High-resolution HLA genotyping improves PIRCHE-II assessment of molecular mismatching in kidney transplantation.

HLA matching in solid organ transplant is performed with the aim of assessing immunologic compatibility in order to avoid hyperacute rejection and assess the risk of future rejection events. Molecular mismatch algorithms are intended to improve granularity in histocompatibility assessment and risk stratification. PIRCHE-II uses HLA genotyping to predict indirectly presented mismatched donor HLA peptides, though most clinical validation studies rely on imputing high resolution (HR) genotypes from low resolution (LR) typing data. We hypothesized that use of bona fide HR typing could overcome limitations in imputation, improving accuracy and predictive ability for donor-specific antibody development and acute rejection. We performed a retrospective analysis of adult and pediatric kidney transplant donor/recipient pairs (N = 419) with HR typing and compared the use of imputed LR genotyping verses HR genotyping for PIRCHE-II analysis and outcomes. Imputation success was highly dependent on the reference population used, as using historic Caucasian reference populations resulted in 10 % of pairs with unsuccessful imputation while multiethnic reference populations improved successful imputation with only 1 % unable to be imputed. Comparing PIRCHE-II analysis with HR and LR genotyping produced notably different results, with 20 % of patients discrepantly classified to immunologic risk groups. These data emphasize the importance of using multiethnic reference panels when performing imputation and indicate HR HLA genotyping has clinically meaningful benefit for PIRCHE-II analysis compared to imputed LR typing.

Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation.

KEY MESSAGE: Pooling and imputation are computational methods that can be combined for achieving cost-effective and accurate high-density genotyping of both common and rare variants, as demonstrated in a MAGIC wheat population. The plant breeding industry has shown growing interest in using the genotype data of relevant markers for performing selection of new competitive varieties. The selection usually benefits from large amounts of marker data, and it is therefore crucial to dispose of data collection methods that are both cost-effective and reliable. Computational methods such as genotype imputation have been proposed earlier in several plant science studies for addressing the cost challenge. Genotype imputation methods have though been used more frequently and investigated more extensively in human genetics research. The various algorithms that exist have shown lower accuracy at inferring the genotype of genetic variants occurring at low frequency, while these rare variants can have great significance and impact in the genetic studies that underlie selection. In contrast, pooling is a technique that can efficiently identify low-frequency items in a population, and it has been successfully used for detecting the samples that carry rare variants in a population. In this study, we propose to combine pooling and imputation and demonstrate this by simulating a hypothetical microarray for genotyping a population of recombinant inbred lines in a cost-effective and accurate manner, even for rare variants. We show that with an adequate imputation model, it is feasible to accurately predict the individual genotypes at lower cost than sample-wise genotyping and time-effectively. Moreover, we provide code resources for reproducing the results presented in this study in the form of a containerized workflow.

A rapid and reference-free imputation method for low-cost genotyping platforms.

Most current genotype imputation methods are reference-based, which posed several challenges to users, such as high computational costs and reference panel inaccessibility. Thus, deep learning models are expected to create reference-free imputation methods performing with higher accuracy and shortening the running time. We proposed a imputation method using recurrent neural networks integrating with an additional discriminator network, namely GRUD. This method was applied to datasets from genotyping chips and Low-Pass Whole Genome Sequencing (LP-WGS) with the reference panels from The 1000 Genomes Project (1KGP) phase 3, the dataset of 4810 Singaporeans (SG10K), and The 1000 Vietnamese Genome Project (VN1K). Our model performed more accurately than other existing methods on multiple datasets, especially with common variants with large minor allele frequency, and shrank running time and memory usage. In summary, these results indicated that GRUD can be implemented in genomic analyses to improve the accuracy and running-time of genotype imputation.

Cost-effective and reliable genomic DNA extraction from plant seedlings for high-throughput genotyping in seed industries.

Genetic purity of seeds is one of the critical aspects in the seed industry. Molecular seed testing laboratories are utilizing PCR based diagnostic tools for genetic purity analysis. High quality DNA is an essential prerequisite for such analyses. Here, we demonstrate a robust and inexpensive DNA extraction method to isolate genomic DNA from variety of crops. Current method (M2) was compared with four commonly used DNA isolation methods for PCR-based genetic characterization and High Resolution Melt (HRM) based hybridity analysis of cotton, okra, tomato and maize using SSR markers. DNA extracted through current method showed excellent yield and quality as compared to other methods. High quality, PCR ready DNA was isolated within 30-50 min and displayed best results for genetic purity analysis using HRM. In contrast, several genomic DNA samples extracted using other methods were found unsuitable for HRM analysis. Our method can be a perfect choice in seed industry, where thousands of samples are processed every day. Notably, using our method single technician can extract DNA from 96 leaf samples within 30-50 min, at a cost of only $0.11/sample. Overall, current DNA extraction method is a reliable and cost-effective solution for large-scale genotyping experiments in the agricultural industry.

Teste de genotipagem HLA-DQ2 e/ou DQ8 para o diagnóstico de doença celíaca em pacientes com fatores de risco / HLA-DQ2 and/or DQ8 genotyping test for the diagnosis of celiac disease in patients with risk factors

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.

Development of molecular inversion probes for soybean progeny genomic selection genotyping.

Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome-wide single-nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) are a targeted genotyping-by-sequencing (GBS) method that could be used for soybean [Glycine max (L.) Merr.] that is both cost-effective, high-throughput, and provides high data quality to screen breeder's germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the northern-central and middle-southern regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line (RIL) population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. The MIP genotyping accuracy was 93% overall, whereas homozygous call accuracy was 98% with <10% missing data. The accuracy of MIPs combined with its low per-sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs.

Assessment of genotyping markers in the molecular characterization of a population of clinical isolates of Fusarium in Colombia / Evaluación de marcadores de genotipificación en la caracterización molecular de una población de aislamientos clínicos de Fusarium en Colombia

Introduction: Fusarium is a very heterogeneous group of fungi, difficult to classify, with a wide range of living styles, acting as saprophytes, parasites of plants, or pathogens for humans and animals. Prevalence of clinical fusariosis and lack of effective treatments have increased the interest in the precise diagnosis, which implies a molecular characterization of Fusarium populations. Objective: We compared different genotyping markers in their assessment of the genetic variability and molecular identification of clinical isolates of Fusarium. Materials and methods: We evaluated the performance of the fingerprinting produced by two random primers: M13, which amplifies a minisatellite sequence, and (GACA)4, which corresponds to a simple repetitive DNA sequence. Using the Hunter Gaston Discriminatory Index (HGDI), an analysis of molecular variance (AMOVA), and a Mantel test, the resolution of these markers was compared to the reference sequencing-based and PCR genotyping methods. Results: The highest HGDI value was associated with the M13 marker followed by (GACA)4. AMOVA and the Mantel tests supported a strong correlation between the M13 classification and the reference method given by the partial sequencing of the transcription elongation factor 1-alpha (TEF1-α) and rDNA 28S. Conclusion: The strong correlation between the M13 classification and the sequencing-based reference together with its higher resolution demonstrates its adequacy for the characterization of Fusarium populations.

Introducción. Fusarium es un grupo heterogéneo de hongos, difícil de clasificar y con una amplia gama de estilos de vida, que actúa como saprófito, parásito de plantas o patógeno de humanos y animales. La prevalencia de la fusariosis clínica y la falta de tratamientos han incrementado el interés en su diagnóstico preciso, lo que conlleva la caracterización molecular de las poblaciones. Objetivo. Comparar marcadores de genotipificación en la evaluación de la variabilidad genética e identificación de aislamientos clínicos de Fusarium. Materiales y métodos. Se evaluó la huella genética producida por dos cebadores aleatorios: M13, que amplifica una secuencia minisatélite, y (GACA)4, que corresponde a una secuencia repetitiva de ADN. Utilizando el índice discriminatorio de Hunter Gaston (HGDI), el análisis de varianza molecular (AMOVA) y una prueba de Mantel, se comparó la resolución de estos marcadores con métodos de genotipificación basados en secuenciación y PCR. Resultados. El mayor HGDI se asoció con el marcador M13, seguido de (GACA)4. Las pruebas AMOVA y Mantel mostraron correlación entre las clasificaciones obtenidas con M13 y la referencia basada en la secuenciación parcial del factor de elongación de transcripción 1-alfa (TEF1-α) y el ADNr 28S. Conclusión. La fuerte correlación entre la clasificación obtenida con M13 y el método de referencia, así como su alta resolución, demuestran su idoneidad para la caracterización de poblaciones de Fusarium.

Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species.

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS).

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

PRIMA: a rapid and cost-effective genotyping method to detect single-nucleotide differences using probe-induced heteroduplexes.

Targeted mutagenesis by programmable site-specific nucleases like CRISPR typically produce 1-base pair (bp) insertion or deletion (indel) mutations. Although several methods have been developed to detect such 1-bp indels, each method has pros and cons in terms of cost and/or resolution. Heteroduplex mobility assay (HMA) is a traditional technique detecting small base pair differences but it has a limited resolution of mutation size and the band patterns are often complex. Here, we developed a new method called PRIMA (Probe-Induced HMA) using a short single-stranded DNA molecule as a probe in HMA. By utilizing a 40-mer probe containing a 5-nucleotide deletion, we assessed the mobility of a heteroduplex with a target DNA fragment from a plant, bacterium, and human. This method allowed us to detect a 1-bp indel mutation consistently. We also showed that SNPs can be detected using PRIMA. PRIMA provides a rapid and cost-effective solution for the genotyping.

The cost-effectiveness of genotyping versus sequencing for prenatal cystic fibrosis carrier screening.

OBJECTIVE: We investigated the cost-effectiveness of three sequential prenatal cystic fibrosis (CF) carrier screening strategies: genotyping both partners, genotyping one partner then sequencing the second, and sequencing both partners. METHOD: A decision-analytic model compared the strategies in a theoretical cohort of four million pregnant couples in the US population and five racial/ethnic sub-populations. Inputs were obtained from literature and varied in sensitivity analysis. Outcomes included cost per quality-adjusted life year (QALY), missed carrier couples, affected newborns, missed prenatal diagnoses, terminations, and procedure-related losses. The cost-effectiveness threshold was $100,000/QALY. RESULTS: Sequencing both partners identified 1099 carrier couples that were missed by genotyping both partners, leading to 273 fewer missed prenatal diagnoses, 152 more terminations, and 152 fewer affected newborns. A similar trend was observed in the genotyping followed by sequencing strategy. The incremental cost-effectiveness ratio of genotyping followed by sequencing compared to genotyping both partners was $180,004/QALY and the incremental cost-effectiveness ratio of sequencing both partners compared to genotyping followed by sequencing was $17.6 million/QALY. Sequencing both partners was cost-effective below $339 per test, genotyping/sequencing between $340 and $1837, and genotyping both partners above $1838. Sequencing was not cost-effective among five racial/ethnic sub-populations. CONCLUSION: Despite improved outcomes, sequencing for prenatal CF carrier screening was not cost-effective compared to genotyping. The clinical significance of the incremental cost-effectiveness of CF carrier screening is a matter of deliberation for public policy debate.

A deterministic genotyping workflow reduces waste of transgenic individuals by two-thirds.

We present a deterministic workflow for genotyping single and double transgenic individuals directly upon nascence that prevents overproduction and reduces wasted animals by two-thirds. In our vector concepts, transgenes are accompanied by two of four clearly distinguishable transformation markers that are embedded in interweaved, but incompatible Lox site pairs. Following Cre-mediated recombination, the genotypes of single and double transgenic individuals were successfully identified by specific marker combinations in 461 scorings.

Celiac disease screening in children and adolescents with type 1 diabetes mellitus: What test should be performed?

INTRODUCTION: Children and adolescents with type 1 diabetes mellitus (T1DM) are at high risk for the development of celiac disease (CD) because of the common genetic characteristics of both conditions. The study objectives were to investigate the frequency of the human leukocyte antigen system (HLA) for CD in pediatric T1DM patients and to determine whether HLA testing is suitable for CD screening in that population and is cost-effective as compared to serological screening for CD. PATIENTS AND METHODS: A retrospective, descriptive study was conducted in 296 patients (148 girls; 148 boys) with T1DM aged <18 years who attended a Madrid hospital. Data on the frequency of genotypes DQ2/DQ8 in a subgroup of 92 patients and the additional cost of performing HLA typing for screening CD were collected. Only when the risk HLA haplotype (DQ2/DQ8) is negative no further serological screening for CD is required. RESULTS: Twenty-three patients with T1DM (7.77%) also had CD. Alleles DQ2 or DQ8 were found in 91.3% of patients in whom the HLA haplotype was studied. Thus, only 8.7% with a negative haplotype would have benefited from HLA testing. The additional cost of HLA typing was € 105.2 for each patient with positive DQ2 or DQ8 in our population. CONCLUSIONS: HLA typing is not a cost-effective screening method for CD in T1DM because of the frequent association of T1DM with risk genotypes for CD.

Rapid genotype imputation from sequence with reference panels.

Inexpensive genotyping methods are essential to modern genomics. Here we present QUILT, which performs diploid genotype imputation using low-coverage whole-genome sequence data. QUILT employs Gibbs sampling to partition reads into maternal and paternal sets, facilitating rapid haploid imputation using large reference panels. We show this partitioning to be accurate over many megabases, enabling highly accurate imputation close to theoretical limits and outperforming existing methods. Moreover, QUILT can impute accurately using diverse technologies, including long reads from Oxford Nanopore Technologies, and a new form of low-cost barcoded Illumina sequencing called haplotagging, with the latter showing improved accuracy at low coverages. Relative to DNA genotyping microarrays, QUILT offers improved accuracy at reduced cost, particularly for diverse populations that are traditionally underserved in modern genomic analyses, with accuracy nearly doubling at rare SNPs. Finally, QUILT can accurately impute (four-digit) human leukocyte antigen types, the first such method from low-coverage sequence data.

Testes comerciais de sondas em linha para detecção do complexo Mycobacterium tuberculosis (MTB), de mutações nas regiões determinantes de resistência a rifampicina e isoniazida (1ª linha) e a fluoroquinolonas e aminoglicosídeos (2ª linha) / Commercial on-line probe tests for detection of Mycobacterium tuberculosis complex (MTB), mutations in rifampicin and isoniazid-resistance-determining regions (1st line) and fluoroquinolones and aminoglycosides (2nd line)

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

Assessment of intra-sample variability in HIV-1 DNA drug resistance genotyping.

BACKGROUND AND OBJECTIVES: HIV-1 drug resistance testing can be performed in proviral DNA. The non-homogenous distribution of viral variants in cells can impact the performance of this method. We assessed the variability of HIV-1 DNA genotyping results in the same blood sample using a next-generation sequencing (NGS) method. METHODS: For each included patient, a blood sample from a single venipuncture was split into five 1 mL aliquots, which were independently tested in the same run. HIV-1 DNA was quantified in blood samples using real-time PCR, and NGS was performed with the Sentosa platform combined with the Sentosa SQ HIV genotyping Assay. RESULTS: A total of 60 aliquots from 12 samples (12 patients) were tested. The median age was 45.50 years old, and all patients were treated with antiretrovirals. A significant variability can sometimes be observed in HIV-1 DNA quantification between aliquots from the same sample, with a coefficient of variation ranging from 23% to 89%. The analysis of resistance-associated mutations (RAMs) with a 20% cut-off found some discordances in RAMs profile between aliquots from the same sample for 5, 3 and 3 patients in the reverse transcriptase, protease and integrase genes, respectively. The analysis with a lower cut-off (10%) showed additional mutations, but did not improve the intra-sample concordance. CONCLUSIONS: There is an intra-sample variability in HIV-1 DNA resistance test results, and repetition may sometimes bring additional information, but the extent of its clinical impact still requires further investigation.

A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power.

BACKGROUND: Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array technologies, and a different assay must be developed for each backcross strain combination. "Next generation" high throughput DNA sequencing technologies have the potential to decrease cost and increase flexibility and power of speed congenics, but thus far have not been utilized for this purpose. RESULTS: We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1640 genome-wide SNPs known to be polymorphic across > 100 mouse strains, with an expected average of 549 ± 136 SD diagnostic SNPs between each pair of strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c strain into the C57BL/6J strain (807-819 SNPs), and a sufficient density of diagnostic SNPs for backcrossing the closely related substrains C57BL/6N and C57BL/6J (123-139 SNPs). Furthermore, the assay can easily be modified to include additional diagnostic SNPs for backcrossing other closely related substrains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. We demonstrated the effectiveness of the assay and bioinformatic pipeline with a backcross experiment of BALB/c-IL4/IL13 into C57BL/6J; after six generations of backcrosses, offspring were up to 99.8% congenic. CONCLUSIONS: The SNP genotyping assay and bioinformatic pipeline developed here present a valuable tool for increasing the power and decreasing the cost of many studies that depend on speed congenics. The assay is highly flexible and can be used for combinations of strains that are commonly used for speed congenics. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics.

Assessment of the Genetic Potential of the Peregrine Falcon (Falco peregrinus peregrinus) Population Used in the Reintroduction Program in Poland.

Microsatellite DNA analysis is a powerful tool for assessing population genetics. The main aim of this study was to assess the genetic potential of the peregrine falcon population covered by the restitution program. We characterized individuals from breeders that set their birds for release into the wild and birds that have been reintroduced in previous years. This was done using a well-known microsatellite panel designed for the peregrine falcon containing 10 markers. We calculated the genetic distance between individuals and populations using the UPGMA (unweighted pair group method with arithmetic mean) method and then performed a Principal Coordinates Analysis (PCoA) and constructed phylogenetic trees, to visualize the results. In addition, we used the Bayesian clustering method, assuming 1-15 hypothetical populations, to find the model that best fit the data. Units were segregated into groups regardless of the country of origin, and the number of alleles and observed heterozygosity were different in different breeding groups. The wild and captive populations were grouped independent of the original population.

High-Throughput and Low-Cost Genotyping Method for Plant Genome Editing.

Genome editing technologies have revolutionized genetic studies in the life sciences community in recent years. The application of these technologies allows researchers to conveniently generate mutations in almost any gene of interest. This is very useful for species such as maize that have complex genomes and lack comprehensive mutant collections. With the improvement of genome editing tools and transformation methods, these technologies are also widely used to assist breeding research and implementation in maize. However, the detection and genotyping of genomic edits rely on low-throughput, high-cost methods, such as traditional agarose gel electrophoresis and Sanger sequencing. This article describes a method to barcode the target regions of genomic edits from many individuals by low-cost polymerase chain reaction (PCR) amplification. It also employs next-generation sequencing (NGS) to genotype the genome-edited plants at high throughput and low cost. This protocol can be used for initial screening of genomic edits as well as derived population genotyping on a small or large scale, at high efficiency and low cost. © 2021 Wiley Periodicals LLC. Basic Protocol 1: A fast genomic DNA preparation method from genome edited plants Basic Protocol 2: Barcoding the amplicons of edited regions from each individual by two rounds of PCR Basic Protocol 3: Bioinformatics analysis.

Pharmacogenetic-guided glimepiride therapy in type-2 diabetes mellitus: a cost-effectiveness study.

The demonstration of the link between certain genetic variations and drug response has allowed the emergence of pharmacogenetics, which offers many opportunities to improve patient care. Type-2 diabetes mellitus is a disease for which several gene polymorphisms have been reported to be associated with drug response. Sulfonylureas are commonly used for the management of this disease. Genetic polymorphisms of CYP2C9, the main enzyme involved in the metabolism of sulfonylureas, have been associated with the risk of severe hypoglycaemia, particularly in poor metabolizers carrying CYP2C9 *3/*3 genotype, and especially in the case of patients treated with glimepiride. The objectives of the present study were to evaluate the potential clinical and economic outcomes of using CYP2C9 genotype data to guide the management of SU regimen in patients initiating glimepiride therapy, and to identify factors affecting the cost-effectiveness of this treatment scheme. The analysis was conducted using a decision tree, considering a 1-year time horizon, and taking as perspective that of the French national health insurance system. With pharmacogenetic-guided therapy, the cost to avoid an episode of severe hypoglycaemia event per 100 000 patients treated was €421 834. Genotyping cost was the most influential factor on the incremental cost-effectiveness ratio. In conclusion, the potential cost of CYP2C9 genotype-guided dosing for glimepiride therapy is relatively high, and associated with modest improvements with respect to the number of hypoglycaemia avoided, as compared with standard dosing. Additional economic studies are required to better specify the usefulness of CYP2C9 genotyping prior to glimepiride regimen initiation.