RESUMO
Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator ZMYM3, located on the X chromosome. Most (n = 24) individuals were males, 17 of which have a maternally inherited variant; six individuals (4 male, 2 female) harbor de novo variants. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n = 26) are missense, including six that recurrently affect two residues. Four unrelated probands were identified with inherited variation affecting Arg441, a site at which variation has been previously seen in NDD-affected siblings, and two individuals have de novo variation resulting in p.Arg1294Cys (c.3880C>T). All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is widely expressed across human tissues, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one variant, p.Arg1274Trp, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. While we are unable to perform statistical evaluations to definitively support a causative role for variation in ZMYM3, the totality of the evidence, including 27 affected individuals, recurrent variation at two codons, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally confirmed functional effects strongly support ZMYM3 as an NDD-associated gene.
Assuntos
Deficiência Intelectual , Malformações do Sistema Nervoso , Transtornos do Neurodesenvolvimento , Humanos , Masculino , Feminino , Transtornos do Neurodesenvolvimento/genética , Deficiência Intelectual/genética , Fenótipo , Regulação da Expressão Gênica , Face , Proteínas Nucleares/genética , Histona Desmetilases/genéticaRESUMO
Alpha-mannosidosis is a rare autosomal recessive lysosomal storage disorder caused by biallelic mutations in the MAN2B1 gene and characterized by a wide clinical heterogeneity. Diagnosis for this multisystemic disorder is confirmed by the presence of either a deficiency in the lysosomal enzyme acid alpha-mannosidase or biallelic mutations in the MAN2B1 gene. This diagnosis confirmation is crucial for both clinical management and genetic counseling purposes. Here we describe a late diagnosis of alpha-mannosidosis in a patient presenting with syndromic intellectual disability, and a rare retinopathy, where reverse phenotyping played a pivotal role in interpreting the exome sequencing result. While a first missense variant was classified as a variant of uncertain significance, the phenotype-guided analysis helped us detect and interpret an in-trans apparent alu-element insertion, which appeared to be a copy number variant (CNV) not identified by the CNV caller. A biochemical analysis showing abnormal excretion of urinary mannosyloligosaccharide and an enzyme assay permitted the re-classification of the missense variant to likely pathogenic, establishing the diagnosis of alpha-mannosidosis. This work emphasizes the importance of reverse phenotyping in the context of exome sequencing.
Assuntos
alfa-Manosidose , Humanos , alfa-Manosidose/diagnóstico , alfa-Manosidose/genética , Variações do Número de Cópias de DNA/genética , alfa-Manosidase/genética , Mutação de Sentido Incorreto/genética , FenótipoRESUMO
Duplications of the 3q29 cytoband are rare chromosomal copy number variations (CNVs) (overlapping or recurrent ~1.6 Mb 3q29 duplications). They have been associated with highly variable neurodevelopmental disorders (NDDs) with various associated features or reported as a susceptibility factor to the development of learning disabilities and neuropsychiatric disorders. The smallest region of overlap and the phenotype of 3q29 duplications remain uncertain. We here report a French cohort of 31 families with a 3q29 duplication identified by chromosomal microarray analysis (CMA), including 14 recurrent 1.6 Mb duplications, eight overlapping duplications (>1 Mb), and nine small duplications (<1 Mb). Additional genetic findings that may be involved in the phenotype were identified in 11 patients. Focusing on apparently isolated 3q29 duplications, patients present mainly mild NDD as suggested by a high rate of learning disabilities in contrast to a low proportion of patients with intellectual disabilities. Although some are de novo, most of the 3q29 duplications are inherited from a parent with a similar mild phenotype. Besides, the study of small 3q29 duplications does not provide evidence for any critical region. Our data suggest that the overlapping and recurrent 3q29 duplications seem to lead to mild NDD and that a severe or syndromic clinical presentation should warrant further genetic analyses.
Assuntos
Duplicação Cromossômica , Cromossomos Humanos Par 3 , Variações do Número de Cópias de DNA , Fenótipo , Humanos , Feminino , Masculino , Cromossomos Humanos Par 3/genética , Duplicação Cromossômica/genética , Criança , Variações do Número de Cópias de DNA/genética , Pré-Escolar , Transtornos do Neurodesenvolvimento/genética , Transtornos do Neurodesenvolvimento/patologia , Adolescente , Estudos de Coortes , Deficiência Intelectual/genética , Deficiência Intelectual/patologia , Adulto , LactenteRESUMO
Chromosome 1p36 deletion syndrome (1p36DS) is one of the most common terminal deletion syndromes (incidence between 1/5000 and 1/10,000 live births in the American population), due to a heterozygous deletion of part of the short arm of chromosome 1. The 1p36DS is characterized by typical craniofacial features, developmental delay/intellectual disability, hypotonia, epilepsy, cardiomyopathy/congenital heart defect, brain abnormalities, hearing loss, eyes/vision problem, and short stature. The aim of our study was to (1) evaluate the incidence of the 1p36DS in the French population compared to 22q11.2 deletion syndrome and trisomy 21; (2) review the postnatal phenotype related to microarray data, compared to previously publish prenatal data. Thanks to a collaboration with the ACLF (Association des Cytogénéticiens de Langue Française), we have collected data of 86 patients constituting, to the best of our knowledge, the second-largest cohort of 1p36DS patients in the literature. We estimated an average of at least 10 cases per year in France. 1p36DS seems to be much less frequent than 22q11.2 deletion syndrome and trisomy 21. Patients presented mainly dysmorphism, microcephaly, developmental delay/intellectual disability, hypotonia, epilepsy, brain malformations, behavioral disorders, cardiomyopathy, or cardiovascular malformations and, pre and/or postnatal growth retardation. Cardiac abnormalities, brain malformations, and epilepsy were more frequent in distal deletions, whereas microcephaly was more common in proximal deletions. Mapping and genotype-phenotype correlation allowed us to identify four critical regions responsible for intellectual disability. This study highlights some phenotypic variability, according to the deletion position, and helps to refine the phenotype of 1p36DS, allowing improved management and follow-up of patients.
Assuntos
Síndrome de DiGeorge , Síndrome de Down , Epilepsia , Deficiência Intelectual , Microcefalia , Humanos , Cromossomos Humanos Par 1 , Hipotonia Muscular , Deleção Cromossômica , FenótipoRESUMO
BACKGROUND: DEL phenotype is a rare Rh variant that cannot be detected by routine serological typing, and DEL individuals are thus typed D-negative (D-). Anti-D alloimmunization has been reported in "true" D- patients receiving DEL red blood cells (RBCs). CASE PRESENTATION: A 17-year-old, D- Thai male patient suffering from immunodeficiency syndrome with negative antibody screening received RBC units from 17 serological D- donors over a period of seven months due to acute respiratory failure with anemia. Before the 12th transfusion, anti-D production was detected. He was later transfused with RBCs from six other apparent D- donors. In order to elucidate anti-D production, all 17 blood donors were investigated by replicative serological testing and molecular analysis to identify potential RHD gene variants. All donors were confirmed D- by routine method, but as many as 12/17 were positive by adsorption-elution testing. Molecular analysis showed that five donors, including four whose blood was transfused before anti-D production occurred, carry the Asia type DEL allele, and are thus predicted to express a DEL phenotype. These data clearly suggest that 1/ the alloimmunized D- patient was exposed to D antigen, 2/ our adsorption-elution test is currently defective to identify DEL RBCs, and 3/ molecular analysis is highly valuable for Asia type DEL allele screening. CONCLUSION: For the first time in Thailand, we report anti-D alloimmunization in a serological D- patient transfused by Asia type DEL RBC units. This work definitely supports the implementation of a dedicated policy for DEL blood management including molecular testing.
Assuntos
Eritrócitos , População do Sudeste Asiático , Humanos , Masculino , Adolescente , Tailândia , Transfusão de Sangue , Doadores de Sangue , Sistema do Grupo Sanguíneo Rh-Hr/genéticaRESUMO
BACKGROUND: Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. RESULTS: We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 × 10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. CONCLUSIONS: In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.
Assuntos
Transtorno Autístico/genética , Predisposição Genética para Doença , Hipotonia Muscular/genética , Transtornos do Neurodesenvolvimento/genética , Fatores de Transcrição/genética , Transtorno Autístico/epidemiologia , Transtorno Autístico/patologia , Elementos Facilitadores Genéticos/genética , Exoma/genética , Feminino , Redes Reguladoras de Genes/genética , Humanos , Masculino , Hipotonia Muscular/epidemiologia , Hipotonia Muscular/patologia , Mutação/genética , Transtornos do Neurodesenvolvimento/epidemiologia , Transtornos do Neurodesenvolvimento/patologia , Neurônios/metabolismo , Neurônios/patologiaRESUMO
13q12.3 microdeletion syndrome is a rare cause of syndromic intellectual disability. Identification and genetic characterization of patients with 13q12.3 microdeletion syndrome continues to expand the phenotypic spectrum associated with it. Previous studies identified four genes within the approximately 300 Kb minimal critical region including two candidate protein coding genes: KATNAL1 and HMGB1. To date, no patients carrying a sequence-level variant or a single gene deletion in HMGB1 or KATNAL1 have been described. Here we report six patients with loss-of-function variants involving HMGB1 and who had phenotypic features similar to the previously described 13q12.3 microdeletion syndrome cases. Common features included developmental delay, language delay, microcephaly, obesity and dysmorphic features. In silico analyses suggest that HMGB1 is likely to be intolerant to loss-of-function, and previous in vitro data are in line with the role of HMGB1 in neurodevelopment. These results strongly suggest that haploinsufficiency of the HMGB1 gene may play a critical role in the pathogenesis of the 13q12.3 microdeletion syndrome.
Assuntos
Deficiências do Desenvolvimento/diagnóstico , Deficiências do Desenvolvimento/genética , Heterozigoto , Mutação com Perda de Função , Microcefalia/diagnóstico , Microcefalia/genética , Adolescente , Criança , Pré-Escolar , Variações do Número de Cópias de DNA , Éxons , Fácies , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença , Proteína HMGB1 , Humanos , Hibridização in Situ Fluorescente , Padrões de Herança , Cariótipo , Masculino , Fenótipo , Sequenciamento do ExomaRESUMO
Ephrin receptor and their ligands, the ephrins, are widely expressed in the developing brain. They are implicated in several developmental processes that are crucial for brain development. Deletions in genes encoding for members of the Eph/ephrin receptor family were reported in several neurodevelopmental disorders. The ephrin receptor A7 gene (EPHA7) encodes a member of ephrin receptor subfamily of the protein-tyrosine kinase family. EPHA7 plays a role in corticogenesis processes, determines brain size and shape, and is involved in development of the central nervous system. One patient only was reported so far with a de novo deletion encompassing EPHA7 in 6q16.1. We report 12 additional patients from nine unrelated pedigrees with similar deletions. The deletions were inherited in nine out of 12 patients, suggesting variable expressivity and incomplete penetrance. Four patients had tiny deletions involving only EPHA7, suggesting a critical role of EPHA7 in a neurodevelopmental disability phenotype. We provide further evidence for EPHA7 deletion as a risk factor for neurodevelopmental disorder and delineate its clinical phenotype.
Assuntos
Estudos de Associação Genética , Predisposição Genética para Doença , Haploinsuficiência , Transtornos do Neurodesenvolvimento/diagnóstico , Transtornos do Neurodesenvolvimento/genética , Fenótipo , Receptor EphA7/genética , Cromossomos Humanos Par 6 , Hibridização Genômica Comparativa , Feminino , Estudos de Associação Genética/métodos , Humanos , Hibridização in Situ Fluorescente , Padrões de Herança , Masculino , Mutação , Linhagem , Sequenciamento do ExomaAssuntos
Anormalidades do Olho , Deficiência Intelectual , Microcefalia , Humanos , Fácies , Ubiquitina-Proteína LigasesRESUMO
BACKGROUND: Although genetic polymorphism of the RH blood group system is well known in sub-Saharan Africa, national/regional specificities still remain to be described precisely. For the first time in Cameroon, Central Africa, and in order to better characterize the molecular basis driving RH phenotype variability, as well as to identify the main antigens that may be potentially responsible for alloimmunization, we sought 1) to study the RH genes in a cohort of 109 patients with sickle cell disease; 2) to study the same genes in the corresponding donors whose red blood cells (RBCs) were transfused to the patients (108 donors in 98 patients); 3) to predict RH phenotype on the basis of the molecular data and compare the results with serologic testing; and 4) to identify retrospectively patients at risk for alloimmunization. MATERIALS AND METHODS: In order to generate an exhaustive dataset, the RH genes of all patient and donor samples were systematically investigated 1) by quantitative multiplex PCR of short fluorescent fragments (QMPSF) for characterization of RHD gene zygosity and potential structural variants (SVs), and 2) by Sanger sequencing for identification of single nucleotide variants (SNVs). Subsequent to molecular analysis, the genotypes and RH phenotype were deduced and predicted, respectively, from reference databases. RESULTS: In a total of 217 Cameroonian individuals, as many as 24 and up to 22 variant alleles were identified in the RHD and RHCE genes, respectively, in addition to the reference alleles. Interestingly, 65 patients with SCD (66.3%) were assumed to be exposed to one or more undesirable RH antigen(s) with varying degrees of clinical relevance. DISCUSSION: Beyond the comprehensive report of the nature and distribution of RH variant alleles in a subset of Cameroonian patients treated by transfusion therapy, this work highlights the need for an extensive review of current practice, including routine serologic typing procedures, preferably in the near future.
RESUMO
Novel variants associated with chronic pancreatitis are being increasingly reported. However, most studies have so far only analyzed point mutations and small insertions or deletions. Here we report the characterization of two distinct deletions of the CTRC locus. Variants in four chronic pancreatitis genes, PRSS1, SPINK1, CTRC and CFTR, were systematically analyzed in the studied cases. Copy number change of the CTRC gene was analyzed by quantitative fluorescent multiplex PCR (QFM-PCR). Walking QFM-PCR followed by long-range PCR and direct sequencing were employed to identify the deletion breakpoints at the nucleotide level. A heterozygous CTRC-deleting complex rearrangement, which was co-inherited with different trans variants in SPINK1, CFTR or PRSS1, is associated with variable phenotypes (chronic pancreatitis; pancreatic cancer and chronic pancreatitis; and type 1 diabetes). Moreover, a different homozygous deletion of the CTRC locus was found in an unrelated patient with asymptomatic chronic pancreatitis. Our findings revealed a hitherto unrecognized level of complexity of genotype-phenotype correlation in chronic pancreatitis. The CTRC-deleting complex rearrangement probably resulted from LINE-1-mediated Alu insertion, which represents a novel mutational mechanism causing chronic pancreatitis.
Assuntos
Quimotripsina/genética , Deleção de Genes , Loci Gênicos , Adulto , Análise Mutacional de DNA , Heterozigoto , Homozigoto , Humanos , Masculino , Pancreatite Crônica/diagnóstico , Pancreatite Crônica/genética , Linhagem , Adulto JovemRESUMO
BACKGROUND: Discriminating individuals with "Asian type DEL" from those who are "true D-negative" (D-) among serologically D- donors/patients in Asia would be very valuable, as clinical outcomes are different in these groups. Here we investigated the molecular basis of D-negativity in Thai blood donors, designing a specific strategy for this purpose. MATERIALS AND METHODS: After routine testing, a total of 1,270 serologically D- blood donors originating from Central, Northeastern and South Thailand underwent analysis of the RHD gene by (i) quantitative multiplex polymerase chain reaction of short fluorescent fragments (QMPSF); (ii) direct sequencing of exon 9 to identify the c.1227G>A variant defining the Asian type DEL allele; and (iii) direct sequencing of the other exons. RESULTS: The most common observation was whole deletion of the gene (i.e. RHD*01N.01; allele frequency: 86.81%), followed by the Asian type DEL allele (RHD*01EL.01; 7.60%) and a D-negative hybrid allele (RHD*01N.03; 3.46%). Four novel alleles, including one with a 13.1 kilobase-deletion, were identified and characterized. All but one RHD*01EL.01 allele carriers (183/184) were C-positive (C+), suggesting that this latter subset may be screened specifically when investigating the c.1227G>A variant, which can be identified with 100% accuracy by a specific Tm-shift genotyping assay. DISCUSSION: On the basis of our extensive molecular findings, we have designed a dedicated diagnostic strategy based on Rh C antigen typing followed by a genotyping test. Implementation of this method in all or selected groups of serologically D- donors/patients will contribute to improve the management of transfusion and pregnancy in Thailand.
Assuntos
Doadores de Sangue , Antígenos de Grupos Sanguíneos , Humanos , Fenótipo , Tailândia/epidemiologia , Sistema do Grupo Sanguíneo Rh-Hr/genética , Reação em Cadeia da Polimerase Multiplex/métodos , Alelos , GenótipoRESUMO
BACKGROUND: Hybrid genes are responsible for the formation of Rh variants and are common in patients with sickle cell disease (SCD). However, it is not usually possible to detect them by conventional molecular protocols. In the present study, hybrid genes were investigated using the Quantitative Multiplex Polymerase chain reaction of Short Fluorescent Fragments (QMPSF), a molecular protocol that quantifies the copy number of RHD and RHCE exons. In addition, we explored additional relevant information obtained with QMPSF, such as recognition of variant RHCE and RHD zygosity. MATERIALS AND METHODS: Three groups of subjects were selected for the study: patients with SCD, self-declared African descent donors (SDA), and D-negative donors. RHD and RHCE hybrids genes were investigated by the QMPSF method. Real-time multiplex polymerase chain reaction (PCR) assay was used to confirm the copy number of the RHD in two samples. Cloning was performed to investigate the allele. Relative RhD antigen density was investigated by flow cytometry, and RhCE phenotyping was performed with both tube and gel methods. RESULTS: In the 507 samples analysed, hybrid allele frequencies were found in 20.08% of patients with SCD, in 18.22% of individuals in the SDA group, and 3.67% of D-negative donors. The SCD and SDA groups had a higher frequency of hybrid alleles, most commonly involving exon 8, with which we found an association with c.733C>G, a common polymorphism observed in individuals of African descent. Of note, two patients with SCD were shown to carry three gene copies, as confirmed by quantitative PCR; no increase in D expression was observed in these patients. In addition, the QMPSF guided the investigation of 144 RHCE variants and RHD zygosity, and two novel alleles were identified. DISCUSSION: The QMPSF was shown to identify hybrid alleles involved in altered Rh phenotypes in Brazilian donors and patients with SCD. The association of the hybrid RHCE-D(8)-CE allele with c.733C>G suggests this hybrid allele may be used as a marker to detect the most frequent variants found in patients with SCD.
Assuntos
Anemia Falciforme , Antígenos de Grupos Sanguíneos , Humanos , Sistema do Grupo Sanguíneo Rh-Hr/genética , Brasil , Antígenos de Grupos Sanguíneos/genética , Frequência do Gene , Anemia Falciforme/genética , Alelos , GenótipoRESUMO
Autosomal dominant polycystic kidney disease (ADPKD), the most common inherited kidney disorder, is caused by mutations in PKD1 or PKD2. The molecular diagnosis of ADPKD is complicated by extensive allelic heterogeneity and particularly by the presence of six highly homologous sequences of PKD1 exons 1-33. Here, we screened PKD1 and PKD2 for both conventional mutations and gross genomic rearrangements in up to 700 unrelated ADPKD patients--the largest patient cohort to date--by means of direct sequencing, followed by quantitative fluorescent multiplex polymerase chain reaction or array-comparative genomic hybridization. This resulted in the identification of the largest number of new pathogenic mutations (n = 351) in a single publication, expanded the spectrum of known ADPKD pathogenic mutations by 41.8% for PKD1 and by 23.8% for PKD2, and provided new insights into several issues, such as the population-dependent distribution of recurrent mutations compared with founder mutations and the relative paucity of pathogenic missense mutations in the PKD2 gene. Our study, together with others, highlights the importance of developing novel approaches for both mutation detection and functional validation of nondefinite pathogenic mutations to increase the diagnostic value of molecular testing for ADPKD.
Assuntos
Análise Mutacional de DNA/métodos , Rim Policístico Autossômico Dominante/genética , Canais de Cátion TRPP/genética , Hibridização Genômica Comparativa , Feminino , Humanos , Reação em Cadeia da Polimerase Multiplex , Mutação/genética , Mutação de Sentido Incorreto/genéticaRESUMO
BACKGROUND: A considerable number of RHD alleles responsible for weak and partial D phenotypes have been identified over the past decade. Two particular concerns, namely, 1) that red blood cells of these phenotypes may cause anti-D immunization when transfused to D- recipients and 2) that serologic determination of these phenotypes is often doubtful, make genetic analysis of the RHD gene highly desirable. STUDY DESIGN AND METHODS: Blood samples that displayed D phenotype ambiguity (as determined by serologic analyses) were collected from several sites of the Etablissement Français du Sang and subjected to RHD variant screening by means of a previously established denaturing high-performance liquid chromatography method followed by direct sequencing. RESULTS: Systematic screening of the RHD coding sequences as well as the exon-intron boundaries identified DNA variants in 755 of the 806 samples analyzed. In particular, this resulted in the identification of 10 novel single-nucleotide substitutions and seven novel complex alleles. CONCLUSION: This study further increased the already large repertoire of RHD allelic variants. Whereas most of the newly found variants are putative weak or partial D alleles, most of the complex alleles are readily understandable in the present phylogenetic model of RHD.
Assuntos
Alelos , Sistema do Grupo Sanguíneo Rh-Hr/genética , Regiões 3' não Traduzidas , Estudos de Coortes , Variação Genética , Humanos , Fenótipo , Estudos Prospectivos , Sistema do Grupo Sanguíneo Rh-Hr/imunologiaAssuntos
Encefalopatias/genética , Proteínas de Transporte/genética , Epilepsia/genética , Fenótipo , Transtornos Psicomotores/genética , Deleção de Sequência , Alelos , Encéfalo/anormalidades , Encefalopatias/diagnóstico , Criança , Códon , Epilepsia/diagnóstico , Genótipo , Humanos , Imageamento por Ressonância Magnética , Masculino , Transtornos Psicomotores/diagnóstico , Índice de Gravidade de DoençaRESUMO
Over the last 20 years since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, more than 1,600 different putatively pathological CFTR mutations have been identified. Until now, however, copy number mutations (CNMs) involving the CFTR gene have not been methodically analyzed, resulting almost certainly in the underascertainment of CFTR gene duplications compared with deletions. Here, high-resolution array comparative genomic hybridization (averaging one interrogating probe every 95 bp) was used to analyze the entire length of the CFTR gene (189 kb) in 233 cystic fibrosis chromosomes lacking conventional mutations. We succeeded in identifying five duplication CNMs that would otherwise have been refractory to analysis. Based upon findings from this and other studies, we propose that deletion and duplication CNMs in the human autosomal genome are likely to be generated in the proportion of approximately 2-3:1. We further postulate that intragenic gene duplication CNMs in other disease loci may have been routinely underascertained. Finally, our analysis of +/-20 bp flanking each of the 40 CFTR breakpoints characterized at the DNA sequence level provide support for the emerging concept that non-B DNA conformations in combination with specific sequence motifs predispose to both recurring and nonrecurring genomic rearrangements.
Assuntos
Regulador de Condutância Transmembrana em Fibrose Cística/genética , Variações do Número de Cópias de DNA/genética , Loci Gênicos/genética , Mutação/genética , Sequência de Bases , Hibridização Genômica Comparativa , Predisposição Genética para Doença , HumanosAssuntos
Cromossomos Humanos Par 18/genética , Cromossomos Humanos Par 2/genética , Cromossomos Humanos Par 3/genética , Rearranjo Gênico , Adulto , Líquido Amniótico/citologia , Troca Genética , Feminino , Humanos , Cariotipagem , Linfócitos/fisiologia , Masculino , Gravidez , Recombinação Genética , Translocação GenéticaRESUMO
We report here a de novo 16q24.1 interstitial duplication in a woman with a severe phenotype consistent with mental retardation, spastic paraplegia, severe epilepsy, a narrow and arched palate, malar hypoplasia, little subcutaneous fat and arachnodactyly. Although conventional karyotyping was found to be normal, array-CGH detected a small duplication on chromosome 16. Using QFM-PCR, we characterised its proximal and distal breakpoints. The duplication, which is approximately 250 kb, encompasses seven genes (KIAA0182, GINS2, c16orf74, COX4NB, COX4I1, MIR1910 and IRF8). Several reports have previously described large 16q duplications, and some of these overlap with our region in 16q24.1. Due to the variability of the described phenotypes, the characterisation of small 16q duplications may help to determine critical regions and the genes they contain that are associated with the components of complex phenotypes.