RESUMEN
Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.
Asunto(s)
Secuenciación del Exoma , Panthera , Polimorfismo de Nucleótido Simple , Animales , Panthera/genética , Secuenciación del Exoma/métodos , Técnicas de Genotipaje/métodos , Genética de Población , Tamaño de la Muestra , Secuenciación de Nucleótidos de Alto Rendimiento , Variación Genética , Animales Salvajes/genéticaRESUMEN
Single-tube nested PCR (STnPCR) is a technique that improves nested PCR, reducing potential contamination and false-positive results, enhancing the amplification sensitivity. Despite being commonly used for the detection of microorganisms, STnPCR can be a valuable tool for bovine genotyping, encompassing essential targets as ROSA26 and TSPY, pivotal in the fields of animal reproduction, genetic improvement, and transgenic research. The objective of this study was to improve and innovate STnPCR for gene detection in cattle. We aimed to detect the ROSA26 and TSPY genes using low-concentration DNA samples, including single cells, small cell groups (one to five cells), in vitro-produced embryos, and bovine tissue samples. Moreover, we refined STnPCR for gene detection in up to single cells by conducting sensitivity testing with different concentration ratios of internal and external primers. Successful amplification of the ROSA26 and TSPY genes was achieved across all tested primer concentrations, even in single cells, with more consistent results observed at lower primer concentrations. Additionally, simultaneous gene amplification was achieved through STnPCR multiplexing, representing the first study of multiplex STnPCR in cattle. These outcomes not only confirm its effectiveness in detecting genetic markers for animal genetic improvement and transgenic elements but also pave the way for its widespread adoption in reproductive studies in bovines.
Asunto(s)
Técnicas de Genotipaje , Reacción en Cadena de la Polimerasa , Animales , Bovinos/genética , Reacción en Cadena de la Polimerasa/métodos , Técnicas de Genotipaje/métodos , Embrión de Mamíferos , Análisis de la Célula Individual/métodos , GenotipoRESUMEN
BACKGROUND: Advances in laboratory techniques for HPV diagnosis necessitate a thorough assessment of the efficiency, replicability, sensitivity, and specificity of those methods. This study aims to validate and compare HPV detection/genotyping using the Anyplex™ II HPV28 Detection assay (Seegene) assay and the Linear Array HPV Genotyping test (Roche Diagnostics) on genital samples for use in epidemiological studies. METHODS: From 6,388 penile and cervical DNA samples collected in the POP-Brazil, 1,745 were randomly selected to be included in this study. The samples were submitted to HPV detection and genotyping following the manufacturers' protocols. DNA was genotyped using the Anyplex™ II HPV28 Detection kit (Seegene), and the results were compared to those obtained using the Linear Array HPV Genotyping test (Roche Diagnostics). Concordance of HPV genotyping results was assessed by the percentage agreement and Cohen's kappa score (κ). RESULTS: The agreement between the two methodologies was deemed good for HPV detection (κ = 0.78). Notably, Anyplex™ II HPV28 demonstrated enhanced capability in detecting a broader spectrum of genotypes compared to Linear Array. CONCLUSION: Anyplex™ II HPV28 exhibited comparable results to the Linear Array assay in clinical specimens, showcasing its potential suitability for a diverse array of research applications requiring the detection and genotyping of HPV. The study supports the utility of Anyplex™ II HPV28 as an effective tool for HPV screening in epidemiological studies, emphasizing its robust performance in comparison to established diagnostic tests.
Asunto(s)
Genotipo , Técnicas de Genotipaje , Papillomaviridae , Infecciones por Papillomavirus , Humanos , Brasil/epidemiología , Infecciones por Papillomavirus/diagnóstico , Infecciones por Papillomavirus/virología , Infecciones por Papillomavirus/epidemiología , Femenino , Técnicas de Genotipaje/métodos , Masculino , Papillomaviridae/genética , Papillomaviridae/clasificación , Papillomaviridae/aislamiento & purificación , ADN Viral/genética , Adulto , Persona de Mediana Edad , Sensibilidad y Especificidad , AlphapapillomavirusRESUMEN
Proper cacao (Theobroma cacao L.) plant genotyping is mandatory for the conservation and use of the species genetic resources. A set of 15 international standard SSR markers was assumed as universal cacao genotyping system. Recently, different SNPs and SNP genotyping techniques have been exploited in cacao. However, a consensus on which to use has not been reached yet, driving the search for new approaches. To validate a new ddRADseq protocol for cacao genotyping, we compared the performances for population analysis of a dataset with 7,880 SNPs obtained from ddRADseq and the genotypic data from the aforementioned SSR set, using 158 cacao plants from productive farms and gene bank. Four genetic groups were identified with STRUCTURE and ADMIXTURE softwares using SSR and SNP data, respectively. Similarities of cacao ancestries among these groups allowed the identification of analogous pairs of groups of individuals, referred to as: G1SSR/G1SNP, G2SSR/G2SNP, G3SSR/G3SNP, G4SSR/G4SNP, whether SSRs or SNPs were used. Both marker systems identified Amelonado and Criollo as the most abundant cacao ancestries among all samples. Genetic distance matrices from both data types were significantly similar to each other according to Mantel test (p < 0.0001). PCoA and UPGMA clustering mostly confirmed the identified genetic groups. AMOVA and FST pairwise comparison revealed a moderate to very large genetic differentiation among identified groups from SSR and SNP data. Genetic diversity parameters from SSR (Hobs = 0.616, Hexp = 0.524 and PIC = 0.544) were higher than that from SNP data (0.288, 0.264, 0.230). In both cases, genetic groups carrying the highest Amelonado proportion (G1SSR and G1SNP) had the lowest genetic diversity parameters among the identified groups. The high congruence among population analysis results using both systems validated the ddRADseq protocol employed for cacao SNP genotyping. These results could provide new ways for developing a universal SNP-based genotyping system very much needed for cacao genetic studies.
Asunto(s)
Cacao , Técnicas de Genotipaje , Repeticiones de Microsatélite , Polimorfismo de Nucleótido Simple , Cacao/genética , Repeticiones de Microsatélite/genética , Técnicas de Genotipaje/métodos , Genotipo , Marcadores GenéticosRESUMEN
Astyanax mexicanus is an emerging model system used to study development, evolution, and behavior of multiple cavefish populations that have repeatedly evolved from conspecific surface fish. Although surface and cavefish live and breed in the laboratory, there are no rapid methods for distinguishing between different cavefish populations. We present 2 methods for genotyping fish for a total of 16 population-specific markers using methods that are easy and inexpensive to implement in a basic molecular biology laboratory. This resource will help researchers maintain independent stocks within the laboratory and distinguish between fish from different populations.
Asunto(s)
Characidae , Animales , Characidae/genética , Marcadores Genéticos , Cuevas , Técnicas de Genotipaje/métodos , GenotipoRESUMEN
INTRODUÇÃO: A doença celíaca é uma doença autoimune de caráter inflamatório, causada pela sensibilidade ao glúten e proteínas associadas. É considerada um problema de saúde pública devido à sua prevalência, frequente associação a morbidade e surgimento de complicações graves. Apresenta-se na forma clássica e não clássica, e as manifestações clínicas variam desde diarreia crônica, vômitos, irritabilidade, anorexia, déficit de crescimento, distensão abdominal, diminuição do tecido celular subcutâneo, atrofia da musculatura glútea, podendo até gerar baixa estatura, anemia por deficiência de ferro, constipação intestinal, osteoporose, esterilidade, artralgia ou artrite e alguns tipos de epilepsia. A doença celíaca pode estar associada a fatores ambientais e genéticos, sendo que o último possui correlação com a presença dos alelos do Complexo Principal de Histocompatibilidade da Classe II que codificam os heterodímeros HLA-DQ2 e HLA-DQ8. Dentro do contexto de predisposição genética, destacam-se os parentes de primeiro grau, que possuem um risco entre 5% a 20% de desenvolver a doença. Ademais, outras doenças autoimunes podem ser listadas como fatores de risco de desenvolver, a saber: como diabetes mellitus tipo 1, tireoidite autoimune, deficiência seletiva de IgA, Síndrome de Sjögren, colestase autoimune e miocardite autoimune; síndrome de Down, síndrome de Turner e síndrome de Williams. Atualmente, o diagnóstico é feito com base nas manifestações clínicas, dosagem sorológica de anticorpos anti-transglutaminase IgA e exame anatomopatológico por biópsia. Na maioria dos casos, o diagnóstico é subnotificado devido a dificuldades inerentes aos testes disponíveis. TECNOLOGIA: : Teste de genotipagem HLA (Antígeno Leucocitário Humano - do inglês Human Leukocyte Antigen) DQ2 e HLA-DQ8. PERGUNTA DE PESQUISA: Qual a acurácia diagnóstica dos exames de genotipagem HLA-DQ2 e HLA-DQ8 para o diagnóstico de doença celíaca em pacientes com fatores de risco para esta condição? EVIDÊNCIAS CIENTÍFICAS: A revisão sistematizada recuperou 3.333 registros dos quais 108 foram selecionados por revisores independentes para leitura completa dos textos e cinco estudos foram incluídos. Dos estudos incluídos ao final da seleção, três apresentavam delineamento transversal e duas coortes prospectivas. A partir desses cinco estudos, foi possível avaliar os desfechos primários (sensibilidade e especificidade) e os desfechos secundários (valor preditivo positivo, valor preditivo negativo, acurácia, razão de verossimilhança positiva e razão de verossimilhança negativa) comparando a genotipagem de HLA-DQ2, HLA-DQ8 e/ou HLA-DQ2:DQ8 com biópsia e teste sorológico de anticorpos anti-transglutaminase IgA. O risco de viés individual de cada estudo foi avaliado utilizando a ferramenta QUADAS-2, sendo que os cincos estudos incluídos apresentaram alto risco de viés com relação ao critério de seleção e à interpretação do teste index. Foi conduzida a análise de acurácia diagnóstica comparando biópsia versus HLA-DQ2 e/ou DQ8 e IgA e o resultado da meta-análise genotipagem do HLA-DQ2/DQ8 versus IgA mostrou-se com alta sensibilidade e baixa especificidade. Por fim, foi mensurada a qualidade da evidência utilizando a metodologia GRADE que, no geral, mostrou uma qualidade baixa e muito baixa. AVALIAÇÃO ECONÔMICA (AE): A análise de custo-efetividade, para anos de vida ajustados pela qualidade, demonstrou que, ao comparar com o exame diagnóstico atualmente disponíveis no SUS (tTG-IgA associado a biopsia), o HLA DQ2/8 apresenta maior custo e menor efetividade. Desta forma, considerando o contexto do SUS, a adição do HLA DQ2/8 não irá promover melhora da qualidade de vida destes pacientes, assim como não será reduzido nenhum custo além do atualmente disponível. ANÁLISE DE IMPACTO ORÇAMENTÁRIO (AIO): Foi realizada análise para estimar o impacto orçamentário com a incorporação do teste de genotipagem HLA-DQ2 e DQ8, comparado a biópsia duodenal ou a testagem de tTG-IgA. Foi adotado o horizonte temporal de cinco anos (2023 a 2027), com estimativas de impacto orçamentário ano a ano. Considerando o cenário 1 biópsia + HLA, o impacto orçamentário incremental acumulado em cinco anos seria de cerca de 713 milhões de reais. Já no cenário 2 ttg-IgA + HLA, com market share de 30%, o impacto orçamentário acumulado em cinco anos seria de 818 milhões de reais. No cenário 3 ttg-IgA + HLA + Biópsia, com o market share de 30%, o impacto orçamentário em cinco anos seria de 677 milhões de reais. Por fim, com o cenário 4 ttg-IgA + HLA + Biópsia considerando a população que relata ter reações adversas ao glúten, o impacto orçamentário acumulado em cinco anos seria de sete bilhões de reais. A análise de sensibilidade revelou que o custo do teste HLA-DQ2/DQ8 é a variável com maior potencial de afetar a estimativa de impacto orçamentário. CONSIDERAÇÕES FINAIS: A qualidade da evidência da presente revisão sistemática foi considerada baixa e os estudos incluídos apresentaram alto risco de viés em vários domínios do QUADAS-2. As análises mostraram que a genotipagem do HLA-DQ2 e/ou DQ8 apresentou alta sensibilidade e baixa especificidade, sendo capaz de identificar os indivíduos verdadeiramente positivos, sugerindo a aplicabilidade do teste como complementar ao diagnóstico da doença celíaca. A razão de custo-efetividade incremental foi de R$ 286,86 para o cenário IgA versus HLA e de R$214,64 por ano de vida ajustado pela qualidade ganho no cenário Biópsia versus HLA. Na análise de impacto orçamentário, o custo incremental calculado para o SUS foi de R$ 120.060,76 para os cinco anos no cenário Biópsia versus HLA, com market share inicial de 30%. Ressalta-se que as limitações apresentadas em relação ao exame esofagogastroduodenoscopia podem apresentar resultados superestimados. Já o impacto incremental no cenário IgA versus HLA foi de R$ 144.358,27 ao final dos cinco anos. RECOMENDAÇÃO PRELIMINAR DA CONITEC: O tema foi avaliado na 113ª Reunião Ordinária da Conitec em 5 de outubro de 2022. A recomendação inicial foi desfavorável à incorporação do teste de genotipagem HLA-DQ2 e/ou DQ8, por não fornecer diagnóstico conclusivo e ter grande impacto orçamentário em cinco anos. CONSULTA PÚBLICA: Foram recebidas 46 contribuições, sendo 25 pelo formulário para contribuições técnico-científicas e 21 pelo formulário para contribuições sobre experiência ou opinião de pacientes, familiares, amigos ou cuidadores de pacientes, profissionais de saúde ou pessoas interessadas no tema. No total, 24 expressaram que o teste de genotipagem HLA DQ2/DQ8 deve ser incorporado ao SUS e 1 participante não tinha opinião formada. De maneira geral, as contribuições abordaram a acessibilidade restrita aos exames clínicos para o diagnóstico de doença celíaca tanto na rede privada quanto pública e a necessidade de o exame ser ofertado a familiares de 1º grau. RECOMENDAÇÃO FINAL DA CONITEC: As contribuições da consulta pública foram apresentadas à Conitec por ocasião da 117ª Reunião Ordinária, realizada em 29 de março de 2023. Os membros presentes do Comitê de Produtos e Procedimentos, deliberaram, por unanimidade, recomendar a não incorporação do teste de genotipagem HLA-DQ2 e/ou DQ8 para diagnóstico da doença celíaca em pacientes com fatores de risco. Por fim, foi assinado o Registro de Deliberação Nº 812 / 2023. DECISÃO: Não incorporar, no âmbito do Sistema Único de Saúde - SUS, o teste de genotipagem HLA-DQ2 e/ou DQ8 para o diagnóstico de doença celíaca em pacientes com fatores de risco, publicada no Diário Oficial da União nº 81, seção 1, página 111, em 28 de abril de 2023.
Asunto(s)
Humanos , Antígenos HLA-DQ , Enfermedad Celíaca/diagnóstico , Técnicas de Genotipaje/métodos , Sistema Único de Salud , Brasil , Factores de Riesgo , Análisis Costo-Beneficio/economíaRESUMEN
The detection of the most significant erythrocyte antigens present in each one of the individuals is fundamental when carrying out a transfusion or a transplant. Detection to date is performed by conventional serological methods through the antigen-antibody reaction. But several drawbacks may arise depending on the pathology under study, limiting the availability of blood components. Molecular methods such as genotyping is a tool that complements sensitivity and specificity and has come to revolutionize immunohematology in the blood bank, allowing not only the detection of erythrocyte antigens but also platelet antigens. These methodologies are applicable in patients and in large-scale donors, starting from the allelic variants present in each of the genes that code for the antigens of clinical interest, using microarray systems or systems based on particles labeled with specific probes or their variants that allow an analysis from the immunohematological point of view.
La detección de los antígenos eritrocitarios más significativos presentes en cada uno de los individuos es fundamental cuando se lleva a cabo una transfusión o un trasplante. La detección a la fecha se realiza mediante métodos serológicos convencionales a través de la reacción de antígeno-anticuerpo. Pero se pueden presentar varios inconvenientes dependiendo de la patología en estudio, lo cual limita la disponibilidad de los hemocomponentes. Los métodos moleculares, como la genotipificación, son una herramienta que complementa la sensibilidad y especificidad y que han venido a revolucionar la inmunohematología en el banco de sangre, lo cual permite no solo la detención de antígenos eritrocitarios sino también la de antígenos plaquetarios. Estas metodologías son aplicables en pacientes y en donantes a gran escala, partiendo de las variantes alélicas presentes en cada uno de los genes que codifican para los antígenos de interés clínico, utilizando los sistemas de microarreglos o los sistemas basados en partículas marcadas con sondas específicas o sus variantes que permiten un análisis desde el punto de vista inmunohematológico.
Asunto(s)
Antígenos de Plaqueta Humana , Humanos , Genotipo , Antígenos de Plaqueta Humana/análisis , Antígenos de Plaqueta Humana/genética , Bancos de Sangre , Transfusión Sanguínea , Técnicas de Genotipaje/métodosRESUMEN
The native marmoset of the Southeastern Atlantic Forest in Brazil is among the 25 most endangered primates of the world. Hybridization with alien species is one of its main threats registered since the early 2000s based on phenotype, so far, without genetic confirmation. Using uniparental molecular markers, we analyzed 18 putative hybrids, captured from 2004 to 2013 in different localities of the Atlantic Forest. A nine base pair deletion in the SRY gene of C. aurita was used to investigate paternal ancestry. Maternal ancestry was assessed by DNA sequencing of ca. 455 bp from the COX2 gene. Hybridization was confirmed for 16 out of the 18 marmosets since they inherited COX2 haplotypes of the alien C. penicillata or C. jacchus and the SRY deletion specific to C. aurita. Two individuals inherited both parental lineages of C. aurita, which is probably related to backcrossing or hybrid interbreeding. The direction of hybridization of females with the matrilineal lineage of invasive species with males descending from the native lineage was predominant in our sampling. This is the first time that hybridization between C. aurita and invasive species has been confirmed through genetic analysis.
Asunto(s)
Callithrix/genética , Hibridación Genética , Especies Introducidas , Animales , Brasil , Ciclooxigenasa 2/genética , ADN Mitocondrial , Femenino , Marcadores Genéticos , Técnicas de Genotipaje/métodos , Patrón de Herencia , Masculino , FilogeniaRESUMEN
BACKGROUND: Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. RESULTS: We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent). CONCLUSIONS: We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.
Asunto(s)
Técnicas de Genotipaje , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Genotipo , Técnicas de Genotipaje/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Mapeo Cromosómico/métodos , Programas Informáticos , Polimorfismo de Nucleótido SimpleRESUMEN
Based on molecular markers, genomic prediction enables us to speed up breeding schemes and increase the response to selection. There are several high-throughput genotyping platforms able to deliver thousands of molecular markers for genomic study purposes. However, even though its widely applied in plant breeding, species without a reference genome cannot fully benefit from genomic tools and modern breeding schemes. We used a method to assemble a population-tailored mock genome to call single-nucleotide polymorphism (SNP) markers without an available reference genome, and for the first time, we compared the results with standard genotyping platforms (array and genotyping-by-sequencing (GBS) using a reference genome) for performance in genomic prediction models. Our results indicate that using a population-tailored mock genome to call SNP delivers reliable estimates for the genomic relationship between genotypes. Furthermore, genomic prediction estimates were comparable to standard approaches, especially when considering only additive effects. However, mock genomes were slightly worse than arrays at predicting traits influenced by dominance effects, but still performed as well as standard GBS methods that use a reference genome. Nevertheless, the array-based SNP markers methods achieved the best predictive ability and reliability to estimate variance components. Overall, the mock genomes can be a worthy alternative for genomic selection studies, especially for those species where the reference genome is not available.
Asunto(s)
Biología Computacional , Técnicas de Genotipaje , Modelos Genéticos , Animales , Quimera/genética , Biología Computacional/métodos , Biología Computacional/normas , Conjuntos de Datos como Asunto , Genoma , Estudio de Asociación del Genoma Completo/métodos , Estudio de Asociación del Genoma Completo/normas , Genómica/métodos , Genómica/normas , Genotipo , Técnicas de Genotipaje/métodos , Técnicas de Genotipaje/normas , Fenotipo , Estándares de Referencia , Reproducibilidad de los Resultados , Selección Genética , Especificidad de la Especie , Zea mays/clasificación , Zea mays/genéticaRESUMEN
In order to improve the diagnosis of giardiasis, fecal samples (high/medium/low concentration of cysts) were processed by the parasitological methods used in the routine: Faust, Lutz e Ritchie modified (replacement of formaldehyde by distilled water). The cysts were quantified; the DNA was extracted and amplified by semi-nested PCR (GDH gene). Fifteen clinical samples were analyzed to validate the study by PCR-RFLP. The results showed that the parasite was only detected and genotyped correctly when samples from children with high, medium, and low parasitic load, belonging to genotype AII, were processed by the modified Ritchie method, different from what was observed for the other methods used in laboratory routine (Faust and Lutz). The modified Ritchie method proved to be more suitable, recovering a greater number of cysts from samples, regardless of parasitic load, which reduces the chance of false negative results and has epidemiological repercussions since individuals with low parasite load are usually asymptomatic and the main disseminators of this infection.
Asunto(s)
Técnicas de Genotipaje/métodos , Giardia lamblia/crecimiento & desarrollo , Giardia lamblia/aislamiento & purificación , Giardiasis/parasitología , Reacción en Cadena de la Polimerasa/métodos , Preescolar , Heces/parasitología , Femenino , Genotipo , Giardia lamblia/genética , Giardiasis/diagnóstico , Humanos , Lactante , Estadios del Ciclo de Vida , Masculino , Técnicas de Diagnóstico Molecular/métodos , Carga de Parásitos , Proteínas Protozoarias/genéticaRESUMEN
BACKGROUND: Human papillomavirus (HPV) is the main cause of cervical cancer. Polymerase chain reaction (PCR)-based techniques are associated with accurate results with respect to HPV detection and genotyping, being able to identify viral DNA at low levels. However, differences in primer design influence their sensibility and specificity, depending on the HPV type assessed. OBJECTIVE: The aim of the study was to comparatively evaluate the effectiveness of three different PCR-based strategies for HPV detection and genotyping from cervical samples. STUDY DESIGN: The procedures were based on different primer design strategies, using MY09/MY11, EntroA, and type specific multiplex PCR primers. RESULTS: Out of 411 samples of cervical scrapings, 45 (10.9%), 50 (12.2%), and 117 (28.5%) were positive for MY09/MY11, EntroA, and multiplex PCR, respectively. For MY09/MY11 positive samples, 36 were negative for EntroA and 23 for multiplex PCR. For EntroA positive samples, 40 were negative for MY09/MY11 and 26 for multiplex PCR. For multiplex PCR positive samples, 96 were negative for MY09/MY11 and 94 for EntroA. MY09/MY11 identified 12 different HPV types, EntroA detected eight types and multiplex PCR detected 11 HPV types. EntroA primers were able to detect HPV in more samples than MY09/MY11, while multiplex PCR, despite the limited targeted HPV types, presented higher sensibility than the other methods. CONCLUSIONS: The three methods presented different advantages and disadvantages, and the present study reinforces the need to use more than one molecular strategy for HPV detection and genotyping, and the development of novel methods which could overcome the limitations of the existing tests.
Asunto(s)
Cuello del Útero/virología , Genotipo , Técnicas de Genotipaje/normas , Papillomaviridae/genética , Reacción en Cadena de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa/normas , Estudios Transversales , Cartilla de ADN/genética , ADN Viral/genética , Femenino , Técnicas de Genotipaje/métodos , Humanos , Papillomaviridae/clasificación , Sensibilidad y EspecificidadRESUMEN
INTRODUÇÃO: Os testes de sonda em linha (LPA) são ensaios qualitativos que utilizam membranas de nitrocelulose com sondas de regiões parciais de genes de resistência. O GenoType MTBDRplus® , a partir de amostras de escarro positivo ou de culturas positivas, identifica o complexo M. tuberculosis e as principais mutações que conferem resistência à rifampicina e isoniazida a partir de sondas das regiões parciais de resistência de determinados genes. O GenoType MTBDRsl® possibilita a identificação de resistência também aos medicamentos injetáveis e de segunda linha, por meio de sondas de genes de resistência conhecidos. A população alvo desse abarca indivíduos com comorbidades ou não, de ambos os sexos, todas as idades, provenientes de qualquer país independentemente da incidência e prevalência regionais da doença, com suspeita de tuberculose pulmonar ou extrapulmonar ou indivíduos diagnosticados com tuberculose, independentemente da baciloscopia, tratados previamente ou não, e suspeita de resistência a drogas de primeira ou segunda linha utilizadas no tratamento das formas resistentes da doença. EQUIPAMENTO: Testes comerciais de sondas em linha para detecção do complexo Mycobacterium tuberculosis (MTB), de mutações nas regiões determinan
Asunto(s)
Humanos , Rifampin/efectos adversos , Fluoroquinolonas/efectos adversos , Técnicas de Genotipaje/métodos , Aminoglicósidos/efectos adversos , Isoniazida/efectos adversos , Infecciones por Mycobacterium/diagnóstico , Mycobacterium tuberculosis/aislamiento & purificación , Sistema Único de Salud , Brasil , Análisis Costo-BeneficioRESUMEN
Human pigmentation is a complex trait, probably involving more than 100 genes. Predicting phenotypes using SNPs present in those genes is important for forensic purpose. For this, the HIrisPlex tool was developed for eye and hair color prediction, with both models achieving high accuracy among Europeans. Its evaluation in admixed populations is important, since they present a higher frequency of intermediate phenotypes, and HIrisPlex has demonstrated limitations in such predictions; therefore, the performance of this tool may be impaired in such populations. Here, we evaluate the set of 24 markers from the HIrisPlex system in 328 individuals from Ribeirão Preto (SP) region, predicting eye and hair color and comparing the predictions with their real phenotypes. We used the HaloPlex Target Enrichment System and MiSeq Personal Sequencer platform for massively parallel sequencing. The prediction of eye and hair color was accomplished by the HIrisPlex online tool, using the default prediction settings. Ancestry was estimated using the SNPforID 34-plex to observe if and how an individual's ancestry background would affect predictions in this admixed sample. Our sample presented major European ancestry (70.5%), followed by African (21.1%) and Native American/East Asian (8.4%). HIrisPlex presented an overall sensitivity of 0.691 for hair color prediction, with sensitivities ranging from 0.547 to 0.782. The lowest sensitivity was observed for individuals with black hair, who present a reduced European contribution (48.4%). For eye color prediction, the overall sensitivity was 0.741, with sensitivities higher than 0.85 for blue and brown eyes, although it failed in predicting intermediate eye color. Such struggle in predicting this phenotype category is in accordance with what has been seen in previous studies involving HIrisPlex. Individuals with brown eye color are more admixed, with European ancestry decreasing to 62.6%; notwithstanding that, sensitivity for brown eyes was almost 100%. Overall sensitivity increases to 0.791 when a 0.7 threshold is set, though 12.5% of the individuals become undefined. When combining eye and hair prediction, hit rates between 51.3 and 68.9% were achieved. Despite the difficulties with intermediate phenotypes, we have shown that HIrisPlex results can be very helpful when interpreted with caution.
Asunto(s)
Color del Ojo/genética , Genotipo , Técnicas de Genotipaje/instrumentación , Técnicas de Genotipaje/métodos , Color del Cabello/genética , Fenotipo , Brasil/etnología , Genética Forense/métodos , HumanosRESUMEN
The genome of the SARS-CoV-2 virus, the causal agent of the COVID-19 pandemic, has diverged due to multiple mutations since its emergence as a human pathogen in December 2019. Some mutations have defined several SARS-CoV-2 clades that seem to behave differently in terms of regional distribution and other biological features. Next-generation sequencing (NGS) approaches are used to classify the sequence variants in viruses from individual human patients. However, the cost and relative scarcity of NGS equipment and expertise in developing countries prevent studies aimed to associate specific clades and variants to clinical features and outcomes in such territories. As of March 2021, the GR clade and its derivatives, including the B.1.1.7 and B.1.1.28 variants, predominate worldwide. We implemented the post-PCR small-amplicon high-resolution melting analysis to genotype SARS-CoV-2 viruses isolated from the saliva of individual patients. This procedure was able to clearly distinguish two groups of samples of SARS-CoV-2-positive samples predicted, according to their melting profiles, to contain GR and non-GR viruses. This grouping of the samples was validated by means of amplification-refractory mutation system (ARMS) assay as well as Sanger sequencing.
Asunto(s)
COVID-19/virología , Técnicas de Genotipaje/métodos , SARS-CoV-2/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Mutación , Desnaturalización de Ácido Nucleico , ARN Viral/aislamiento & purificaciónRESUMEN
The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.
Asunto(s)
Genoma de Planta , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Prunus persica/enzimología , Prunus persica/genética , Análisis de Secuencia de ADN/métodos , Biología Computacional/métodos , ADN de Plantas/genética , ADN de Plantas/aislamiento & purificación , Desoxirribonucleasas de Localización Especificada Tipo II/genética , Sitios Genéticos , Técnicas de Genotipaje/métodos , Fitomejoramiento , Polimorfismo de Nucleótido SimpleRESUMEN
As raças taurinas de origem ibérica Limonero e Carora (Bos primigenius taurus) possuem o fenótipo de pelo curto, liso e com baixa densidade folicular, o que confere a esses animais maior tolerância térmica e melhor produtividade em regiões quentes. Diferentes mutações associadas a esse fenótipo foram descritas no gene do receptor de prolactina PRLR, localizado no cromossomo bovino BTA20. Uma mutação recentemente encontrada é a substituição do nucleotídeo C por T, SNP 39136666 (p. R497*), no exon 11, que gera um códon de parada e, consequentemente, uma menor isoforma desse receptor. Neste trabalho, desenvolveu-se um protocolo rápido e de baixo custo para detecção desse SNP, utilizando-se a técnica de tetra-primer ARMS-PCR. Assim, foi possível detectar essa mutação nas raças brasileiras de origem ibérica localmente adaptadas: Caracu, Crioulo Lageano, Mocho Nacional e Pantaneiro. O alelo T foi mais frequente na raça Caracu (80%), enquanto o alelo C foi mais frequente na raça Crioulo Lageano (84%). Essa simples metodologia pode ser usada para genotipar esse SNP e ajudar na aplicação dessas informações moleculares em programas de melhoramento focados na tolerância térmica em bovinos taurinos e seus mestiços.(AU)
Asunto(s)
Animales , Bovinos , Receptores de Prolactina/genética , Cartilla de ADN/análisis , Polimorfismo de Nucleótido Simple/genética , Técnicas de Genotipaje/métodos , Reacción en Cadena de la Polimerasa Multiplex/veterinariaRESUMEN
Whole genome sequencing (WGS) has been shown to be superior to traditional procedures of genotyping in tuberculosis (TB), nevertheless, reports of its use in drug resistant TB (DR-TB) isolates circulating in Mexico, are practically unknown. Considering the above the main of this work was to identify and characterize the lineages and genomic transmission clusters present in 67 DR-TB isolates circulating in southeastern Mexico. The results show the presence of three major lineages: L1 (3%), L2 (3%) and L4 (94%), the last one included 16 sublineages. Sublineage 4.1.1.3 (X3) was predominant in 18 (27%) of the isolates, including one genomic cluster, formed by eleven multidrug resistant isolates and sharing the SIT 3278, which seems to be restricted to Mexico. By the use of WGS, it was possible to identify the high prevalence of L4 and a high number of sublineages circulating in the region, also was recognized the presence of a novel X3 sublineage, formed exclusively by multidrug resistant isolates and with restrictive circulation in Mexico for at least the past 17 years.
Asunto(s)
Farmacorresistencia Bacteriana Múltiple/genética , Técnicas de Genotipaje/métodos , Mycobacterium tuberculosis/genética , Secuenciación Completa del Genoma/métodos , Adulto , Antituberculosos/farmacología , Estudios Transversales , ADN Bacteriano/química , ADN Bacteriano/genética , Farmacorresistencia Bacteriana Múltiple/efectos de los fármacos , Femenino , Genómica/métodos , Genotipo , Humanos , Masculino , México , Persona de Mediana Edad , Familia de Multigenes/genética , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/fisiología , Filogenia , Polimorfismo de Nucleótido Simple , Tuberculosis Resistente a Múltiples Medicamentos/tratamiento farmacológico , Tuberculosis Resistente a Múltiples Medicamentos/microbiologíaRESUMEN
Genotyping-by-sequencing (GBS) provides the marker density required for genomic predictions (GP). However, GBS gives a high proportion of missing SNP data which, for species without a chromosome-level genome assembly, must be imputed without knowing the SNP physical positions. Here, we compared GP accuracy with seven map-independent and two map-dependent imputation approaches, and when using all SNPs against the subset of genetically mapped SNPs. We used two rubber tree (Hevea brasiliensis) datasets with three traits. The results showed that the best imputation approaches were LinkImputeR, Beagle and FImpute. Using the genetically mapped SNPs increased GP accuracy by 4.3%. Using LinkImputeR on all the markers allowed avoiding genetic mapping, with a slight decrease in GP accuracy. LinkImputeR gave the highest level of correctly imputed genotypes and its performances were further improved by its ability to define a subset of SNPs imputed optimally. These results will contribute to the efficient implementation of genomic selection with GBS. For Hevea, GBS is promising for rubber yield improvement, with GP accuracies reaching 0.52.
Asunto(s)
Técnicas de Genotipaje/métodos , Hevea/genética , Fitomejoramiento/métodos , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN/métodos , Marcadores GenéticosRESUMEN
CRISPR-Cas9 is a method for genome editing that can be used efficiently for in vivo applications; the basic implementation of this method is used to generate genome site-directed sequence eliminations. Here we describe a protocol for genome editing using CRISPR-Cas9 in zebrafish (Danio rerio) one-cell embryos.