Open-Access Worldwide Population STR Database Constructed Using High-Coverage Massively Parallel Sequencing Data Obtained from the 1000 Genomes Project.

Achieving accurate STR genotyping by using next-generation sequencing data has been challenging. To provide the forensic genetics community with a reliable open-access STR database, we conducted a comprehensive genotyping analysis of a set of STRs of broad forensic interest obtained from 1000 Genome populations. We analyzed 22 STR markers using files of the high-coverage dataset of Phase 3 of the 1000 Genomes Project. We used HipSTR to call genotypes from 2504 samples obtained from 26 populations. We were not able to detect the D21S11 marker. The Hardy-Weinberg equilibrium analysis coupled with a comprehensive analysis of allele frequencies revealed that HipSTR was not able to identify longer alleles, which resulted in heterozygote deficiency. Nevertheless, AMOVA, a clustering analysis that uses STRUCTURE, and a Principal Coordinates Analysis showed a clear-cut separation between the four major ancestries sampled by the 1000 Genomes Consortium. Except for larger Penta D and Penta E alleles, and two very small Penta D alleles (2.2 and 3.2) usually observed in African populations, our analyses revealed that allele frequencies and genotypes offered as an open-access database are consistent and reliable.

Prevalencia de anticuerpos antinucleares en médicos residentes aparentemente sanos del Hospital de Clínicas, San Lorenzo

RESUMEN Introducción: los anticuerpos antinucleares son muy utilizados en la práctica médica como marcadores de autoinmunidad y en el diagnóstico de enfermedades autoinmunes. Sin embargo, estos anticuerpos son la expresión de otros trastornos más allá de las colagenopatías e incluso pueden estar presentes en la población aparentemente sana sin representar un riesgo para la salud de estos en el futuro. Objetivo: determinar la prevalencia de anticuerpos antinucleares en médicos residentes aparentemente sanos del Hospital de Clínicas, San Lorenzo, en el año 2021. Material y métodos: se realizó un estudio descriptivo prospectivo y transversal en 150 médicos residentes aparentemente sanos en el Hospital de Clínicas de la ciudad de San Lorenzo, Paraguay, en el periodo de junio a septiembre de 2021. Se determinaron los anticuerpos antinucleares tipo inmunoglobulina G mediante inmunofluorescencia indirecta en células HEp-2. Resultados: la prevalencia de anticuerpos antinucleares fue 11,3%. La mayoría de los sujetos con resultados positivos fueron mujeres (76,5%, p<0,05). Las titulaciones más frecuentes fueron 1:80 y 1:160 por igual (35,3% cada una) y entre los sujetos reactivos el patrón nuclear granular fino denso (AC2) fue el más prevalente (52,9%). Conclusión: la prevalencia de anticuerpos nucleares fue 11,3%, la mayor frecuencia se vio en mujeres, las titulaciones más comunes fueron 1:80 y 1:160 y el patrón más habitual fue el nuclear granular fino denso.

ABSTRACT Introduction: Antinuclear antibodies are widely used in medical practice as autoimmunity markers and in the diagnosis of autoimmune diseases. However, these antibodies are the expression of other disorders beyond collagenopathies and may even be present in the apparently healthy population without representing a risk to their health in the future. Objective: To determine the prevalence of antinuclear antibodies in apparently healthy residents of the Hospital de Clínicas, San Lorenzo, in 2021. Material and methods: A descriptive, prospective and cross-sectional study was carried out in 150 apparently healthy resident physicians at the Hospital de Clínicas in the city of San Lorenzo, Paraguay, from June to September 2021. Immunoglobulin G-type antinuclear antibodies were determined using Indirect immunofluorescence in HEp-2 cells. Results: The prevalence of antinuclear antibodies was 11.3%. Most of the subjects with positive results were women (76.5%, p <0.05). The most frequent titrations were 1:80 and 1:160 equally (35.3% each) and among the reactive subjects the nuclear dense fine speckled pattern (AC2) was the most prevalent (52.9%). Conclusion: The prevalence of nuclear antibodies was 11.3%, the highest frequency was seen in women, the most common titers were 1:80 and 1: 160 and the most common pattern was the nuclear dense fine speckled.

Analysis and comparison of the STR genotypes called with HipSTR, STRait Razor and toaSTR by using next generation sequencing data in a Brazilian population sample.

Short tandem repeats (STRs) are particularly difficult to genotype with rapid evolving next-generation sequencing (NGS) technology. Long amplicons containing repetitive sequences result in alignment and genotyping errors. Stutters arising from polymerase slippage often result in reads with additional or missing repeat copies. Many tools are available for analysis of STR markers from NGS data. This study has evaluated the concordance of the HipSTR, STRait Razor, and toaSTR tools for STR genotype calling; NGS data obtained from a highly genetically diverse Brazilian population sample have been used. We found that toaSTR can retrieve a larger number of genotypes (93.8%), whereas HipSTR (84.9%) and STRait Razor present much lower genotype calling (75.3%). Accuracy levels for genotype calling are very similar (identical genotypes ~95% and correct alleles ~ 97.5%) across the three methods. All the markers presenting the same genotype through the methods are in Hardy-Weinberg equilibrium. We found that combined match probability and combined exclusion power are 2.90 × 10-28 and 0.99999999982, respectively. Although toaSTR has varying locus-specific differences and better overall performance of toaSTR, the three programs are reliable genotyping tools. Notwithstanding, additional effort is necessary to improve the genotype calling accuracy of next-generation sequencing datasets.

Rapid growth atypical mycobacteria infection associated with growth hormone injections: a case report.

INTRODUCTION: Infections caused by fast growing mycobacteria have increased markedly worldwide. They are normally associated with trauma, surgery or cosmetic interventions. Paraguay has a deficit in sanitary control including clinics, private practices, and aesthetic centres. This situation is accompanied by the easy access to drugs, which leads to the performance of exclusively medical aesthetic procedures by people without professional knowledge or training. CASE REPORT: A 26-year-old female patient comes to a medical consultation with pain and bruising in the abdominal area with more than 3 months of progression, without fever or apparent cause. Later, she confessed to the application of subcutaneous injections of 'growth hormones' at the gym. Excisional biopsy of the lesions was carried out for anatomopathological and microbiological studies. In addition, the use of polymerase chain reaction analysis was indicated because of the strong suspicion of an atypical mycobacterial infection. The Ziehl-Neelsen staining was negative for BAAR, and the PAS-Hematoxylin negative for fungal elements. When performing the culture, the growth of atypical mycobacteria was observed on chocolate and blood agar medium culture. Through the polymerase chain reaction study, it was possible to identify the atypical mycobacterium as 'Mycobacterium abscessus'. CONCLUSION: The irresponsible application of medications by people without professional authorization or biosafety precautions can lead to the development atypical infections that are difficult to diagnose and treat. This situation could lead to serious complications and even death.

Forensic parameters and allele frequency distributions of 16 STR in a Paraguayan population.

Paraguay is a Latin American country located in the central zone of South America. There is no official data on the ethnic composition of its population. The European colonization and the wars through which the country crossed were fundamental for its current genetic composition. Here, we analyzed sixteen short tandem repeats (STRs) used in the CODIS system in 259 Paraguayan individuals.