its impact on human reproduction.

Design: Database and literature analysis.

Setting: University hospital.

Patient(s): Carriers of massive and complex chromosomal rearrangements.

Intervention(s): Cytogenetic analysis and molecular testing (fluorescence in situ hybridization, microarray, whole-genome sequencing).

Main Outcome Measure(s): Chromothripsis occurrence in human gametes and preimplantation embryos, with regard to the potential causative mechanisms described in literature.

Result(s): Databases were searched for the literature published up to March 2014. Chromothripsis is characterized by the shattering of one (or a few) chromosome segments followed by a haphazard reassembly of the fragments generated, arising through a single initial catastrophic event. Several mechanisms involving abortive apoptosis, telomere erosion, mitotic errors, micronuclei formation, and p53 inactivation might cause chromothripsis. The remarkable point is that all these plausible mechanisms have been identified in the field of human reproduction as causal factors for reproductive failures and the genesis of chromosomal abnormalities. Specific features of gametogenesis and early embryonic development such as the weakness of cell cycle and mitosis checkpoints and the rapid kinetics of division in germ cells and early cleavage embryos may contribute to the emergence of chromothripsis.

Conclusion(s): The discovery of this new class of massive chromosomal rearrangement has deeply modified our understanding on the genesis of complex genomic rearrangements. Data presented in this review support the assumption that chromothripsis could operate in human germlines and during early embryonic development. Chromothripsis might arise more frequently than previously thought in both gametogenesis and early human embryogenesis.
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http://dx.doi.org/10.1016/j.fertnstert.2014.09.006DOI Listing
December 2014

[Chromothripsis, an unexpected novel form of complexity for chromosomal rearrangements].

Med Sci (Paris) 2014 Mar 31;30(3):266-73. Epub 2014 Mar 31.

Laboratoire de génétique chromosomique, hôpital Arnaud de Villeneuve, CHRU de Montpellier, 371, avenue du doyen Gaston Giraud, 34295 Montpellier, France.

The recent discovery of a new kind of massive chromosomal rearrangement in different cancers, named "chromothripsis" (chromo for chromosome, thripsis for shattering) has questioned the established models for a progressive development of tumors. Indeed, this phenomenon, which is characterized by the shattering of one (or a few) chromosome segments followed by a random reassembly of the fragments generated, occurs during one unique cellular event. The same phenomenon was identified in constitutional genetics in patients with various developmental pathologies, indicating that chromothripsis also occurs at the germ cell level. Diverse situations can cause chromothripsis (radiations, telomere erosion, abortive apoptosis, etc.), and two express "repair routes" are used by the cell to chaotically reorganise the chromosomal regions concerned: non-homologous end-joining and repair by replicative stress. The in-depth analysis of the DNA sequences involved in the regions of chromothripsis leads to a better understanding of the molecular basis of chromothripsis and also helps to better apprehend its unexpected role in the development of constitutional pathologies and the progression of cancers.
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http://dx.doi.org/10.1051/medsci/20143003014DOI Listing
March 2014

[Complex chromosomal rearrangements: a paradigm for the study of chromosomal instability].

Med Sci (Paris) 2014 Jan 24;30(1):55-63. Epub 2014 Jan 24.

Laboratoire de génétique chromosomique, hôpital Arnaud de Villeneuve, CHRU de Montpellier, 371, avenue du doyen Gaston Giraud, 34295 Montpellier, France.

Complex chromosomal rearrangements (CCR) include diverse structural anomalies leading to complex karyotypes which are difficult to interpret. Although karyotype analysis has been able to identify a large number of these rearrangements and to distinguish de novo and familial events, it is the advent of molecular cytogenetic and sequence analysis techniques which have led to an understanding of the molecular mechanisms underlying the formation of CCR. The diversity and high level of complexity inherent to CCR raises questions about their origin, their ties to chromosome instability and their impact in pathology. Today it is possible to precisely characterize CCR and to offer carriers sophisticated diagnostic techniques, such as preimplantation diagnosis. However, the meiotic segregation of these rearrangements remains very complex.
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http://dx.doi.org/10.1051/medsci/20143001014DOI Listing
January 2014

CEP57 mutation in a girl with mosaic variegated aneuploidy syndrome.

Am J Med Genet A 2014 Jan 20;164A(1):177-81. Epub 2013 Nov 20.

Département de Génétique Médicale, Centre Hospitalier Universitaire, Montpellier, France.

Mosaic variegated aneuploidy (MVA) is a rare autosomal recessive disorder characterized by constitutional aneuploidies. Mutations in BUB1B and CEP57 genes, which are involved in mitotic spindle and microtubule stabilization, respectively, are responsible for a subset of patients with MVA. To date, CEP57 mutations have been reported only in four probands. We report on a girl with this disorder due to c.915-925dup11 mutation in CEP57, which predicts p.Leu309ProfsX9 and review the literature in order to facilitate genotype-phenotype correlation. Rhizomelic shortening of the upper limbs, skull anomalies with conserved head circumference, and absence of tumor development could be features suggesting a need for molecular screening of the CEP57 gene in patients with this disorder.
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http://dx.doi.org/10.1002/ajmg.a.36166DOI Listing
January 2014

Early-onset obesity and paternal 2pter deletion encompassing the ACP1, TMEM18, and MYT1L genes.

Eur J Hum Genet 2014 Apr 16;22(4):471-9. Epub 2013 Oct 16.

Département de Génétique Médicale, CHRU Montpellier, Faculté de Médecine de Montpellier-Nimes, Université Montpellier 1, Montpellier, France.

Obesity is a common but highly, clinically, and genetically heterogeneous disease. Deletion of the terminal region of the short arm of chromosome 2 is rare and has been reported in about 13 patients in the literature often associated with a Prader-Willi-like phenotype. We report on five unrelated patients with 2p25 deletion of paternal origin presenting with early-onset obesity, hyperphagia, intellectual deficiency, and behavioural difficulties. Among these patients, three had de novo pure 2pter deletions, one presented with a paternal derivative der(2)t(2;15)(p25.3;q26) with deletion in the 2pter region and the last patient presented with an interstitial 2p25 deletion. The size of the deletions was characterized by SNP array or array-CGH and was confirmed by fluorescence in situ hybridization (FISH) studies. Four patients shared a 2p25.3 deletion with a minimal critical region estimated at 1.97 Mb and encompassing seven genes, namely SH3HYL1, ACP1, TMEMI8, SNTG2, TPO, PXDN, and MYT1L genes. The fifth patient had a smaller interstitial deletion encompassing the TPO, PXDN, and MYT1L genes. Paternal origin of the deletion was determined by genotyping using microsatellite markers. Analysis of the genes encompassed in the deleted region led us to speculate that the ACP1, TMEM18, and/or MYT1L genes might be involved in early-onset obesity. In addition, intellectual deficiency and behavioural troubles can be explained by the heterozygous loss of the SNTG2 and MYT1L genes. Finally, we discuss the parent-of-origin of the deletion.
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http://dx.doi.org/10.1038/ejhg.2013.189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953915PMC
April 2014

Congenital linear streaks on the face and neck and microphthalmia in an infant girl.

Acta Derm Venereol 2014 May;94(3):342-3

Department of Dermatology,, Skin and Allergy Hospital, Helsinki University Central Hospital, Meilahdentie 2, PO Box 160, FIN-00029 Helsinki, Finland.

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http://dx.doi.org/10.2340/00015555-1688DOI Listing
May 2014

Large deletions encompassing the TCOF1 and CAMK2A genes are responsible for Treacher Collins syndrome with intellectual disability.

Eur J Hum Genet 2014 Jan 22;22(1):52-6. Epub 2013 May 22.

Département de Génétique Médicale, CHRU Montpellier, Faculté de Médecine de Montpellier-Mimes, Université Montpellier 1, Montpellier, France.

Mandibulofacial dysostosis is part of a clinically and genetically heterogeneous group of disorders of craniofacial development, which lead to malar and mandibular hypoplasia. Treacher Collins syndrome is the major cause of mandibulofacial dysostosis and is due to mutations in the TCOF1 gene. Usually patients with Treacher Collins syndrome do not present with intellectual disability. Recently, the EFTUD2 gene was identified in patients with mandibulofacial dysostosis associated with microcephaly, intellectual disability and esophageal atresia. We report on two patients presenting with mandibulofacial dysostosis characteristic of Treacher Collins syndrome, but associated with unexpected intellectual disability, due to a large deletion encompassing several genes including the TCOF1 gene. We discuss the involvement of the other deleted genes such as CAMK2A or SLC6A7 in the cognitive development delay of the patients reported, and we propose the systematic investigation for 5q32 deletion when intellectual disability is associated with Treacher Collins syndrome.
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http://dx.doi.org/10.1038/ejhg.2013.98DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3865420PMC
January 2014

Expanding the phenotype of IQSEC2 mutations: truncating mutations in severe intellectual disability.

Eur J Hum Genet 2014 Feb 15;22(2):289-92. Epub 2013 May 15.

Departement de Genetique Medicale, Centre de Reference Maladies Rares Anomalies du Developpement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hopital Arnaud de Villeneuve CHRU Montpellier, Faculte de Medecine Universite Montpellier 1, Montpellier, France.

Intellectual disability (ID) is frequent in the general population, with 1 in 50 individuals directly affected worldwide. The multiple etiologies include X-linked ID (XLID). Among syndromic XLID, few syndromes present severe ID associated with postnatal microcephaly and midline stereotypic hand movements. We report on three male patients with ID, midline stereotypic hand movements, hypotonia, hyperkinesia, strabismus, as well as seizures (2/3), and non-inherited and postnatal onset microcephaly (2/3). Using array CGH and exome sequencing we characterised two truncating mutations in IQSEC2, namely two de novo intragenic duplication mapped to the Xp11.22 region and a nonsense mutation in exon 7. We propose that truncating mutations in IQSEC2 are responsible for syndromic severe ID in male patients and should be screened in patients without mutations in MECP2, FOXG1, CDKL5 and MEF2C.
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http://dx.doi.org/10.1038/ejhg.2013.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895633PMC
February 2014

Somatic mosaicism in trichorhinophalangeal syndrome: a lesson for genetic counseling.

Eur J Hum Genet 2014 Jan 10;22(1):136-9. Epub 2013 Apr 10.

1] Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, CHRU Montpellier, Faculté de Médecine Université Montpellier 1, Montpellier, France [2] Unité INSERM U844, Institut des Neurosciences de Montpellier, Montpellier, France.

Trichorhinophalangeal syndrome type I (TRPSI) is a genetic disorder characterized by sparse hair, a bulbous nasal tip, short stature with severe generalized shortening of all phalanges, metacarpal and metatarsal bones and cone-shaped epiphyses. This syndrome is caused by autosomal dominant mutations in the TRPS1 gene. However, because recurrence has been observed in siblings from healthy parents, an autosomal recessive mode of inheritance has also been suggested. We report on a male patient, born to healthy unrelated parents, with TRPSI. Using Sanger sequencing, we identified a mutation in the TRPS1 gene (c.2735 G>A, P.Cys912Tyr). The same mutation was detected as a 10% mosaic mutation by Pyrosequencing in blood-derived DNA from his healthy mother. To our knowledge, this is the first time that somatic mosaicism has been identified in TRPSI. This data combined with the observations of recurrences in siblings from healthy parents modifies the genetic counseling for TRPSI, which should discuss a 5-10 percent recurrence risk for healthy parents with an affected child because of the possibility of germinal mosaicism.
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http://dx.doi.org/10.1038/ejhg.2013.56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3865400PMC
January 2014