RESUMO
The splicing of pre-mRNAs into mature transcripts is remarkable for its precision, but the mechanisms by which the cellular machinery achieves such specificity are incompletely understood. Here, we describe a deep neural network that accurately predicts splice junctions from an arbitrary pre-mRNA transcript sequence, enabling precise prediction of noncoding genetic variants that cause cryptic splicing. Synonymous and intronic mutations with predicted splice-altering consequence validate at a high rate on RNA-seq and are strongly deleterious in the human population. De novo mutations with predicted splice-altering consequence are significantly enriched in patients with autism and intellectual disability compared to healthy controls and validate against RNA-seq in 21 out of 28 of these patients. We estimate that 9%-11% of pathogenic mutations in patients with rare genetic disorders are caused by this previously underappreciated class of disease variation.
Assuntos
Previsões/métodos , Precursores de RNA/genética , Splicing de RNA/genética , Algoritmos , Processamento Alternativo/genética , Transtorno Autístico/genética , Aprendizado Profundo , Éxons/genética , Humanos , Deficiência Intelectual/genética , Íntrons/genética , Redes Neurais de Computação , Precursores de RNA/metabolismo , Sítios de Splice de RNA/genética , Sítios de Splice de RNA/fisiologiaRESUMO
The nuclear receptor subfamily 5, Group A, Member 1 (NR5A1) gene encodes steroidogenic factor 1 (SF1), which is necessary for development of steroid hormone-producing tissues including the gonad and adrenal gland. An induced pluripotent stem cell line (iPSC) LCHi002-B was generated from a participant with differences (disorders) of sex development (DSD) and multiple genetic variants including a large deletion in NR5A1, and three single nucleotide changes in DYNC2H1, PDE4D, and ZFPM2. The line presented typical morphology, expressed stem cell markers, differentiated into three germ layers, had normal karyotype, was mycoplasma-free, and carried mutations in NR5A1, DYNC2H1, PDE4D, and ZFPM2.
Assuntos
Transtorno 46,XY do Desenvolvimento Sexual , Células-Tronco Pluripotentes Induzidas , Humanos , Fator Esteroidogênico 1/genética , Transtorno 46,XY do Desenvolvimento Sexual/genética , Mutação , Desenvolvimento Sexual/genéticaRESUMO
BACKGROUND: To identify genes associated with congenital diaphragmatic hernia (CDH) to help understand the etiology and inform prognosis. METHODS: We performed exome sequencing on fetuses with CDH and their parents to identify rare genetic variants likely to mediate risk. We reviewed prenatal characteristics and neonatal outcomes. RESULTS: Data were generated for 22 parent-offspring trios. Six Likely Damaging (LD) variants were identified in five families (23 %). Three LD variants were in genes that contain variants in other CDH cohorts (NR2F2, PTPN11, WT1), while three were in genes that do not (CTR9, HDAC6, TP53). Integrating these data bolsters the evidence of association of NR2F2, PTPN11, and WT1 with CDH in humans. Of the five fetuses with a genetic diagnosis, one was terminated, two underwent perinatal demise, while two survived until repair. CONCLUSIONS: Exome sequencing expands the diagnostic yield of genetic testing in CDH. Correlating CDH patients' exomes with clinical outcomes may enable personalized counseling and therapies.
Assuntos
Fator II de Transcrição COUP/genética , Hérnias Diafragmáticas Congênitas/genética , Proteína Tirosina Fosfatase não Receptora Tipo 11/genética , Proteínas WT1/genética , Exoma/genética , Feminino , Feto/anormalidades , Feto/diagnóstico por imagem , Testes Genéticos/métodos , Testes Genéticos/estatística & dados numéricos , Hérnias Diafragmáticas Congênitas/diagnóstico , Humanos , Masculino , Gravidez , Ultrassonografia Pré-NatalRESUMO
Complete Androgen Insensitivity Syndrome (CAIS) is a difference of sex development (DSD) caused by loss of function of the androgen receptor (AR) gene. Patients typically identify as female and have a 46,XY karyotype. Two induced pluripotent stem cell lines (iPSCs), LCHi001-A and LCHi001-B, were generated from a participant with CAIS with AR mutation: c.2698A>T (p.Ile900Phe). Both lines presented typical morphology, expressed stem cell markers, differentiated into three germ layers, had a normal 46,XY karyotype, were mycoplasma-free, and carried the expected mutation in AR. These iPSC lines are an important resource for studying CAIS pathogenesis and possible treatment options.
Assuntos
Síndrome de Resistência a Andrógenos , Células-Tronco Pluripotentes Induzidas , Síndrome de Resistência a Andrógenos/genética , Feminino , Humanos , Masculino , Mutação , Nucleotídeos , Receptores Androgênicos/genéticaRESUMO
Clinical exome sequencing is frequently used to identify gene-disrupting variants in individuals with neurodevelopmental disorders. While splice-disrupting variants are known to contribute to these disorders, clinical interpretation of cryptic splice variants outside of the canonical splice site has been challenging. Here, we discuss papers that improve such detection.
Assuntos
Transtornos do Neurodesenvolvimento/genética , Splicing de RNA , HumanosRESUMO
Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contribution of de novo noncoding mutations to complex disorders. Using WGS, we identified 255,106 de novo mutations among sample genomes from members of 1902 quartet families in which one child, but not a sibling or their parents, was affected by autism spectrum disorder (ASD). In contrast to coding mutations, no noncoding functional annotation category, analyzed in isolation, was significantly associated with ASD. Casting noncoding variation in the context of a de novo risk score across multiple annotation categories, however, did demonstrate association with mutations localized to promoter regions. We found that the strongest driver of this promoter signal emanates from evolutionarily conserved transcription factor binding sites distal to the transcription start site. These data suggest that de novo mutations in promoter regions, characterized by evolutionary and functional signatures, contribute to ASD.
Assuntos
Transtorno do Espectro Autista/genética , Mutação , Regiões Promotoras Genéticas/genética , Sítios de Ligação/genética , Sequência Conservada , Análise Mutacional de DNA , Loci Gênicos , Variação Genética , Humanos , Linhagem , Risco , Fatores de Transcrição/metabolismoRESUMO
Genomic association studies of common or rare protein-coding variation have established robust statistical approaches to account for multiple testing. Here we present a comparable framework to evaluate rare and de novo noncoding single-nucleotide variants, insertion/deletions, and all classes of structural variation from whole-genome sequencing (WGS). Integrating genomic annotations at the level of nucleotides, genes, and regulatory regions, we define 51,801 annotation categories. Analyses of 519 autism spectrum disorder families did not identify association with any categories after correction for 4,123 effective tests. Without appropriate correction, biologically plausible associations are observed in both cases and controls. Despite excluding previously identified gene-disrupting mutations, coding regions still exhibited the strongest associations. Thus, in autism, the contribution of de novo noncoding variation is probably modest in comparison to that of de novo coding variants. Robust results from future WGS studies will require large cohorts and comprehensive analytical strategies that consider the substantial multiple-testing burden.