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1.
BMC Evol Biol ; 19(1): 144, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311498

RESUMO

BACKGROUND: Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depends on the analysis of sequence homology at the nucleotide or protein level. RESULTS: We analyzed mRNA GC content, codon usage and divergence of orthologous proteins in 55 vertebrate genomes. Data were visualized in genome-wide landscapes using a sliding window approach. Landscapes of GC content reveal both evolutionary conservation of clustered genes, and lineage-specific changes, so that it was possible to construct a phylogenetic tree that closely matched the classic "tree of life". Landscapes of GC content also strongly correlated to landscapes of amino acid usage: positive correlation with glycine, alanine, arginine and proline and negative correlation with phenylalanine, tyrosine, methionine, isoleucine, asparagine and lysine. Peaks of GC content correlated strongly with increased protein divergence. CONCLUSIONS: Landscapes of base- and amino acid composition of the coding genome opens a new approach in comparative genomics, allowing identification of discrete regions in which protein evolution accelerated over deep evolutionary time. Insight in the evolution of genome structure may spur novel studies assessing the evolutionary benefit of genes in particular genomic regions.


Assuntos
Composição de Bases/genética , Evolução Molecular , Exoma/genética , Proteínas/genética , Vertebrados/genética , Animais , Códon/genética , Genoma , Humanos , Mamíferos/genética , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Répteis/genética
2.
BMC Bioinformatics ; 20(1): 342, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208315

RESUMO

BACKGROUND: Whole exome sequencing (WES) is a cost-effective method that identifies clinical variants but it demands accurate variant caller tools. Currently available tools have variable accuracy in predicting specific clinical variants. But it may be possible to find the best combination of aligner-variant caller tools for detecting accurate single nucleotide variants (SNVs) and small insertion and deletion (InDels) separately. Moreover, many important aspects of InDel detection are overlooked while comparing the performance of tools, particularly its base pair length. RESULTS: We assessed the performance of variant calling pipelines using the combinations of four variant callers and five aligners on human NA12878 and simulated exome data. We used high confidence variant calls from Genome in a Bottle (GiaB) consortium for validation, and GRCh37 and GRCh38 as the human reference genome. Based on the performance metrics, both BWA and Novoalign aligners performed better with DeepVariant and SAMtools callers for detecting SNVs, and with DeepVariant and GATK for InDels. Furthermore, we obtained similar results on human NA24385 and NA24631 exome data from GiaB. CONCLUSION: In this study, DeepVariant with BWA and Novoalign performed best for detecting accurate SNVs and InDels. The accuracy of variant calling was improved by merging the top performing pipelines. The results of our study provide useful recommendations for analysis of WES data in clinical genomics.


Assuntos
Simulação por Computador , Polimorfismo de Nucleotídeo Único/genética , Sequenciamento Completo do Exoma , Pareamento de Bases/genética , Exoma/genética , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutação INDEL/genética , Curva ROC
3.
Nature ; 570(7759): 71-76, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31118516

RESUMO

Protein-coding genetic variants that strongly affect disease risk can yield relevant clues to disease pathogenesis. Here we report exome-sequencing analyses of 20,791 individuals with type 2 diabetes (T2D) and 24,440 non-diabetic control participants from 5 ancestries. We identify gene-level associations of rare variants (with minor allele frequencies of less than 0.5%) in 4 genes at exome-wide significance, including a series of more than 30 SLC30A8 alleles that conveys protection against T2D, and in 12 gene sets, including those corresponding to T2D drug targets (P = 6.1 × 10-3) and candidate genes from knockout mice (P = 5.2 × 10-3). Within our study, the strongest T2D gene-level signals for rare variants explain at most 25% of the heritability of the strongest common single-variant signals, and the gene-level effect sizes of the rare variants that we observed in established T2D drug targets will require 75,000-185,000 sequenced cases to achieve exome-wide significance. We propose a method to interpret these modest rare-variant associations and to incorporate these associations into future target or gene prioritization efforts.


Assuntos
Diabetes Mellitus Tipo 2/genética , Exoma/genética , Sequenciamento Completo do Exoma , Animais , Estudos de Casos e Controles , Técnicas de Apoio para a Decisão , Feminino , Frequência do Gene , Estudo de Associação Genômica Ampla , Humanos , Masculino , Camundongos , Camundongos Knockout
4.
PLoS Comput Biol ; 15(4): e1006953, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30986244

RESUMO

Determining the cancer type and molecular subtype has important clinical implications. The primary site is however unknown for some malignancies discovered in the metastatic stage. Moreover liquid biopsies may be used to screen for tumoral DNA, which upon detection needs to be assigned to a site-of-origin. Classifiers based on genomic features are a promising approach to prioritize the tumor anatomical site, type and subtype. We examined the predictive ability of causal (driver) somatic mutations in this task, comparing it against global patterns of non-selected (passenger) mutations, including features based on regional mutation density (RMD). In the task of distinguishing 18 cancer types, the driver mutations-mutated oncogenes or tumor suppressors, pathways and hotspots-classified 36% of the patients to the correct cancer type. In contrast, the features based on passenger mutations did so at 92% accuracy, with similar contribution from the RMD and the trinucleotide mutation spectra. The RMD and the spectra covered distinct sets of patients with predictions. In particular, introducing the RMD features into a combined classification model increased the fraction of diagnosed patients by 50 percentage points (at 20% FDR). Furthermore, RMD was able to discriminate molecular subtypes and/or anatomical site of six major cancers. The advantage of passenger mutations was upheld under high rates of false negative mutation calls and with exome sequencing, even though overall accuracy decreased. We suggest whole genome sequencing is valuable for classifying tumors because it captures global patterns emanating from mutational processes, which are informative of the underlying tumor biology.


Assuntos
Biologia Computacional/métodos , Neoplasias/classificação , Neoplasias/genética , Algoritmos , DNA de Neoplasias/classificação , DNA de Neoplasias/genética , Exoma/genética , Genômica , Humanos , Aprendizado de Máquina , Mutação/genética , Software , Sequenciamento Completo do Exoma/métodos , Sequenciamento Completo do Genoma/métodos
5.
BMC Cancer ; 19(1): 313, 2019 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-30947698

RESUMO

BACKGROUND: In the majority of familial breast cancer (BC) families, the etiology of the disease remains unresolved. To identify missing BC heritability resulting from relatively rare variants (minor allele frequency ≤ 1%), we have performed whole exome sequencing followed by variant analysis in a virtual panel of 492 cancer-associated genes on BC patients from BRCA1 and BRCA2 negative families with elevated BC risk. METHODS: BC patients from 54 BRCA1 and BRCA2-negative families with elevated BC risk and 120 matched controls were considered for germline DNA whole exome sequencing. Rare variants identified in the exome and in a virtual panel of cancer-associated genes [492 genes associated with different types of (hereditary) cancer] were compared between BC patients and controls. Nonsense, frame-shift indels and splice-site variants (strong protein-damaging variants, called PDAVs later on) observed in BC patients within the genes of the panel, which we estimated to possess the highest probability to predispose to BC, were further validated using an alternative sequencing procedure. RESULTS: Exome- and cancer-associated gene panel-wide variant analysis show that there is no significant difference in the average number of rare variants found in BC patients compared to controls. However, the genes in the cancer-associated gene panel with nonsense variants were more than two-fold over-represented in women with BC and commonly involved in the DNA double-strand break repair process. Approximately 44% (24 of 54) of BC patients harbored 31 PDAVs, of which 11 were novel. These variants were found in genes associated with known or suspected BC predisposition (PALB2, BARD1, CHEK2, RAD51C and FANCA) or in predisposing genes linked to other cancer types but not well-studied in the context of familial BC (EXO1, RECQL4, CCNH, MUS81, TDP1, DCLRE1A, DCLRE1C, PDE11A and RINT1) and genes associated with different hereditary syndromes but not yet clearly associated with familial cancer syndromes (ABCC11, BBS10, CD96, CYP1A1, DHCR7, DNAH11, ESCO2, FLT4, HPS6, MYH8, NME8 and TTC8). Exome-wide, only a few genes appeared to be enriched for PDAVs in the familial BC patients compared to controls. CONCLUSIONS: We have identified a series of novel candidate BC predisposition variants/genes. These variants/genes should be further investigated in larger cohorts/case-control studies. Other studies including co-segregation analyses in affected families, locus-specific loss of heterozygosity and functional studies should shed further light on their relevance for BC risk.


Assuntos
Neoplasias da Mama/genética , Exoma/genética , Predisposição Genética para Doença , Adulto , Idoso , Proteína BRCA1/genética , Proteína BRCA2/genética , Estudos de Casos e Controles , Feminino , Humanos , Pessoa de Meia-Idade , Mutação , Sequenciamento Completo do Exoma
6.
Cell Mol Biol (Noisy-le-grand) ; 65(3): 84-88, 2019 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-30942159

RESUMO

The aim of this study was to identify the novel missense eya4 mutation which cause autosomal dominant non syndromic hearing loss In a Chinese family. Hearing loss is the most common sensory deficit in humans, but the middle-frequency sensorineural hearing loss (MFSNHL) is rare among hereditary non-syndromic hearing loss, and EYA4 is one of the genes reported to be associated with MFSNHL. A genetic analysis of a Chinese family with autosomal dominant non­syndromic progressive hearing impairment was conducted and assessed. Targeted exome sequencing, conducted using DNA samples of an affected member in this family, revealed a novel heterozygous missense mutation c.1855T>G in exon 20 of EYA4, causing amino-acid (aa) substitution Gly for Trp at a conserved position aa-619. The p.W619G mutation related to hearing loss in this Chinese family was validated by Sanger sequencing. Bioinformatic analysis confirmed the pathogenic effects of this mutation. We identified the novel missense mutation c.1855T>G (p.W619G) in EYA4 causing autosomal dominant non-syndromic hearing impairment in the selected Chinese family.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Genes Dominantes , Perda Auditiva/genética , Mutação de Sentido Incorreto/genética , Transativadores/genética , Adulto , Idoso , Simulação por Computador , Exoma/genética , Família , Feminino , Loci Gênicos , Humanos , Masculino , Pessoa de Meia-Idade , Software
7.
Nat Methods ; 16(5): 401-404, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30988467

RESUMO

Profiling of both the genome and the transcriptome promises a comprehensive, functional readout of a tissue sample, yet analytical approaches are required to translate the increased data dimensionality, heterogeneity and complexity into patient benefits. We developed a statistical approach called Texomer ( https://github.com/KChen-lab/Texomer ) that performs allele-specific, tumor-deconvoluted transcriptome-exome integration of autologous bulk whole-exome and transcriptome sequencing data. Texomer results in substantially improved accuracy in sample categorization and functional variant prioritization.


Assuntos
Perfilação da Expressão Gênica/métodos , Genoma Humano , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias/genética , Transcriptoma/genética , Alelos , DNA de Neoplasias/genética , Exoma/genética , Humanos , Mutação , Polimorfismo de Nucleotídeo Único
8.
Biomed Res Int ; 2019: 7235914, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30834272

RESUMO

Leukodystrophies (LDs) are heterogeneous genetic disorders characterized by abnormal white matter in the central nervous system. Some of the LDs are progressive and often fatal. In general, LD is primarily diagnosed based on the neuroimaging; however, definitive diagnosis of the LD type is done using genetic testing such as next-generation sequencing. The aim of this study is to identify the genetic causes of LD in two independent Jordanian cases that exhibit MRI findings confirming LD with no definitive diagnosis using whole exome sequencing (WES). The most likely causative variants were identified. In one case, the homozygous pathogenic variant NM_000049.2:c.914C>A;p.Ala305Glu, which is previously reported in ClinVar, in the gene ASPA was identified causing Canavan disease. In the second case, the homozygous novel variant NM_000487.5:c.256C>G;p.Arg86Gly in the gene ARSA was identified causing metachromatic leukodystrophy. The two variants segregate in their families. The phenotypes of the two studied cases overlap with assigned diseases. The present study raises the importance of using WES to identify the precise neurodevelopmental diseases in Jordan.


Assuntos
Amidoidrolases/genética , Cerebrosídeo Sulfatase/genética , Leucodistrofia Metacromática/genética , Sequenciamento Completo do Exoma , Adulto , Variações do Número de Cópias de DNA/genética , Exoma/genética , Feminino , Predisposição Genética para Doença , Homozigoto , Humanos , Lactente , Jordânia , Leucodistrofia Metacromática/diagnóstico , Leucodistrofia Metacromática/diagnóstico por imagem , Leucodistrofia Metacromática/patologia , Masculino , Mutação , Linhagem , Fenótipo , Substância Branca/patologia
9.
Nat Biotechnol ; 37(5): 555-560, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30858580

RESUMO

Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part of the Global Alliance for Genomics and Health (GA4GH), we present a benchmarking framework for variant calling. We provide guidance on how to match variant calls with different representations, define standard performance metrics, and stratify performance by variant type and genome context. We describe limitations of high-confidence calls and regions that can be used as truth sets (for example, single-nucleotide variant concordance of two methods is 99.7% inside versus 76.5% outside high-confidence regions). Our web-based app enables comparison of variant calls against truth sets to obtain a standardized performance report. Our approach has been piloted in the PrecisionFDA variant-calling challenges to identify the best-in-class variant-calling methods within high-confidence regions. Finally, we recommend a set of best practices for using our tools and evaluating the results.


Assuntos
Benchmarking , Exoma/genética , Genoma Humano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Algoritmos , Genômica/tendências , Células Germinativas , Humanos , Polimorfismo de Nucleotídeo Único/genética , Software
10.
Biomed Pharmacother ; 111: 983-992, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30841478

RESUMO

Genetic polymorphisms in cytochrome P450 (CYP) or UDP-glucuronosyltransferase (UGT) genes can lead to changes in endocrine regulation or drug metabolism. Based on the recently published allele frequency data of the Exome Aggregation Consortium (ExAC), we extracted all common SNP variants that lead to missense mutations in CYPs and UGTs or in their helping proteins CPR, AdR, Adx, and UGDH. With a total of 737 alleles from 83 genes we provide the most comprehensive overview of missense variation distributions in drug metabolizing enzymes published to date. In all variants the most common allele was always considered to be the wild-type (WT), even if it was not identical to the *1-allele and/or the reference standard sequence of the RefSeq project. Surprisingly, in 15 cases (AdR, CYP2A7, CYP2C19, CYP2D6, CYP4A22, CYP4F11, CYP4F12, CYP4V2, CYP8B1, CYP20A1, UGT1A3, UGT1A7, UGT2A3, UGT2B7, and UGT2B15), the WT protein sequences were found to differ from reference standard sequences in up to four amino acids. We expect that these findings will have an impact on the definition of reference sequence standards for these genes, on the corresponding naming of alleles, and on the definition of reference standard activities.


Assuntos
Sistema Enzimático do Citocromo P-450/genética , Glucuronosiltransferase/genética , Mutação de Sentido Incorreto/genética , Alelos , Aminoácidos/genética , Exoma/genética , Frequência do Gene/genética , Humanos , Polimorfismo de Nucleotídeo Único/genética
11.
Hum Genet ; 138(8-9): 799-830, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-30762128

RESUMO

Eye formation is the result of coordinated induction and differentiation processes during embryogenesis. Disruption of any one of these events has the potential to cause ocular growth and structural defects, such as anophthalmia and microphthalmia (A/M). A/M can be isolated or occur with systemic anomalies, when they may form part of a recognizable syndrome. Their etiology includes genetic and environmental factors; several hundred genes involved in ocular development have been identified in humans or animal models. In humans, around 30 genes have been repeatedly implicated in A/M families, although many other genes have been described in single cases or families, and some genetic syndromes include eye anomalies occasionally as part of a wider phenotype. As a result of this broad genetic heterogeneity, with one or two notable exceptions, each gene explains only a small percentage of cases. Given the overlapping phenotypes, these genes can be most efficiently tested on panels or by whole exome/genome sequencing for the purposes of molecular diagnosis. However, despite whole exome/genome testing more than half of patients currently remain without a molecular diagnosis. The proportion of undiagnosed cases is even higher in those individuals with unilateral or milder phenotypes. Furthermore, even when a strong gene candidate is available for a patient, issues of incomplete penetrance and germinal mosaicism make diagnosis and genetic counseling challenging. In this review, we present the main genes implicated in non-syndromic human A/M phenotypes and, for practical purposes, classify them according to the most frequent or predominant phenotype each is associated with. Our intention is that this will allow clinicians to rank and prioritize their molecular analyses and interpretations according to the phenotypes of their patients.


Assuntos
Anoftalmia/genética , Anormalidades do Olho/genética , Microftalmia/genética , Animais , Exoma/genética , Olho/patologia , Humanos , Fenótipo , Síndrome
12.
Gene ; 695: 12-17, 2019 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-30738969

RESUMO

Microcephaly is a rare condition in which the occipitofrontal circumference in a child is more than two standard deviations below the mean of children of the same age and gender. It is mainly caused by genetic abnormalities that interfere with the growth of the cerebral cortex during early months of fetal development. We present a case of a 12 years old patient with microcephaly. To identify a possible genetic origin of the phenotype, we performed array CGH and exome sequencing in the patient. Exome sequencing revealed the presence of a de novo missense mutation in the TUBB5 gene (E401K). Mutations in the TUBB5 are mainly responsible for microcephaly but the clinical spectrum is wide, from patients with severe developmental delay, and the presence of different brain malformations, to patients with only slightly cognitive impairment and normal motor development. Our patient shows a milder phenotype than other patients carrying the same mutation. These differences in the clinical features suggest that other factors, presumably genetic or epigenetic, could be modulating clinical expressivity of TUBB5. It is therefore evident that more functional studies are needed to understand the pathology that underlies the clinical spectrum of tubulin associated disease states.


Assuntos
Deficiências do Desenvolvimento/genética , Microcefalia/genética , Malformações do Sistema Nervoso/genética , Tubulina (Proteína)/genética , Criança , Deficiências do Desenvolvimento/diagnóstico , Deficiências do Desenvolvimento/fisiopatologia , Exoma/genética , Feminino , Humanos , Masculino , Microcefalia/diagnóstico , Microcefalia/fisiopatologia , Mutação , Malformações do Sistema Nervoso/diagnóstico , Malformações do Sistema Nervoso/fisiopatologia
13.
BMC Bioinformatics ; 20(1): 65, 2019 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-30727941

RESUMO

BACKGROUND: Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In these methods, pathogenicity prediction is combined with a semantic similarity measure to prioritize not only variants that are likely to be dysfunctional but those that are likely involved in the pathogenesis of a patient's phenotype. RESULTS: We have developed DeepPVP, a variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data. We demonstrate that DeepPVP performs significantly better than existing methods, including phenotype-based methods that use similar features. DeepPVP is freely available at https://github.com/bio-ontology-research-group/phenomenet-vp . CONCLUSIONS: DeepPVP further improves on existing variant prioritization methods both in terms of speed as well as accuracy.


Assuntos
Aprendizado Profundo , Variação Genética , Software , Exoma/genética , Frequência do Gene/genética , Humanos , Redes Neurais (Computação) , Fenótipo , Sequenciamento Completo do Exoma
14.
Genet Test Mol Biomarkers ; 23(3): 204-208, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30758234

RESUMO

AIMS: Autosomal recessive nonsyndromic hearing loss (ARNSHL) is the most common form of hereditary deafness. Despite its frequency, the diagnosis of this disorder continues to be a challenging task given its extreme genetic heterogeneity. The purpose of this study was to identify the causative mutation in a consanguineous United Arab Emirates (UAE) family with ARNSHL. MATERIALS AND METHODS: Clinical exome sequencing (CES) followed by segregation analysis via Sanger sequencing was used to identify the causative mutation. In addition, 109 deaf individuals and 50 deafness-free controls from the UAE population were screened for the identified mutation. RESULTS AND DISCUSSION: CES identified the STRC frameshift mutation c.4510del (p.Glu1504Argfs*32) as the causative mutation in this family. Moreover, segregation analysis confirmed the above finding. In addition, the absence of this variant in 109 unrelated deaf individuals and 50 healthy controls indicates that it is rare in the UAE population. CONCLUSION: The present study represents the first STRC mutation reported in the UAE population. It also reinforces the power of next-generation sequencing in the diagnosis of heterogenous disorders such as nonsyndromic hearing loss.


Assuntos
Surdez/genética , Proteínas de Membrana/genética , Adulto , Exoma/genética , Feminino , Mutação da Fase de Leitura/genética , Genes Recessivos/genética , Perda Auditiva Neurossensorial/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Masculino , Proteínas de Membrana/fisiologia , Mutação , Linhagem , Emirados Árabes Unidos , Sequenciamento Completo do Exoma
15.
Nat Genet ; 51(3): 506-516, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30718927

RESUMO

Esophageal adenocarcinoma (EAC) is a poor-prognosis cancer type with rapidly rising incidence. Understanding of the genetic events driving EAC development is limited, and there are few molecular biomarkers for prognostication or therapeutics. Using a cohort of 551 genomically characterized EACs with matched RNA sequencing data, we discovered 77 EAC driver genes and 21 noncoding driver elements. We identified a mean of 4.4 driver events per tumor, which were derived more commonly from mutations than copy number alterations, and compared the prevelence of these mutations to the exome-wide mutational excess calculated using non-synonymous to synonymous mutation ratios (dN/dS). We observed mutual exclusivity or co-occurrence of events within and between several dysregulated EAC pathways, a result suggestive of strong functional relationships. Indicators of poor prognosis (SMAD4 and GATA4) were verified in independent cohorts with significant predictive value. Over 50% of EACs contained sensitizing events for CDK4 and CDK6 inhibitors, which were highly correlated with clinically relevant sensitivity in a panel of EAC cell lines and organoids.


Assuntos
Adenocarcinoma/genética , Biomarcadores Tumorais/genética , Neoplasias Esofágicas/genética , Estudos de Coortes , Variações do Número de Cópias de DNA/genética , Exoma/genética , Feminino , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica/genética , Genômica/métodos , Humanos , Masculino , Mutação/genética
16.
Nat Genet ; 51(4): 755-763, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30804562

RESUMO

Exome analysis of patients with a likely monogenic disease does not identify a causal variant in over half of cases. Splice-disrupting mutations make up the second largest class of known disease-causing mutations. Each individual (singleton) exome harbors over 500 rare variants of unknown significance (VUS) in the splicing region. The existing relevant pathogenicity prediction tools tackle all non-coding variants as one amorphic class and/or are not calibrated for the high sensitivity required for clinical use. Here we calibrate seven such tools and devise a novel tool called Splicing Clinically Applicable Pathogenicity prediction (S-CAP) that is over twice as powerful as all previous tools, removing 41% of patient VUS at 95% sensitivity. We show that S-CAP does this by using its own features and not via meta-prediction over previous tools, and that splicing pathogenicity prediction is distinct from predicting molecular splicing changes. S-CAP is an important step on the path to deriving non-coding causal diagnoses.


Assuntos
Variação Genética/genética , Processamento de RNA/genética , Exoma/genética , Humanos , Mutação/genética
17.
Nat Genet ; 51(3): 452-469, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30778226

RESUMO

Body-fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body-fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF ≥5%) and nine low-frequency or rare (MAF <5%) coding novel variants. Pathway/gene set enrichment analyses identified lipid particle, adiponectin, abnormal white adipose tissue physiology and bone development and morphology as important contributors to fat distribution, while cross-trait associations highlight cardiometabolic traits. In functional follow-up analyses, specifically in Drosophila RNAi-knockdowns, we observed a significant increase in the total body triglyceride levels for two genes (DNAH10 and PLXND1). We implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants.


Assuntos
Predisposição Genética para Doença/genética , Variação Genética/genética , Homeostase/genética , Lipídeos/genética , Proteínas/genética , Animais , Distribuição da Gordura Corporal/métodos , Índice de Massa Corporal , Estudos de Casos e Controles , Drosophila/genética , Exoma/genética , Feminino , Frequência do Gene/genética , Estudo de Associação Genômica Ampla/métodos , Humanos , Masculino , Fatores de Risco , Relação Cintura-Quadril/métodos
18.
Hum Immunol ; 80(4): 237-242, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30684568

RESUMO

Cervical cancer is more strongly associated with a specific virus, Human Papilloma Virus (HPV), in otherwise healthy individuals, than is any other cancer. Thus, there is an expectation that an adaptive immune signature of cervical cancer would be highly apparent. Here we used a genomics approach to investigate the relationship between T-cell receptor (TCR) V and J usage and survival for patients diagnosed with cervical cancer, relying exclusively on tissue and blood exome files. Specific TCR V or J segments, identified in recombination reads recovered from the exome files, were combined with the patient HLA alleles to identify V or J, HLA allele combination groups associated with distinct survival rates. For examples, the T-cell receptor-ß (TRB) V6-5, HLA-A*02:01 combination was associated with a positive outcome, and the TRBV6-1, HLA-A*01:01 combination was associated with a negative outcome. Overall, these results point to V or J usage, HLA allele combinations as survival biomarkers, likely conveniently accessible with a noninvasive procedure, and the results may point the way towards immunological reagents useful in therapy designs.


Assuntos
Exoma/genética , Genes Codificadores da Cadeia beta de Receptores de Linfócitos T/genética , Antígenos HLA/genética , Linfócitos T/imunologia , Neoplasias do Colo do Útero/genética , Adulto , Alelos , Feminino , Estudos de Associação Genética , Humanos , Técnicas de Diagnóstico Molecular , Prognóstico , Taxa de Sobrevida , Neoplasias do Colo do Útero/diagnóstico , Neoplasias do Colo do Útero/mortalidade
19.
BMC Med Genet ; 20(1): 3, 2019 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-30612563

RESUMO

BACKGROUND: Tandem mass spectrometry (MS MS) and simple fluorometric assays are currently used in newborn screening programs to detect inborn errors of metabolism (IEM). The aim of the study was to evaluate the clinical utility of exome sequencing as a second tier screening method to assist clinical diagnosis of the newborn. METHODS: A novel PCR-exome amplification and re-sequencing (PEARS) assay was designed and used to detect mutations in 122 genes associated with 101 IEM. Newborn bloodspots positive by biochemical testing were analysed by PEARS assay to detect pathogenic mutations relevant to the IEM. RESULTS: In initial validation studies of genomic DNA samples, PEARS assay correctly detected 25 known mutations associated with 17 different IEM. Retrospective gene analysis of newborns with clinical phenylketonuria (PKU), identified compound heterozygote phenylalanine hydroxylase (PAH) gene mutations in eight of nine samples (89%). Prospective analysis of 211 bloodspots correctly identified the two true PKU samples, yielding positive and negative predictive values of 100%. Testing of 8 true positive MS MS samples correctly identified potentially pathogenic compound heterozygote genotypes in 2 cases of citrullinemia type 1 and one case each of methylmalonic acidemia, isobutyryl-CoA dehydrogenase deficiency, short chain acyl-CoA dehydrogenase deficiency and glutaric acid type II and heterozygous genotypes in 2 cases of autosomal dominant methioninemia. Analysis of 11 of 12 false positive MS MS samples for other IEM identified heterozygous carriers in 8 cases for the relevant genes associated with the suspected IEM. In the remaining 3 cases, the test revealed compound heterozygote mutations in other metabolic genes not associated with the suspected IEM, indicating a misinterpretation of the original MS MS data. CONCLUSIONS: The PEARS assay has clinical utility as a rapid and cost effective second-tier test to assist the clinician to accurately diagnose newborns with a suspected IEM.


Assuntos
Exoma/genética , Erros Inatos do Metabolismo/diagnóstico , Erros Inatos do Metabolismo/genética , Reação em Cadeia da Polimerase Multiplex/métodos , Triagem Neonatal/métodos , Sequenciamento Completo do Exoma/métodos , Acil-CoA Desidrogenase/deficiência , Acil-CoA Desidrogenase/genética , Erros Inatos do Metabolismo dos Aminoácidos/genética , Citrulinemia/genética , Aconselhamento Genético , Genótipo , Glutaratos , Glicina N-Metiltransferase/deficiência , Glicina N-Metiltransferase/genética , Heterozigoto , Humanos , Recém-Nascido , Erros Inatos do Metabolismo Lipídico/genética , Masculino , Técnicas de Diagnóstico Molecular/métodos , Mutação , Fenilalanina Hidroxilase/genética , Fenilcetonúrias/diagnóstico , Fenilcetonúrias/genética , Estudos Prospectivos , Estudos Retrospectivos , Espectrometria de Massas em Tandem/métodos
20.
Life Sci ; 219: 74-81, 2019 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-30611784

RESUMO

AIMS: Progressive cardiac conduction disease (PCCD) is a rare heart disease that usually shows familial inheritance. Potential genetic risk factors for PCCD have been mostly limited to genes that encode ion channels, cardiac transcription factors, T-box transcription factors, gap junction proteins, energy metabolism regulators and structural proteins. MAIN METHODS: Subjects in the present study came from a family who exhibited the autosomal dominant inheritance of PCCD. The primary proband had syncope and an electrocardiogram typical for PCCD, which started in the left bundle branch block, and passed to the atrioventricular block. The patient received a permanent pacemaker in 2013. Pathogenic mutations in the proband's family were identified using whole-exome sequencing and Sanger sequencing. KEY FINDINGS: The results for the family members were verified using Sanger sequencing, while the results for healthy unrelated individuals were verified using SNaPShot. All patients in the family shared two adjacent missense mutations in the preprodynorphin (PDYN) gene (c.581A > T, c.580G > C; p.D194L). SIGNIFICANCE: The PDYN double mutation c.581A > T and c.580G > C (p.D194L) may be linked to the onset of familial PCCD. The effects of these mutations on electrophysiology require further investigation.


Assuntos
Doença do Sistema de Condução Cardíaco/genética , Dinorfinas/genética , Exoma/genética , Mutação de Sentido Incorreto/genética , Precursores de Proteínas/genética , Adulto , Doença do Sistema de Condução Cardíaco/fisiopatologia , Eletrocardiografia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Linhagem , Reação em Cadeia da Polimerase , Análise de Sequência de DNA
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