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1.
Nat Genet ; 53(3): 313-321, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33664507

RESUMO

Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.


Assuntos
Variação Genética , Células-Tronco Pluripotentes Induzidas/fisiologia , Locos de Características Quantitativas , Síndrome de Bardet-Biedl/genética , Canais de Cálcio/genética , Linhagem Celular , Ataxia Cerebelar/genética , Metilação de DNA , Expressão Gênica , Humanos , Células-Tronco Pluripotentes Induzidas/citologia , Polimorfismo de Nucleotídeo Único , Proteínas/genética , Doenças Raras/genética , Sequências Reguladoras de Ácido Nucleico , Análise de Sequência de RNA , Sequenciamento Completo do Genoma
2.
Am J Hum Genet ; 108(3): 482-501, 2021 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-33636100

RESUMO

Rare monogenic disorders of the primary cilium, termed ciliopathies, are characterized by extreme presentations of otherwise common diseases, such as diabetes, hepatic fibrosis, and kidney failure. However, despite a recent revolution in our understanding of the cilium's role in rare disease pathogenesis, the organelle's contribution to common disease remains largely unknown. Hypothesizing that common genetic variants within Mendelian ciliopathy genes might contribute to common complex diseases pathogenesis, we performed association studies of 16,874 common genetic variants across 122 ciliary genes with 12 quantitative laboratory traits characteristic of ciliopathy syndromes in 452,593 individuals in the UK Biobank. We incorporated tissue-specific gene expression analysis, expression quantitative trait loci, and Mendelian disease phenotype information into our analysis and replicated our findings in meta-analysis. 101 statistically significant associations were identified across 42 of the 122 examined ciliary genes (including eight novel replicating associations). These ciliary genes were widely expressed in tissues relevant to the phenotypes being studied, and eQTL analysis revealed strong evidence for correlation between ciliary gene expression levels and laboratory traits. Perhaps most interestingly, our analysis identified different ciliary subcompartments as being specifically associated with distinct sets of phenotypes. Taken together, our data demonstrate the utility of a Mendelian pathway-based approach to genomic association studies, challenge the widely held belief that the cilium is an organelle important mainly in development and in rare syndromic disease pathogenesis, and provide a framework for the continued integration of common and rare disease genetics to provide insight into the pathophysiology of human diseases of immense public health burden.


Assuntos
Cílios/genética , Ciliopatias/genética , Doenças Genéticas Inatas/genética , Doenças Raras/genética , Cílios/patologia , Ciliopatias/patologia , Estudos de Associação Genética , Doenças Genéticas Inatas/patologia , Predisposição Genética para Doença , Genômica , Humanos , Fenótipo , Locos de Características Quantitativas/genética , Doenças Raras/patologia
4.
Nat Commun ; 12(1): 964, 2021 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-33574263

RESUMO

Metabolite levels in urine may provide insights into genetic mechanisms shaping their related pathways. We therefore investigate the cumulative contribution of rare, exonic genetic variants on urine levels of 1487 metabolites and 53,714 metabolite ratios among 4864 GCKD study participants. Here we report the detection of 128 significant associations involving 30 unique genes, 16 of which are known to underlie inborn errors of metabolism. The 30 genes are strongly enriched for shared expression in liver and kidney (odds ratio = 65, p-FDR = 3e-7), with hepatocytes and proximal tubule cells as driving cell types. Use of UK Biobank whole-exome sequencing data links genes to diseases connected to the identified metabolites. In silico constraint-based modeling of gene knockouts in a virtual whole-body, organ-resolved metabolic human correctly predicts the observed direction of metabolite changes, highlighting the potential of linking population genetics to modeling. Our study implicates candidate variants and genes for inborn errors of metabolism.


Assuntos
Erros Inatos do Metabolismo/genética , Erros Inatos do Metabolismo/urina , Variação Genética , Genótipo , Humanos , Rim/metabolismo , Fígado/metabolismo , Masculino , Doenças Raras/genética , Sequenciamento Completo do Exoma
5.
JAMA Netw Open ; 4(2): e2036220, 2021 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-33630084

RESUMO

Importance: The Undiagnosed Diseases Network (UDN) is a national network that evaluates individual patients whose signs and symptoms have been refractory to diagnosis. Providing reliable estimates of admission outcomes may assist clinical evaluators to distinguish, prioritize, and accelerate admission to the UDN for patients with undiagnosed diseases. Objective: To develop computational models that effectively predict admission outcomes for applicants seeking UDN evaluation and to rank the applications based on the likelihood of patient admission to the UDN. Design, Setting, and Participants: This prognostic study included all applications submitted to the UDN from July 2014 to June 2019, with 1209 applications accepted and 1212 applications not accepted. The main inclusion criterion was an undiagnosed condition despite thorough evaluation by a health care professional; the main exclusion criteria were a diagnosis that explained the objective findings or a review of the records that suggested a diagnosis. A classifier was trained using information extracted from application forms, referral letters from health care professionals, and semantic similarity between referral letters and textual description of known mendelian disorders. The admission labels were provided by the case review committee of the UDN. In addition to retrospective analysis, the classifier was prospectively tested on another 288 applications that were not evaluated at the time of classifier development. Main Outcomes and Measures: The primary outcomes were whether a patient was accepted or not accepted to the UDN and application order ranked based on likelihood of admission. The performance of the classifier was assessed by comparing its predictions against the UDN admission outcomes and by measuring improvement in the mean processing time for accepted applications. Results: The best classifier obtained sensitivity of 0.843, specificity of 0.738, and area under the receiver operating characteristic curve of 0.844 for predicting admission outcomes among 1212 accepted and 1210 not accepted applications. In addition, the classifier can decrease the current mean (SD) UDN processing time for accepted applications from 3.29 (3.17) months to 1.05 (3.82) months (68% improvement) by ordering applications based on their likelihood of acceptance. Conclusions and Relevance: A classification system was developed that may assist clinical evaluators to distinguish, prioritize, and accelerate admission to the UDN for patients with undiagnosed diseases. Accelerating the admission process may improve the diagnostic journeys for these patients and serve as a model for partial automation of triaging or referral for other resource-constrained applications. Such classification models make explicit some of the considerations that currently inform the use of whole-genome sequencing for undiagnosed disease and thereby invite a broader discussion in the clinical genetics community.


Assuntos
Aprendizado de Máquina , Seleção de Pacientes , Doenças Raras/diagnóstico , Encaminhamento e Consulta , Doenças não Diagnosticadas/diagnóstico , Adolescente , Adulto , Área Sob a Curva , Criança , Pré-Escolar , Simulação por Computador , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Admissão do Paciente , Estudos Prospectivos , Curva ROC , Doenças Raras/genética , Reprodutibilidade dos Testes , Estudos Retrospectivos , Triagem , Doenças não Diagnosticadas/genética , Sequenciamento Completo do Genoma , Adulto Jovem
8.
Am J Hum Genet ; 108(2): 213, 2021 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-33545026
9.
Am J Hum Genet ; 107(3): 403-417, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32755546

RESUMO

Human Phenotype Ontology (HPO)-based analysis has become standard for genomic diagnostics of rare diseases. Current algorithms use a variety of semantic and statistical approaches to prioritize the typically long lists of genes with candidate pathogenic variants. These algorithms do not provide robust estimates of the strength of the predictions beyond the placement in a ranked list, nor do they provide measures of how much any individual phenotypic observation has contributed to the prioritization result. However, given that the overall success rate of genomic diagnostics is only around 25%-50% or less in many cohorts, a good ranking cannot be taken to imply that the gene or disease at rank one is necessarily a good candidate. Here, we present an approach to genomic diagnostics that exploits the likelihood ratio (LR) framework to provide an estimate of (1) the posttest probability of candidate diagnoses, (2) the LR for each observed HPO phenotype, and (3) the predicted pathogenicity of observed genotypes. LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) placed the correct diagnosis within the first three ranks in 92.9% of 384 case reports comprising 262 Mendelian diseases, and the correct diagnosis had a mean posttest probability of 67.3%. Simulations show that LIRICAL is robust to many typically encountered forms of genomic and phenomic noise. In summary, LIRICAL provides accurate, clinically interpretable results for phenotype-driven genomic diagnostics.


Assuntos
Biologia Computacional , Bases de Dados Genéticas , Genômica , Doenças Raras/diagnóstico , Algoritmos , Exoma/genética , Humanos , Fenótipo , Doenças Raras/genética , Software
10.
Am J Hum Genet ; 107(3): 527-538, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32758447

RESUMO

Generalized pustular psoriasis (GPP) is a severe multi-systemic inflammatory disease characterized by neutrophilic pustulosis and triggered by pro-inflammatory IL-36 cytokines in skin. While 19%-41% of affected individuals harbor bi-allelic mutations in IL36RN, the genetic cause is not known in most cases. To identify and characterize new pathways involved in the pathogenesis of GPP, we performed whole-exome sequencing in 31 individuals with GPP and demonstrated effects of mutations in MPO encoding the neutrophilic enzyme myeloperoxidase (MPO). We discovered eight MPO mutations resulting in MPO -deficiency in neutrophils and monocytes. MPO mutations, primarily those resulting in complete MPO deficiency, cumulatively associated with GPP (p = 1.85E-08; OR = 6.47). The number of mutant MPO alleles significantly differed between 82 affected individuals and >4,900 control subjects (p = 1.04E-09); this effect was stronger when including IL36RN mutations (1.48E-13) and correlated with a younger age of onset (p = 0.0018). The activity of four proteases, previously implicated as activating enzymes of IL-36 precursors, correlated with MPO deficiency. Phorbol-myristate-acetate-induced formation of neutrophil extracellular traps (NETs) was reduced in affected cells (p = 0.015), and phagocytosis assays in MPO-deficient mice and human cells revealed altered neutrophil function and impaired clearance of neutrophils by monocytes (efferocytosis) allowing prolonged neutrophil persistence in inflammatory skin. MPO mutations contribute significantly to GPP's pathogenesis. We implicate MPO as an inflammatory modulator in humans that regulates protease activity and NET formation and modifies efferocytosis. Our findings indicate possible implications for the application of MPO inhibitors in cardiovascular diseases. MPO and affected pathways represent attractive targets for inducing resolution of inflammation in neutrophil-mediated skin diseases.


Assuntos
Inflamação/genética , Interleucinas/genética , Peroxidase/genética , Psoríase/genética , Dermatopatias/genética , Adulto , Animais , Citocinas/genética , Armadilhas Extracelulares/genética , Feminino , Humanos , Inflamação/patologia , Interleucina-1/genética , Interleucinas/metabolismo , Masculino , Camundongos , Mutação/genética , Neutrófilos/metabolismo , Psoríase/patologia , Doenças Raras/enzimologia , Doenças Raras/genética , Doenças Raras/patologia , Pele/enzimologia , Pele/patologia , Dermatopatias/patologia
11.
Nature ; 583(7814): 96-102, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32581362

RESUMO

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.


Assuntos
Internacionalidade , Programas Nacionais de Saúde , Doenças Raras/diagnóstico , Doenças Raras/genética , Sequenciamento Completo do Genoma , Complexo 2-3 de Proteínas Relacionadas à Actina/genética , Proteínas Adaptadoras de Transdução de Sinal/genética , Alelos , Bases de Dados Factuais , Eritrócitos/metabolismo , Fator de Transcrição GATA1/genética , Humanos , Fenótipo , Locos de Características Quantitativas , Receptores de Trombopoetina/genética , Medicina Estatal , Reino Unido
12.
Einstein (Sao Paulo) ; 18: eRC5335, 2020.
Artigo em Inglês, Português | MEDLINE | ID: mdl-32578677

RESUMO

Chromosomal abnormalities are responsible for several congenital malformations in the world, some of these are associated to telomeric/subtelomeric deletions. The abnormalities involving the telomere of chromosome 12 are rare, with few reports of deletions involving 12q24.31 region in the literature, and, to our knowledge, only four of them in the 12q24.31-q24.33 region. We report a further case of interstitial deletion of bands 12q24.31-q24.33 associated with autism spectrum disorder. A 2-year-old boy with global developmental delay associated with multiple congenital anomalies. The Human Genome CGH Microarray 60K confirmed the diagnosis of 12q deletion syndrome. This study made a review of the current literature comparing our patient with previously reported cases. These detailed analyses contribute to the development of genotype/phenotype correlations for 12q deletions that will aid in better diagnosis and prognosis of this deletion.


Assuntos
Transtorno do Espectro Autista/genética , Transtorno Autístico/genética , Transtornos Cromossômicos/patologia , Cromossomos Humanos Par 12/genética , Doenças Raras/genética , Anormalidades Múltiplas , Pré-Escolar , Aberrações Cromossômicas , Deleção Cromossômica , Humanos , Masculino
13.
Nature ; 581(7809): 452-458, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32461655

RESUMO

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the 'proportion expressed across transcripts', which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies.


Assuntos
Doença/genética , Haploinsuficiência/genética , Mutação com Perda de Função/genética , Anotação de Sequência Molecular , Transcrição Genética , Transcriptoma/genética , Transtorno do Espectro Autista/genética , Conjuntos de Dados como Assunto , Deficiências do Desenvolvimento/genética , Éxons/genética , Feminino , Genótipo , Humanos , Deficiência Intelectual/genética , Masculino , Anotação de Sequência Molecular/normas , Distribuição de Poisson , RNA Mensageiro/análise , RNA Mensageiro/genética , Doenças Raras/diagnóstico , Doenças Raras/genética , Reprodutibilidade dos Testes , Sequenciamento Completo do Exoma
14.
Adv Exp Med Biol ; 1233: 311-325, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32274764

RESUMO

The TRIM family comprises proteins characterized by the presence of the tripartite motif composed of a RING domain, one or two B-box domains and a coiled-coil region. The TRIM shared domain structure underscores a common biochemical function as E3 ligase within the ubiquitination cascade. The TRIM proteins represent one of the largest E3 ligase families counting in human more than 70 members. These proteins are implicated in a plethora of cellular processes such as apoptosis, cell cycle regulation, muscular physiology, and innate immune response. Consistently, their alteration results in several pathological conditions emphasizing their medical relevance. Here, the genetic and pathogenetic mechanisms of rare disorders directly caused by mutations in TRIM genes will be reviewed. These diseases fall into different pathological areas, from malformation birth defects due to developmental abnormalities, to neurological disorders and progressive teenage neuromuscular disorders. In many instances, TRIM E3 ligases act on several substrates thus exerting pleiotropic activities: the need of unraveling disease-specific TRIM pathways for a precise targeting therapy avoiding dramatic side effects will be discussed.


Assuntos
Doenças Genéticas Inatas/enzimologia , Doenças Genéticas Inatas/genética , Doenças Raras/enzimologia , Doenças Raras/genética , Proteínas com Motivo Tripartido/química , Proteínas com Motivo Tripartido/metabolismo , Ubiquitina-Proteína Ligases/química , Ubiquitina-Proteína Ligases/metabolismo , Humanos , Domínios Proteicos , Proteínas com Motivo Tripartido/genética , Ubiquitina-Proteína Ligases/genética , Ubiquitinação
15.
PLoS One ; 15(4): e0231728, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32315351

RESUMO

INTRODUCTION: Phenotype-driven rare disease gene prioritization relies on high quality curated resources containing disease, gene and phenotype annotations. However, the effectiveness of gene prioritization tools is constrained by the incomplete coverage of rare disease, phenotype and gene annotations in such curated resources. METHODS: We extracted rare disease correlation pairs involving diseases, phenotypes and genes from MEDLINE abstracts and used the information propagation algorithm GCAS to build an association network. We built a tool called PRIORI-T for rare disease gene prioritization that uses this network for phenotype-driven rare disease gene prioritization. The quality of disease-gene associations in PRIORI-T was compared with resources such as DisGeNET and Open Targets in the context of rare diseases. The gene prioritization performance of PRIORI-T was evaluated using phenotype descriptions of 230 real-world rare disease clinical cases collated from recent publications, as well as compared to other gene prioritization tools such as HANRD and Orphamizer. RESULTS: PRIORI-T contains qualitatively better associations than DisGeNET and Open Targets. Furthermore, the causal genes were captured within Top-50 for more than 40% of the real-world clinical cases and within Top-300 for more than 72% of the cases when PRIORI-T was used for gene prioritization. It outperformed other gene prioritization tools such as HANRD and Orphamizer that primarily rely on curated resources. CONCLUSIONS: PRIORI-T exhibited improved gene prioritization performance without requiring high quality curated data. Thus, it holds great promise in phenotype-driven gene prioritization for rare disease studies.


Assuntos
Algoritmos , Biologia Computacional/métodos , MEDLINE , Doenças Raras/genética , Humanos , Fenótipo
16.
Am J Hum Genet ; 106(5): 717-725, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32330417

RESUMO

We identified three unrelated individuals with de novo missense variants in CDK19, encoding a cyclin-dependent kinase protein family member that predominantly regulates gene transcription. These individuals presented with hypotonia, global developmental delay, epileptic encephalopathy, and dysmorphic features. CDK19 is conserved between vertebrate and invertebrate model organisms, but currently abnormalities in CDK19 are not known to be associated with a human disorder. Loss of Cdk8, the fly homolog of CDK19, causes larval lethality, which is suppressed by expression of human CDK19 reference cDNA. In contrast, the CDK19 p.Tyr32His and p.Thr196Ala variants identified in the affected individuals fail to rescue the loss of Cdk8 and behave as null alleles. Additionally, neuronal RNAi-mediated knockdown of Cdk8 in flies results in semi-lethality. The few eclosing flies exhibit severe seizures and a reduced lifespan. Both phenotypes are fully suppressed by moderate expression of the CDK19 reference cDNA but not by expression of the two variants. Finally, loss of Cdk8 causes an obvious loss of boutons and synapses at larval neuromuscular junctions (NMJs). Together, our findings demonstrate that human CDK19 fully replaces the function of Cdk8 in the fly, the human disease-associated CDK19 variants behave as strong loss-of-function variants, and deleterious CDK19 variants underlie a syndromic neurodevelopmental disorder.


Assuntos
Encefalopatias/genética , Quinases Ciclina-Dependentes/genética , Epilepsia Generalizada/genética , Deficiência Intelectual/genética , Mutação de Sentido Incorreto/genética , Adulto , Sequência de Aminoácidos , Animais , Pré-Escolar , Quinase 8 Dependente de Ciclina/deficiência , Quinase 8 Dependente de Ciclina/genética , Proteínas de Drosophila/deficiência , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Junção Neuromuscular , Doenças Raras/genética , Convulsões/genética , Síndrome , Adulto Jovem
17.
Nucleic Acids Res ; 48(W1): W162-W169, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32338743

RESUMO

VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases.


Assuntos
Variação Genética , Doenças Raras/genética , Software , Humanos , Anotação de Sequência Molecular , Doenças Raras/diagnóstico , Pesquisa , Interface Usuário-Computador
18.
BMC Med Genet ; 21(1): 79, 2020 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-32295532

RESUMO

BACKGROUND: Congenital chloride diarrhea (CLD; OMIM 214700) is a rare autosomal recessive disorder caused by pathogenic variations in the solute carrier family 26 member A3 (SLC26A3) gene. Without salt substitution, this chronic diarrheal disorder causes severe dehydration and electrolyte disturbances. Homozygous variants in the nearby gene SLC26A4 disrupt anion exchange in the inner ear and the thyroid, causing Pendred syndrome (PDS; OMIM 274600), which is the most frequent form of syndromic deafness. CASE PRESENTATION: We report an unusual co-occurrence of two rare homozygous mutations in both the SLC26A3 and SLC26A4 genes, causing a rare combination of both CLD and PDS in two siblings. Although the clinical pictures were typical, the combined loss of these anion transporters might modulate the risk of renal injury associated with CLD. CONCLUSIONS: Familial presentation of two rare autosomal recessive disorders with loss of function of different SLC26 anion transporters is described. Independent homozygous variants in the SLC26A3 and SLC26A4 genes cause CLD and PDS in siblings, shedding light on co-occurrence of rare recessive traits in the progeny of consanguineous couples.


Assuntos
Antiportadores de Cloreto-Bicarbonato/genética , Diarreia/congênito , Bócio Nodular/genética , Perda Auditiva Neurossensorial/genética , Erros Inatos do Metabolismo/genética , Transportadores de Sulfato/genética , Diarreia/diagnóstico , Diarreia/genética , Diarreia/patologia , Feminino , Genes Recessivos/genética , Testes Genéticos , Bócio Nodular/diagnóstico , Bócio Nodular/patologia , Perda Auditiva Neurossensorial/diagnóstico , Perda Auditiva Neurossensorial/patologia , Humanos , Lactente , Erros Inatos do Metabolismo/diagnóstico , Erros Inatos do Metabolismo/patologia , Mutação , Linhagem , Gravidez , Doenças Raras/diagnóstico , Doenças Raras/genética , Doenças Raras/patologia , Irmãos
19.
PLoS One ; 15(4): e0230587, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32271766

RESUMO

As high-throughput sequencing is increasingly applied to the molecular diagnosis of rare Mendelian disorders, a large number of patients with diverse phenotypes have their genetic and phenotypic data pooled together to uncover new gene-phenotype relations. We introduce Phenogenon, a statistical tool that combines, Human Phenotype Ontology (HPO) annotated patient phenotypes, gnomAD allele population frequency, and Combined Annotation Dependent Depletion (CADD) score for variant pathogenicity, in order to jointly predict the mode of inheritance and gene-phenotype associations. We ran Phenogenon on our cohort of 3,290 patients who had undergone whole exome sequencing. Among the top associations, we recapitulated previously known, such as "SRD5A3-Abnormal full-field electroretinogram-recessive" and "GRHL2 -Nail dystrophy-recessive", and discovered one potentially novel, "RRAGA-Abnormality of the skin-dominant". We also developed an interactive web interface available at https://phenogenon.phenopolis.org to visualise and explore the results.


Assuntos
Biologia Computacional/métodos , Estudos de Associação Genética , Doenças Genéticas Inatas , Sequenciamento de Nucleotídeos em Larga Escala , Doenças Raras , 3-Oxo-5-alfa-Esteroide 4-Desidrogenase/genética , Estudos de Coortes , Proteínas de Ligação a DNA/genética , Bases de Dados Genéticas , Frequência do Gene , Estudos de Associação Genética/métodos , Estudos de Associação Genética/estatística & dados numéricos , Doenças Genéticas Inatas/epidemiologia , Doenças Genéticas Inatas/genética , Predisposição Genética para Doença , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos , Humanos , Proteínas de Membrana/genética , Proteínas Monoméricas de Ligação ao GTP/genética , Doenças da Unha/epidemiologia , Doenças da Unha/genética , Fenótipo , Doenças Raras/epidemiologia , Doenças Raras/genética , Distrofias Retinianas/epidemiologia , Distrofias Retinianas/genética , Dermatopatias/epidemiologia , Dermatopatias/genética , Fatores de Transcrição/genética , Sequenciamento Completo do Exoma
20.
Qual Life Res ; 29(9): 2445-2454, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32266555

RESUMO

PURPOSE: The complexity and severity of rare genetic conditions pose substantial burden to families. While the importance of spillovers on carers' health in resource allocation decisions is increasingly recognised, there is significant lack of empirical evidence in the context of rare diseases. The objective of this study was to estimate the health spillovers of paediatric rare genetic conditions on parents. METHODS: Health-related quality-of-life (HRQoL) data from children with rare genetic conditions (genetic kidney diseases, mitochondrial diseases, epileptic encephalopathies, brain malformations) and their parents were collected using the CHU9D and SF-12 measures, respectively. We used two approaches to estimate parental health spillovers. To quantify the 'absolute health spillover', we matched our parent cohort to the Australian general population. To quantify the 'relative health spillover', regression models were applied using the cohort data. RESULTS: Parents of affected children had significantly lower HRQoL compared to matched parents in the general public (- 0.06; 95% CIs - 0.08, - 0.04). Multivariable regression demonstrated a positive association between parental and child health. The mean magnitude of HRQoL loss in parents was estimated to be 33% of the HRQoL loss observed in children (95% CIs 21%, 46%). CONCLUSION: Paediatric rare genetic conditions appear to be associated with substantial parental health spillovers. This highlights the importance of including health effects on family members and caregivers into economic evaluation of genomic technologies and personalised medicine. Overlooking spillover effects may undervalue the benefits of diagnosis and management in this context. This study also expands the knowledge of family spillover to the rare disease spectrum.


Assuntos
Pais/psicologia , Qualidade de Vida/psicologia , Doenças Raras/genética , Adulto , Feminino , Humanos , Masculino
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