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1.
Gene ; 761: 145027, 2020 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-32758583

RESUMO

OBJECTIVES: Oliver-McFarlane syndrome (OMCS) is an autosomal recessive inherited disease resulting from PNPLA6 mutations that results in intellectual impairment and profound short stature. To obtain a better understanding of the genotype-phenotype correlations for PNPLA6-related disorders, we reported the 14th OMCS case and summarized all the reported cases of OMCS. METHODS: We collected clinical biochemical and data and brain MRI data and used whole-exon gene detection and analysis tools to evaluate the pathogenicity of the variants, including PolyPhen-2 and Mutation Taster, and we also generated three-dimensional protein structures and visualized the effects of altered residues with I-TASSER and PyMOL Viewer software. RESULTS: The patient presented with trichomegaly and multiple pituitary hormone deficiencies. Brain MRI showed small pituitary and bilateral paraventricular leukomalacia. Novel variants (c.1491G > T and c.3367G > A) in the PNPLA6 gene were detected in the proband and verified by direct sequencing. Amino acid residues of Gln497 and Gly1123 are predicted to be damaging and destroy the three-dimensional protein structures of the protein. In follow-up, this patient could neither walk nor hold his head erect and had not spoken one word at the age of one year and ten months. Moreover, there is no obvious hot spot mutation in any of the reported allelic variants. Interestingly, the majority of mutations are located in the phospholipid esterase domain, which is responsible for esterase activity. CONCLUSIONS: We identified two novel variants of the PNPLA6 gene in an OMCS patient, which will help to better understand the function of PNPLA6 and genotype-phenotype correlations for PNPLA6-related disorders.


Assuntos
Blefaroptose/diagnóstico , Blefaroptose/genética , Nanismo/diagnóstico , Nanismo/genética , Hipertricose/diagnóstico , Hipertricose/genética , Deficiência Intelectual/diagnóstico , Deficiência Intelectual/genética , Fosfolipases/genética , Retinite Pigmentosa/diagnóstico , Retinite Pigmentosa/genética , Alelos , China , Deficiências do Desenvolvimento/diagnóstico , Deficiências do Desenvolvimento/genética , Frequência do Gene/genética , Estudos de Associação Genética , Genótipo , Humanos , Lactente , Masculino , Mutação , Fenótipo , Fosfolipases/metabolismo
2.
Anticancer Res ; 40(7): 3707-3712, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32620609

RESUMO

BACKGROUND/AIM: Oral cancer incidence is highest worldwide in Taiwan, and practical markers for personalized therapeutic strategies such as immunotherapies, is lacking. Interleukin-12 (IL12) is a cytokine that is reported to exhibit potent tumoricidal effects, however, its genotypic contribution to oral cancer is still largely unknown. We aimed to examine whether IL12A rs568408 and rs2243115 genotypes are associated with oral cancer risk in Taiwan. MATERIALS AND METHODS: Genotypic characteristics of IL12A were determined among 958 oral cancer cases and age- and gender-matched individuals via typical polymerase chain reaction-restriction fragment length polymorphism methodology. RESULTS: The variant genotypes of IL12A rs568408 and rs2243115 were not found to be significantly associated with elevated oral cancer risk (all p>0.05). Moreover, there was no interaction between IL12A genotypes and personal smoking, alcohol drinking and betel quid chewing behaviors (all p>0.05). CONCLUSION: IL12A rs568408 and rs2243115 genotypes may not serve as good predictors for oral cancer risk.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Predisposição Genética para Doença/genética , Subunidade p35 da Interleucina-12/genética , Neoplasias Bucais/genética , Polimorfismo de Nucleotídeo Único/genética , Consumo de Bebidas Alcoólicas/efeitos adversos , Consumo de Bebidas Alcoólicas/genética , Estudos de Casos e Controles , Feminino , Frequência do Gene/genética , Estudos de Associação Genética/métodos , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Fragmento de Restrição/genética , Fatores de Risco , Fumar/efeitos adversos , Fumar/genética , Taiwan
3.
PLoS One ; 15(7): e0236421, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32716958

RESUMO

BACKGROUND: NOD2 variants are the strongest genetic predictors for susceptibility to Crohn's disease (CD). However, the clinical value of NOD2 on an individual patient level remains controversial. We aimed to define the predictive power of the major NOD2 mutations regarding complicated CD in a large single center cohort. METHODS: 1076 CD patients were prospectively genotyped for the three common CD-associated NOD2 mutations rs2066844, rs2066845, and rs2066847, followed by detailed genotype-phenotype analyses. RESULTS: Overall, 434 CD patients (40.3%) carried at least one of the three main NOD2 mutations. A significantly higher minor allele frequency (15.6%) of the NOD2 frameshift mutation p.Leu1007fsX1008 (rs2066847) was seen in patients with aggressive disease compared to 8.2% in patients with mild disease (p = 2.6 x 10-5). Moreover, a total of 54 CD patients (5.0%) were homozygous for this NOD2 frameshift mutation. 100% of these patients had ileal disease compared to 82% of NOD2 wild-type carriers (p<0.0001). In homozygous carriers of the NOD2 frameshift mutation, 87% presented with ileal stenosis, 68.5% had fistulas, and 72.2% required CD-related surgery despite immunosuppressive therapy in 87% of these patients. All homozygous carriers of the 1007fs mutation who were active smokers had ileal stenosis and required CD-related surgery. CONCLUSION: Homozygosity for Leu1007fsX1008 is an excellent biomarker for predicting complicated CD on an individual patient level. Active smoking and homozygosity for this mutation is associated with a 100% risk for developing ileal stenosis requiring CD-related surgery. In these patients, smoking cessation and early initiation of immunosuppressive strategies may be beneficial.


Assuntos
Doença de Crohn/genética , Doença de Crohn/patologia , Doenças do Íleo/cirurgia , Obstrução Intestinal/etiologia , Obstrução Intestinal/cirurgia , Mutação/genética , Proteína Adaptadora de Sinalização NOD2/genética , Fumar/efeitos adversos , Adolescente , Adulto , Estudos de Coortes , Doença de Crohn/complicações , Feminino , Dosagem de Genes , Frequência do Gene/genética , Marcadores Genéticos , Predisposição Genética para Doença , Heterozigoto , Homozigoto , Humanos , Doenças do Íleo/etiologia , Modelos Logísticos , Masculino , Fenótipo , Fatores de Risco , Índice de Gravidade de Doença , Adulto Jovem
4.
PLoS One ; 15(7): e0236343, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32730349

RESUMO

Using pooled DNA genotyping to estimate the proportional contributions from multiple families in a pooled sample is of particular interest for selective breeding in aquaculture. We compared different pooled libraries with separate 2b-RAD sequencing of Litopenaeus vannamei individuals to assess the effect of different population structures (different numbers of individuals and families) on pooled DNA sequencing, the accuracy of parent sequencing of the DNA pools and the effect of SNP numbers on pooled DNA sequencing. We demonstrated that small pooled DNA genotyping of up to 53 individuals by 2b-RAD sequencing could provide a highly accurate assessment of population allele frequencies. The accuracy increased as the number of individuals and families increased. The allele frequencies of the parents from each pool were highly correlated with those of the pools or the corresponding individuals in the pool. We chose 500-28,000 SNPs to test the effect of SNP number on the accuracy of pooled sequencing, and no linear relationship was found between them. When the SNP number was fixed, increasing the number of individuals in the mixed pool resulted in higher accuracy of each pooled genotyping. Our data confirmed that pooled DNA genotyping by 2b-RAD sequencing could achieve higher accuracy than that of individual-based genotyping. The results will provide important information for shrimp breeding programs.


Assuntos
DNA/genética , Técnicas de Genotipagem , Sequenciamento de Nucleotídeos em Larga Escala , Penaeidae/genética , Mapeamento por Restrição , Alelos , Animais , Frequência do Gene/genética , Genética Populacional , Polimorfismo de Nucleotídeo Único/genética , Reprodutibilidade dos Testes
5.
Proc Natl Acad Sci U S A ; 117(29): 17135-17141, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32631983

RESUMO

For social animals, the genotypes of group members affect the social environment, and thus individual behavior, often indirectly. We used genome-wide association studies (GWAS) to determine the influence of individual vs. group genotypes on aggression in honey bees. Aggression in honey bees arises from the coordinated actions of colony members, primarily nonreproductive "soldier" bees, and thus, experiences evolutionary selection at the colony level. Here, we show that individual behavior is influenced by colony environment, which in turn, is shaped by allele frequency within colonies. Using a population with a range of aggression, we sequenced individual whole genomes and looked for genotype-behavior associations within colonies in a common environment. There were no significant correlations between individual aggression and specific alleles. By contrast, we found strong correlations between colony aggression and the frequencies of specific alleles within colonies, despite a small number of colonies. Associations at the colony level were highly significant and were very similar among both soldiers and foragers, but they covaried with one another. One strongly significant association peak, containing an ortholog of the Drosophila sensory gene dpr4 on linkage group (chromosome) 7, showed strong signals of both selection and admixture during the evolution of gentleness in a honey bee population. We thus found links between colony genetics and group behavior and also, molecular evidence for group-level selection, acting at the colony level. We conclude that group genetics dominates individual genetics in determining the fatal decision of honey bees to sting.


Assuntos
Agressão , Abelhas/genética , Frequência do Gene/genética , Genoma de Inseto/genética , Animais , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único/genética , Comportamento Social
6.
Gene ; 758: 144944, 2020 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-32628976

RESUMO

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). The relentless spread and pathogenicity of the virus have become a global public health emergency. One of the striking features of this pandemic is the pronounced impact on specific regions and ethnic groups. In particular, compared with East Asia, where the virus first emerged, SARS-CoV-2 has caused high rates of morbidity and mortality in Europe. This has not been experienced in past global viral infections, such as influenza, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and is unique to SARS-CoV-2. For this reason, we investigated the involvement of genetic factors associated with SARS-CoV-2 infection with a focus on angiotensin-converting enzyme (ACE)-related genes, because ACE2 is a receptor for SARS-CoV-2. We found that the ACE1 II genotype frequency in a population was significantly negatively correlated with the number of SARS-CoV-2 cases. Similarly, the ACE1 II genotype was negatively correlated with the number of deaths due to SARS-CoV-2 infection. These data suggest that the ACE1 II genotype may influence the prevalence and clinical outcome of COVID-19 and serve as a predictive marker for COVID-19 risk and severity.


Assuntos
Infecções por Coronavirus/mortalidade , Peptidil Dipeptidase A/genética , Pneumonia Viral/mortalidade , Ásia/epidemiologia , Ásia/etnologia , Betacoronavirus/metabolismo , Infecções por Coronavirus/epidemiologia , Europa (Continente)/epidemiologia , Europa (Continente)/etnologia , Frequência do Gene/genética , Genótipo , Humanos , Pandemias , Pneumonia Viral/epidemiologia , Polimorfismo de Nucleotídeo Único/genética , Risco , Fatores de Risco , Índice de Gravidade de Doença , Resultado do Tratamento
7.
Am J Hum Genet ; 107(2): 234-250, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32668217

RESUMO

Phenylketonuria (PKU), caused by variants in the phenylalanine hydroxylase (PAH) gene, is the most common autosomal-recessive Mendelian phenotype of amino acid metabolism. We estimated that globally 0.45 million individuals have PKU, with global prevalence 1:23,930 live births (range 1:4,500 [Italy]-1:125,000 [Japan]). Comparing genotypes and metabolic phenotypes from 16,092 affected subjects revealed differences in disease severity in 51 countries from 17 world regions, with the global phenotype distribution of 62% classic PKU, 22% mild PKU, and 16% mild hyperphenylalaninemia. A gradient in genotype and phenotype distribution exists across Europe, from classic PKU in the east to mild PKU in the southwest and mild hyperphenylalaninemia in the south. The c.1241A>G (p.Tyr414Cys)-associated genotype can be traced from Northern to Western Europe, from Sweden via Norway, to Denmark, to the Netherlands. The frequency of classic PKU increases from Europe (56%) via Middle East (71%) to Australia (80%). Of 758 PAH variants, c.1222C>T (p.Arg408Trp) (22.2%), c.1066-11G>A (IVS10-11G>A) (6.4%), and c.782G>A (p.Arg261Gln) (5.5%) were most common and responsible for two prevalent genotypes: p.[Arg408Trp];[Arg408Trp] (11.4%) and c.[1066-11G>A];[1066-11G>A] (2.6%). Most genotypes (73%) were compound heterozygous, 27% were homozygous, and 55% of 3,659 different genotypes occurred in only a single individual. PAH variants were scored using an allelic phenotype value and correlated with pre-treatment blood phenylalanine concentrations (n = 6,115) and tetrahydrobiopterin loading test results (n = 4,381), enabling prediction of both a genotype-based phenotype (88%) and tetrahydrobiopterin responsiveness (83%). This study shows that large genotype databases enable accurate phenotype prediction, allowing appropriate targeting of therapies to optimize clinical outcome.


Assuntos
Predisposição Genética para Doença/genética , Fenilcetonúrias/epidemiologia , Fenilcetonúrias/genética , Alelos , Biopterina/análogos & derivados , Biopterina/genética , Europa (Continente) , Frequência do Gene/genética , Estudos de Associação Genética/métodos , Genótipo , Homozigoto , Humanos , Mutação/genética , Fenótipo , Fenilalanina/sangue , Fenilalanina Hidroxilase/genética , Fenilcetonúrias/sangue
8.
Gene ; 758: 144957, 2020 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-32683081

RESUMO

Leptin receptor (LEPR) gene play a pivotal role in the regulation of fat deposition and energy homeostasis. This study investigated the presence and frequency of polymorphisms of bovine LEPR gene and determine whether the polymorphisms are associated with the fat deposition in two Chinese beef cattle breeds. Quantitative real-time polymerase chain reactions identified that the expression of LEPR gene was highest in the liver and subcutaneous fat. Four single nucleotide polymorphisms (SNPs) were identified including g.24169C > T, g.24256T > A, g.24267 G > C and g.24413T > A. A greater backfat thickness was associated with the AA genotype of g.24256T > A compared to the TT genotype. A greater intramuscular fat content was associated with the GG genotype of g.24267 G > C compared to the CC genotype. Both g.24169C > T and g.24413T > A were not correlated with fat deposition. These results indicated that the SNP g.24256T > A and g.24267 G > C of LEPR gene may be useful markers for genetic improvement of fat deposition in Chinese beef cattle breeds.


Assuntos
Adiposidade/genética , Distribuição da Gordura Corporal , Receptores para Leptina/genética , Receptores para Leptina/metabolismo , Animais , Bovinos , Frequência do Gene/genética , Estudos de Associação Genética , Genótipo , Leptina/metabolismo , Polimorfismo de Nucleotídeo Único/genética
9.
PLoS Biol ; 18(7): e3000745, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32667908

RESUMO

Mutations create genetic variation for other evolutionary forces to operate on and cause numerous genetic diseases. Nevertheless, how de novo mutations arise remains poorly understood. Progress in the area is hindered by the fact that error rates of conventional sequencing technologies (1 in 100 or 1,000 base pairs) are several orders of magnitude higher than de novo mutation rates (1 in 10,000,000 or 100,000,000 base pairs per generation). Moreover, previous analyses of germline de novo mutations examined pedigrees (and not germ cells) and thus were likely affected by selection. Here, we applied highly accurate duplex sequencing to detect low-frequency, de novo mutations in mitochondrial DNA (mtDNA) directly from oocytes and from somatic tissues (brain and muscle) of 36 mice from two independent pedigrees. We found mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo. Mutation frequencies and patterns differed between germline and somatic tissues and among mtDNA regions, suggestive of distinct mutagenesis mechanisms. Additionally, we discovered a more pronounced genetic drift of mitochondrial genetic variants in the germline of older versus younger mice, arguing for mtDNA turnover during oocyte meiotic arrest. Our study deciphered for the first time the intricacies of germline de novo mutagenesis using duplex sequencing directly in oocytes, which provided unprecedented resolution and minimized selection effects present in pedigree studies. Moreover, our work provides important information about the origins and accumulation of mutations with aging/maturation and has implications for delayed reproduction in modern human societies. Furthermore, the duplex sequencing method we optimized for single cells opens avenues for investigating low-frequency mutations in other studies.


Assuntos
Envelhecimento/genética , Mamíferos/genética , Mitocôndrias/genética , Mutação/genética , Oócitos/metabolismo , Especificidade de Órgãos/genética , Animais , Análise Mutacional de DNA , DNA Mitocondrial/genética , Feminino , Frequência do Gene/genética , Deriva Genética , Células Germinativas/metabolismo , Padrões de Herança/genética , Modelos Logísticos , Masculino , Camundongos , Modelos Genéticos , Taxa de Mutação , Nucleotídeos/genética , Linhagem
10.
PLoS Biol ; 18(6): e3000742, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32511234

RESUMO

The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?


Assuntos
DNA Antigo , Lactase/genética , Seleção Genética , Animais , Ásia , Grupos Étnicos/genética , Europa (Continente) , Fermentação , Frequência do Gene/genética , Genótipo , Humanos , Leite , Fatores de Tempo
11.
PLoS One ; 15(6): e0234328, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32579617

RESUMO

FABP4 is a candidate gene for carcass and meat quality traits in livestock and poultry. However, the effects of FABP4 have not been examined in the Yanbian yellow cattle, an economically important local cattle breed in China. In this study, we characterized single nucleotide polymorphisms (SNPs) in FABP4 in this cattle breed and their associations with meat quality traits. Six SNPs (referred to as SNP1-6) were identified in FABP4 by direct sequencing and polymerase chain reaction-restriction fragment length polymorphism. The six SNPs were significantly correlated with meat quality traits. In particular, the GG and GA genotypes of SNP1 were significantly associated with water and fat contents and GG and AA genotypes of SNP1 were significantly associated with protein contents (P < 0.05). The fat content and marbling in heterozygous individuals at SNP2-6 were significantly higher than those in wild-type or mutant individuals (P < 0.05), while protein content was significantly higher in wild-type and mutant individuals than in heterozygous individuals (P < 0.05). A gene expression analysis indicated that the lipid metabolism-related genes FABP4, PPARγ, ANGPTL4, and LPL show similar expression patterns with respect to FABP4 genotypes, with the highest levels in wild-type individuals and the lowest levels in mutants. In conclusion, FABP4 SNPs can be used for marker-assisted selection in Yanbian yellow cattle breeding.


Assuntos
Bovinos/genética , Proteínas de Ligação a Ácido Graxo/genética , Metabolismo dos Lipídeos/genética , Animais , China , Feminino , Qualidade dos Alimentos , Expressão Gênica/genética , Frequência do Gene/genética , Estudos de Associação Genética/métodos , Genótipo , Masculino , Mutação/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Carne Vermelha/análise , Análise de Sequência de DNA/métodos
12.
Am J Hum Genet ; 107(2): 222-233, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32589924

RESUMO

With increasing biobanking efforts connecting electronic health records and national registries to germline genetics, the time-to-event data analysis has attracted increasing attention in the genetics studies of human diseases. In time-to-event data analysis, the Cox proportional hazards (PH) regression model is one of the most used approaches. However, existing methods and tools are not scalable when analyzing a large biobank with hundreds of thousands of samples and endpoints, and they are not accurate when testing low-frequency and rare variants. Here, we propose a scalable and accurate method, SPACox (a saddlepoint approximation implementation based on the Cox PH regression model), that is applicable for genome-wide scale time-to-event data analysis. SPACox requires fitting a Cox PH regression model only once across the genome-wide analysis and then uses a saddlepoint approximation (SPA) to calibrate the test statistics. Simulation studies show that SPACox is 76-252 times faster than other existing alternatives, such as gwasurvivr, 185-511 times faster than the standard Wald test, and more than 6,000 times faster than the Firth correction and can control type I error rates at the genome-wide significance level regardless of minor allele frequencies. Through the analysis of UK Biobank inpatient data of 282,871 white British European ancestry samples, we show that SPACox can efficiently analyze large sample sizes and accurately control type I error rates. We identified 611 loci associated with time-to-event phenotypes of 12 common diseases, of which 38 loci would be missed within a logistic regression framework with a binary phenotype defined as event occurrence status during the follow-up period.


Assuntos
Estudo de Associação Genômica Ampla/métodos , Bancos de Espécimes Biológicos , Estudos de Casos e Controles , Análise de Dados , Grupo com Ancestrais do Continente Europeu/genética , Frequência do Gene/genética , Humanos , Modelos Logísticos , Fenótipo , Modelos de Riscos Proporcionais , Tamanho da Amostra , Reino Unido
13.
BMC Bioinformatics ; 21(1): 227, 2020 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-32498674

RESUMO

BACKGROUND: Mutations arise in the human genome in two major settings: the germline and the soma. These settings involve different inheritance patterns, time scales, chromatin structures, and environmental exposures, all of which impact the resulting distribution of substitutions. Nonetheless, many of the same single nucleotide variants (SNVs) are shared between germline and somatic mutation databases, such as between the gnomAD database of 120,000 germline exomes and the TCGA database of 10,000 somatic exomes. Here, we sought to explain this overlap. RESULTS: After strict filtering to exclude common germline polymorphisms and sites with poor coverage or mappability, we found 336,987 variants shared between the somatic and germline databases. A uniform statistical model explains 34% of these shared variants; a model that incorporates the varying mutation rates of the basic mutation types explains another 50% of shared variants; and a model that includes extended nucleotide contexts (e.g. surrounding 3 bases on either side) explains an additional 4% of shared variants. Analysis of read depth finds mixed evidence that up to 4% of the shared variants may represent germline variants leaked into somatic call sets. 9% of the shared variants are not explained by any model. Sequencing errors and convergent evolution did not account for these. We surveyed other factors as well: Cancers driven by endogenous mutational processes share a greater fraction of variants with the germline, and recently derived germline variants were more likely to be somatically shared than were ancient germline ones. CONCLUSIONS: Overall, we find that shared variants largely represent bona fide biological occurrences of the same variant in the germline and somatic setting and arise primarily because DNA has some of the same basic chemical vulnerabilities in either setting. Moreover, we find mixed evidence that somatic call-sets leak appreciable numbers of germline variants, which is relevant to genomic privacy regulations. In future studies, the similar chemical vulnerability of DNA between the somatic and germline settings might be used to help identify disease-related genes by guiding the development of background-mutation models that are informed by both somatic and germline patterns of variation.


Assuntos
Bases de Dados Genéticas , Mutação em Linhagem Germinativa/genética , Alelos , Evolução Biológica , Epigênese Genética , Frequência do Gene/genética , Humanos , Taxa de Mutação , Neoplasias/genética , Nucleotídeos/genética , Filogenia , Análise de Sequência de DNA
14.
Medicine (Baltimore) ; 99(25): e20756, 2020 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-32569219

RESUMO

The prognostic value of 3 types (total, bioavailable, and free) of 25-hydroxy vitamin D [25(OH)D] and vitamin D binding protein (VDBP) in patients with sepsis is unknown. The aim of this study was to evaluate the association of levels of those 3 types of 25(OH) D and VDBP with 30-day mortality in patients with sepsis. From March to December 2018, patients diagnosed with sepsis and admitted to the medical intensive care unit were enrolled, prospectively. We measured total 25(OH)D and VDBP levels, performed GC genotyping for the polymorphisms rs4588 and rs7041, and calculated bioavailable and free 25(OH)D levels. Total, bioavailable, and free 25(OH)D levels did not differ in 30-days nonsurvivors and survivors. Serum VDBP level was significantly higher in survivors than nonsurvivors (138.6 ug/mL vs 108.2 ug/mL, P = .023) and was associated with 30-day mortality in univariate but not multivariate analysis. VDBP polymorphisms and allele frequencies were not statistically different between the groups. Serum VDBP level was significantly higher in survivors than nonsurvivors over 30-days mortality in septic patients. However, 3 types (total, bioavailable, and free) of 25(OH)D levels did not differ between the survivors and nonsurvivors group.


Assuntos
Sepse/mortalidade , Proteína de Ligação a Vitamina D/sangue , Vitamina D/sangue , Idoso , Idoso de 80 Anos ou mais , Disponibilidade Biológica , Feminino , Frequência do Gene/genética , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Estudos Prospectivos , Sepse/sangue , Sepse/complicações , Sepse/genética , Vitamina D/metabolismo , Deficiência de Vitamina D/complicações , Deficiência de Vitamina D/mortalidade , Proteína de Ligação a Vitamina D/genética , Proteína de Ligação a Vitamina D/metabolismo
15.
PLoS One ; 15(6): e0234547, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32555714

RESUMO

Estimating the prevalence of cardiovascular diseases (CVDs) and risk factors among the Roma population, the largest minority in Europe, and investigating the role of genetic or environmental/behavioral risk factors in CVD development are important issues in countries where they are significant minority. This study was designed to estimate the genetic susceptibility of the Hungarian Roma (HR) population to essential hypertension (EH) and compare it to that of the general (HG) population. Twenty EH associated SNPs (in AGT, FMO3, MTHFR-NPPB, NPPA, NPPA-AS1, AGTR1, ADD1, NPR3-C5orf23, NOS3, CACNB2, PLCE1, ATP2B1, GNB3, CYP1A1-ULK3, UMOD and GNAS-EDN3) were genotyped using DNA samples obtained from HR (N = 1176) and HG population (N = 1178) subjects assembled by cross-sectional studies. Allele frequencies and genetic risk scores (unweighted and weighted genetic risk scores (GRS and wGRS, respectively) were calculated for the study groups and compared to examine the joint effects of the SNPs. The susceptibility alleles were more frequent in the HG population, and both GRS and wGRS were found to be higher in the HG population than in the HR population (GRS: 18.98 ± 3.05 vs. 18.25 ± 2.97, p<0.001; wGRS: 1.4 [IQR: 0.93-1.89] vs. 1.52 [IQR: 0.99-2.00], p<0.01). Twenty-seven percent of subjects in the HR population were in the bottom fifth (GRS ≤ 16) of the risk allele count compared with 21% of those in the HG population. Thirteen percent of people in the HR group were in the top fifth (GRS ≥ 22) of the GRS compared with 21% of those in the HG population (p<0.001), i.e., the distribution of GRS was found to be left-shifted in the HR population compared to the HG population. The Roma population seems to be genetically less susceptible to EH than the general one. These results support preventive efforts to lower the risk of developing hypertension by encouraging a healthy lifestyle.


Assuntos
Estudos de Associação Genética , Predisposição Genética para Doença , Hipertensão/genética , Adulto , Alelos , Biomarcadores/sangue , Feminino , Frequência do Gene/genética , Genótipo , Humanos , Hungria/epidemiologia , Hipertensão/sangue , Hipertensão/patologia , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Fatores de Risco , Roma/genética
16.
Genet Sel Evol ; 52(1): 26, 2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-32414320

RESUMO

BACKGROUND: Estimating the genetic component of a complex phenotype is a complicated problem, mainly because there are many allele effects to estimate from a limited number of phenotypes. In spite of this difficulty, linear methods with variable selection have been able to give good predictions of additive effects of individuals. However, prediction of non-additive genetic effects is challenging with the usual prediction methods. In machine learning, non-additive relations between inputs can be modeled with neural networks. We developed a novel method (NetSparse) that uses Bayesian neural networks with variable selection for the prediction of genotypic values of individuals, including non-additive genetic effects. RESULTS: We simulated several populations with different phenotypic models and compared NetSparse to genomic best linear unbiased prediction (GBLUP), BayesB, their dominance variants, and an additive by additive method. We found that when the number of QTL was relatively small (10 or 100), NetSparse had 2 to 28 percentage points higher accuracy than the reference methods. For scenarios that included dominance or epistatic effects, NetSparse had 0.0 to 3.9 percentage points higher accuracy for predicting phenotypes than the reference methods, except in scenarios with extreme overdominance, for which reference methods that explicitly model dominance had 6 percentage points higher accuracy than NetSparse. CONCLUSIONS: Bayesian neural networks with variable selection are promising for prediction of the genetic component of complex traits in animal breeding, and their performance is robust across different genetic models. However, their large computational costs can hinder their use in practice.


Assuntos
Previsões/métodos , Herança Multifatorial/genética , Fenótipo , Algoritmos , Alelos , Animais , Teorema de Bayes , Frequência do Gene/genética , Genética Populacional/métodos , Genômica/métodos , Genótipo , Humanos , Modelos Genéticos , Redes Neurais de Computação , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Seleção Genética/genética
17.
Genet Sel Evol ; 52(1): 27, 2020 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-32460767

RESUMO

BACKGROUND: Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. RESULTS: We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N'Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. CONCLUSIONS: Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.


Assuntos
Bovinos/genética , DNA Helicases/genética , Alelos , Animais , Sequência de Bases/genética , Cruzamento , Variações do Número de Cópias de DNA/genética , Dano ao DNA/genética , DNA Helicases/metabolismo , Domesticação , Feminino , Frequência do Gene/genética , Genótipo , Masculino , Mutação de Sentido Incorreto/genética , Fases de Leitura Aberta/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Regiões Promotoras Genéticas/genética , Seleção Genética/genética , Sequenciamento Completo do Genoma
18.
Gene ; 752: 144760, 2020 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-32416252

RESUMO

BACKGROUND: PCOS is a common endocrine disorder that is characterized by hyperandrogenism and chronic anovulation and is the leading cause of female infertility. It is a heterogeneous disorder with the involvement of multiple gene and environmental interactions. This study identified variants that are known to confer susceptibility identified by Genome wide association studies (GWAS) in other ethnicities and replicated the same in individuals with PCOS of Indian ethnicity. METHODS: Study subjects (n = 600) were recruited. Blood samples, demographic and clinical details were collected after obtaining informed consent. Fifteen variants were selected from GWA studies from other ethnicities and genotyped in half of the recruited samples (n = 300) using MassARRAYiPLEX™. Replication of significant variants generated from preliminary data was carried out by PCR and direct sequencing in remainder of the samples (n = 300). Insilco analysis for significant variants was performed using software namely CADD, GWAVA, FATHMM-MKL. Relevant statistics were used to ascertain significance. RESULTS: The mean age of patients and controls was 24.26 ± 3.22 and 30.19 ± 11.21 years respectively. Of the 15 variants, 3 variants (rs13405728 in LHCGR; rs13429458 in THADA and rs2209972 IDE genes) were found to be associated with PCOS. The association was successfully replicated in an independent cohort. Insilico analysis categorized two variants (rs13429458-THADA and rs2209972-IDE genes) as deleterious. CONCLUSION: We demonstrate the association of variants in genes namely LHCGR, THADA and IDE with an increased risk of PCOS. Genotyping for these variants aids in identifying at-risk individuals which is crucial as appropriate early interventions may benefit the patient.


Assuntos
Insulisina/genética , Proteínas de Neoplasias/genética , Síndrome do Ovário Policístico/genética , Receptores do LH/genética , Adulto , Alelos , Grupo com Ancestrais do Continente Asiático/genética , Estudos de Casos e Controles , Estudos de Coortes , Grupos Étnicos/genética , Grupo com Ancestrais do Continente Europeu/genética , Feminino , Frequência do Gene/genética , Predisposição Genética para Doença/genética , Testes Genéticos , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Índia/epidemiologia , Insulisina/metabolismo , Proteínas de Neoplasias/metabolismo , Síndrome do Ovário Policístico/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Receptores do LH/metabolismo , Análise de Sequência de DNA/métodos
19.
PLoS One ; 15(5): e0233096, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32421725

RESUMO

Congenital cytomegalovirus (cCMV) infection is the most common intrauterine infection. A non-specific immune response is the first line of host defense mechanism against human cytomegalovirus (HCMV). There is limited data on associations between Single Nucleotide Polymorphisms (SNPs) in genes involving innate immunity and the risk and clinical manifestation of cCMV infection. The aim of the study was to investigate association between selected SNPs in genes encoding cytokines and cytokine receptors, and predisposition to cCMV infection including symptomatic course of disease and symptoms. A panel of eight SNPs: IL1B rs16944, IL12B rs3212227, IL28B rs12979860, CCL2 rs1024611, DC-SIGN rs735240, TLR2 rs5743708, TLR4 rs4986791, TLR9 rs352140 was analyzed in 233 infants (92 cCMV-infected and 141 healthy controls). Associations between genotyped SNPs and predisposition to cCMV infection and symptoms were analyzed. The association analysis was performed using SNPStats software. No statistically significant association was found between any genotyped SNPs and predisposition to cCMV infection and symptomatic course of disease. In relation to particular symptoms, polymorphism of IL12B rs3212227 was linked to decreased risk of prematurity (OR = 0.37;95%CI,0.14-0.98;p = 0.025), while polymorphism of IL1B rs16944 was linked to reduced risk of splenomegaly (OR = 0.36;95%CI,0.14-0.98; p = 0.034) in infants with cCMV infection. An increased risk of thrombocytopenia was associated with IL28B rs12979860 polymorphism (OR = 2.55;95%CI,1.03-6.32;p = 0.042), while hepatitis was associated with SNP of TLR4rs4986791 (OR = 7.80;95%CI,1.49-40,81; p = 0.024). This is the first study to demonstrate four new associations between SNPs in selected genes (IL1B, IL12B, IL28B, TLR4) and particular symptoms in cCMV disease. Further studies on the role of SNPs in the pathogenesis of cCMV infection and incorporation of selected SNPs in the clinical practice might be considered in the future.


Assuntos
Infecções por Citomegalovirus/genética , Interferons/genética , Interleucina-12/genética , Interleucina-1beta/genética , Polimorfismo de Nucleotídeo Único/genética , Receptor 4 Toll-Like/genética , Adulto , Infecções por Citomegalovirus/virologia , Feminino , Frequência do Gene/genética , Genótipo , Técnicas de Genotipagem , Humanos , Masculino , Trombocitopenia/genética , Trombocitopenia/virologia
20.
PLoS One ; 15(5): e0232174, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32380517

RESUMO

BACKGROUND: Previous studies have reported on several genetic variants related to breast cancer, but a substantial proportion of mutation loci have not yet been identified. In the current study, we aimed to evaluate the association between single nucleotide polymorphisms (SNPs) of interleukin-10 (IL-10) and susceptibility to breast cancer in Shaanxi Han women in China. METHODS: Six SNPs were genotyped in 530 breast cancer patients and 628 healthy women from the First Affiliated Hospital of Xi'an Jiaotong University Hospital. Odds ratios and 95% confidence intervals were calculated by unconditional logistic regression analysis to assess the association between breast cancer risk and polymorphisms of six loci. RESULTS: Two SNPs, rs3024490 and rs1800871, were found to be significantly different between breast cancer patients and healthy women. These SNPs also increased the risk of breast cancer in co-dominant and dominant models. Moreover, another SNP, rs1554286, was significantly associated with an increased risk of breast cancer in the co-dominant model. Functional assessments indicated that these three variants may influence the expression and transcription factor binding of IL-10. CONCLUSIONS: Our findings suggest that variants of IL-10 may be likelihood risk factors for the development and progression of breast cancer. Future studies should replicate this study and evaluate functional assessments in Chinese Han women and women from other regions.


Assuntos
Neoplasias da Mama/genética , Interleucina-10/genética , Adulto , Idoso , Alelos , Grupo com Ancestrais do Continente Asiático/genética , Estudos de Casos e Controles , China , Grupos Étnicos/genética , Feminino , Frequência do Gene/genética , Predisposição Genética para Doença/genética , Genótipo , Humanos , Interleucina-10/metabolismo , Pessoa de Meia-Idade , Razão de Chances , Polimorfismo de Nucleotídeo Único/genética , Fatores de Risco
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