Tecnologías de secuenciación de nueva generación en diagnóstico genético pre- y postnatal

Standardization of the use of opsonized zymosan as stimulus in the 1,2,3-dihydrorhodamine technique for the assessment of neutrophil respiratory burst

Introduction

Chronic granulomatous disease is a defect in phagocytosis due to deficiency of gp91phox, p22phox, p47phox, p40phox, and p67phox (classic form of the disease). Recently, EROS and p40phox deficiency were described as responsible for the non-classical form of the disease. The 1,2,3-dihydrorhodamine oxidation technique, with phorbol-12-myristate-13-acetate as a stimulus, is performed to diagnose the classic chronic granulomatous disease. However, oxidation mediated by EROS and p40phox requires stimuli such as zymosan, Escherichia coli, or Staphylococcus aureus.

Objective

To optimize the 1,2,3-dihydrorhodamine technique using zymosan to assess neutrophil respiratory burst and detect the non-classical chronic granulomatous disease.

Materials and method

Blood was obtained from five healthy subjects after the signature of the informed consent. The 1,2,3-dihydrorhodamine technique was performed with phorbol-12-myristate-13-acetate as control and different quantities of opsonized zymosan (150, 100, 50, 20, and 10 μg). We obtained through flow cytometry the mean fluorescence intensity of rhodamine 1,2,3 oxidated in the neutrophil population and calculated the oxidation index. The Kolmogorov-Smirnov test, ANOVA, and Tukey’s post-hoc analysis were used. We considered a p value ≤ 0.05 as statistically significant.

Results

The phorbol-12-myristate-13-acetate increased the rhodamine 1,2,3 mean fluorescence intensity in healthy subjects. Among the different zymosan conditions tested, we selected 50 μg as the optimal and reproducible amount in all controls according to the statistical analysis and cytometric findings.

Conclusions

We present the optimization of the 1,2,3-dihydrorhodamine technique using zymosan. We propose its implementation in clinical diagnostic laboratories to expand the diagnosis of chronic granulomatous disease.

Physiological and Genomic Analysis of Bacillus pumilus UAMX Isolated from the Gastrointestinal Tract of Overweight Individuals

The study aimed to evaluate the metabolism and resistance to the gastrointestinal tract conditions of Bacillus pumilus UAMX (BP-UAMX) isolated from overweight individuals using genomic tools. Specifically, we assessed its ability to metabolize various carbon sources, its resistance to low pH exposure, and its growth in the presence of bile salts. The genomic and bioinformatic analyses included the prediction of gene and protein metabolic functions, a pan-genome and phylogenomic analysis. BP-UAMX survived at pH 3, while bile salts (0.2-0.3% w/v) increased its growth rate. Moreover, it showed the ability to metabolize simple and complex carbon sources (glucose, starch, carboxymethyl-cellulose, inulin, and tributyrin), showing a differentiated electrophoretic profile. Genome was assembled into a single contig, with a high percentage of genes and proteins associated with the metabolism of amino acids, carbohydrates, and lipids. Antibiotic resistance genes were detected, but only one beta-Lactam resistance protein related to the inhibition of peptidoglycan biosynthesis was identified. The pan-genome of BP-UAMX is still open with phylogenetic similarities with other Bacillus of human origin. Therefore, BP-UAMX seems to be adapted to the intestinal environment, with physiological and genomic analyses demonstrating the ability to metabolize complex carbon sources, the strain has an open pan-genome with continuous evolution and adaptation.

Secuenciación de nueva generación (NGS) de ADN: presente y futuro en la práctica clínica

Introducción: el término secuenciación de nueva generación (NGS) hace referencia a las tecnologías diseñadas para analizar gran cantidad de ADN de forma masiva y paralela. Abordamos en esta revisión los conceptos básicos de estas tecnologías, las consideraciones de su uso clínico actual y perspectivas a futuro. Desarrollo: las pruebas basadas en NGS han revolucionado el estudio de los genomas pues permiten la lectura de millones de secuencias de ADN de forma masiva y paralela en un menor lapso de tiempo y a menor costo por base. Estas pruebas incluyen la secuenciación de panel de genes, la secuenciación completa del exoma y la secuenciación completa del genoma. El análisis de sus resultados es complejo y requiere de un proceso bioinformático y clínico exhaustivo para su adecuada interpretación. Las limitaciones de las pruebas NGS incluyen aspectos técnicos como la cobertura, profundidad y longitud de las secuencias, las cuales se pueden solventar implementando buenas prácticas de laboratorio. Conclusiones: las pruebas basadas en la secuenciación por NGS son herramientas diagnósticas que deben partir de una aproximación clínica adecuada para su uso razonado, correcta interpretación y toma de decisiones acertadas. Es de gran trascendencia que los médicos tengan la información básica para poder solicitar e interpretar estas pruebas dada su relevancia clínica actual.

[Leber hereditary optic neuropathy: Usefulness of next generation sequencing to study mitochondrial mutations on apparent homoplasmy]

BACKGROUND AND OBJECTIVE

Leber hereditary optic neuropathy is characterized by acute and subacute visual loss, produced by mitochondrial DNA mutations.

PATIENTS AND METHODS

The molecular study of a family with only one affected member is presented.

RESULTS

In the index case and in her mother, the mitochondrial mutation m.11778G>A in the MT-ND4 was detected in the heteroplasmic state. The index case's sister, without ocular manifestations, asked for genetic counseling. The study of the mentioned mutation by Sanger sequencing identified it in an apparent homoplasmic state. However, by means of next-generation sequencing (NGS), the mutation was actually in a heteroplasmic state.

CONCLUSIONS

Regarding genetic counseling, verifying a mutation in homoplasmic state is really important. We have observed that NGS allows us to discriminate between high levels of heteroplasmy and homoplasmy, meaning that it is a useful technique for the analysis of apparent homoplasmic results obtained with less sensitive technique, as Sanger sequencing.

[Algorithm for the molecular analysis of Bardet-Biedl syndrome in Spain]

BACKGROUND AND OBJECTIVE

Bardet-Biedl syndrome (BBS) is a multisystemic genetic disorder, which is not widespread among the Caucasian population, characterized by a highly variable phenotype and great genetic heterogeneity. BBS belongs to a group of diseases called ciliopathies, caused by defects in the structure and/or function of cilia. Due to the diagnostic complexity of the syndrome, the objective of this study was to analyse our whole group of patients in order to create an algorithm to facilitate the routine molecular diagnosis of BBS. We also calculated several epidemiological parameters in our cohort.

PATIENTS AND METHOD

We analysed 116 BBS patients belonging to 89 families from the whole Spanish geography. All probands fulfilled diagnosis criteria established for BBS. For this, we used: genotyping microarray, direct sequencing and homozygosis mapping (in consanguineous families).

RESULTS

By means of the different approaches, it was possible to diagnose 47% of families (21% by genotyping microarray, 18% by direct sequencing of predominant BBS genes, and 8% by homozygosis mapping). With regard to epidemiological data, a prevalence value of 1:407,000 was obtained for BBS in Spain, and a sex ratio of 1.4:1 (men:women).

CONCLUSIONS

The proposed algorithm, based on the analysis of predominant BBS genes combined with homozygosis mapping, allowed us to confirm the molecular diagnosis in a significant percentage of families with clinically suspected BBS. This diagnostic algorithm will be useful for the improvement of the efficiency of molecular analysis in BBS.