TIROSEC: Molecular, Clinical and Histopathological Profile of Papillary Thyroid Carcinoma in a Colombian Cohort

INTRODUCTION

In Colombia, thyroid cancer ranks among the highest incidences, yet our population lacks studies on its molecular profile. This study aims to characterize clinical, histopathologic and molecular data in a Colombian cohort with papillary thyroid carcinoma (PTC).

METHODS

A retrospective review of clinical history, clinicopathologic characteristics, treatment and 5-10-year follow-up for all patients was done. DNA and RNA were extracted from formalin-fixed paraffin-embedded (FFPE) tissue using the Quick-DNA & RNA FFPE Min iPrep kit (Zymo Research). Next-generation sequencing (NGS) analysis was performed with SOPHiA Solid Tumor Solutions kit (SOPHiA GENETICS). Tumor mutation genomic analysis used SOPHiA DDM™ platform, with descriptive analysis reporting frequencies, means and associations via chi-square analysis.

RESULTS

Among 231 sequenced patients, mean age at diagnosis was 46 (± 12.35) years, with higher frequency in women (81.82%). Two cases were reclassified as non-invasive follicular thyroid neoplasm (NIFT-P); an NRAS mutation was found in one of them. Predominant histologic subtype was classic PTC (57.64%) followed by tall cell (28.82%). Of the 229 sequenced carcinomas, mutations were identified in 186 cases, including BRAF, IDH1, RAS and PIK3CA. Notable copy number variations (CNVs) were PDGFRA, CDK4 and KIT, with RET being the most frequent gene fusion, including CCDC6-RET in two classic subtype cases.

CONCLUSION

This is the first study in Colombia (TIROSEC) to our knowledge that integrates molecular and histopathologic profiles enriching our local comprehension and knowledge of PTC. The identification of target mutations such as BRAF, RET and NTRK fusions holds the potential to guide targeted therapies for tumor recurrence and predict aggressive behavior.

A scoping review of longitudinal airway microbiota studies

INTRODUCTION

The role of the microbiota in inflammatory airway diseases is unclear. Antimicrobial therapies have predominantly been guided by culture results. However, molecular sequencing has shown that the airway microbiota is much more complex and accurate modeling requires longitudinal analysis.

AREAS COVERED

A Preferred Reporting Items for Systematic Reviews and Meta-Analyses scoping review was performed by searching Medline, Scopus, and Web of Science databases for all longitudinal airway microbiota studies that utilized molecular techniques. 38 studies with 1,993 participants were included in this review. Healthy microbial communities were more diverse, individualized and stable over time. Acute infections resulted in changes in the microbiota that were detected earlier and more sensitively by molecular sequencing than culture. Distinct microbiota profiles have been demonstrated in chronic obstructive pulmonary disease patients associated with exacerbation frequency and severity.

EXPERT OPINION

Longitudinal studies provide essential data on the stability of the microbiota over time and valuable information about the dynamic interactions between host, disease and microbes. We believe that molecular sequencing will be increasingly incorporated into research and clinical practice in the future. These advances can lead to improved diagnosis, enhanced prescribing guidance and reduce unnecessary antibiotic usage.

Optimization of a microfluidics-based next generation sequencing assay for clinical oncology diagnostics

Background

Massively parallel, or next-generation, sequencing is a powerful technique for the assessment of somatic genomic alterations in cancer samples. Numerous gene targets can be interrogated simultaneously with a high degree of sensitivity. The clinical standard of care for many advanced solid and hematologic malignancies currently requires mutation analysis of several genes in the front-line setting, making focused next generation sequencing (NGS) assays an effective tool for clinical molecular diagnostic laboratories.

Methods

We have utilized an integrated microfluidics circuit (IFC) technology for multiplex PCR-based library preparation coupled with a bioinformatic method designed to enhance indel detection. A parallel low input PCR-based library preparation method was developed for challenging specimens with low DNA yield. Computational data filters were written to optimize analytic sensitivity and specificity for clinically relevant variants.

Results

Minimum sequencing coverage and precision of variant calls were the two primary criteria used to establish minimum DNA mass input onto the IFC. Wet-bench and bioinformatics protocols were modified based on data from the optimization and familiarization process to improve assay performance. The NGS platform was then clinically validated for single nucleotide and indel (up to 93 base pair) variant detection with overall analytic accuracy of 98% (97% sensitivity; 100% specificity) using as little as 3 ng of formalin-fixed, paraffin-embedded DNA or 0.3 ng of unfixed DNA.

Conclusions

We created a targeted clinical NGS assay for common solid and hematologic cancers with high sensitivity, high specificity, and the flexibility to test very limited tissue samples often encountered in routine clinical practice.

Complete genome sequence of a multi-recombinant echovirus 6 strain isolated from CSF in Ahvaz, Southwestern Iran

BACKGROUND

Echovirus 6 (E6), is one of the main enteroviral serotypes, was initially isolated from patients with aseptic meningitis (AM) and is a major cause of hospitalization among children and adults worldwide.

METHODS

A cerebrospinal fluid (CSF) sample was collected from patient with clinically suspected aseptic meningitis (AM) in August 2011. Following detection of a virus and subsequent virus serotyping, the whole genome sequence was determined. The sequence of the VP1 region of the isolated strain E6 RA/E6/Ahvaz/Iran/2011 showed 79% (>75%) nucleotide and 94% (>85%) amino acid homology with prototype strain D'Amori. The isolated strain was identified as an E6 serotype. A specimen was cultured in a human rhabdomyosarcoma (RD) cell line. Following propagation, the virus was further analyzed using the plaque assay technique, reverse transcription PCR (RT-PCR), rapid amplification of CDNA ends (RACE), TA cloning, sequencing, phylogenetic analysis, Simplot and boot scanning analyses (ver. 3.5) were applied to find evidence of recombination in the isolated strain.

RESULTS

The isolated Echo6 strain RA/E6/Ahvaz/Iran/2011 has been recorded in GenBank with a partial and complete genome accession numbers (KX619440) (KX198605), respectively. The complete genomic sequence was 7435 nt, with a 742 bp 5' UTR, 117 bp 3' UTR, and an open reading frame (ORF) encoding a polypeptide of 2191 amino acids. The nucleotide analysis of the VP1 and structural genomic regions of the isolated strain showed high similarity with strain E6-10887-99 isolated from patient with facial nerve paresis in Russia in 1999. The recombinations evidence were observed in the isolated strain E6 RA/E6/Ahvaz/Iran/2011 and found to have a high levels of inter-serotypic exchanges in 2C and 3A-3C genomic regions with Echovirus13 and Echovirus14, respectively.

CONCLUSION

Full genome sequence analysis of enteroviral is required to understand the epidemiological pattern and to evaluate the new enterovirus circulating in community.

Fatal Pulmonary Mucormycosis due to Rhizopus homothallicus

We report here a case of cavitary pneumonia due to Rhizopus homothallicus in a diabetic patient. This is the first proven case of R. homothallicus infection in Western countries and the third case described worldwide. The organism was isolated from lung biopsy and identified after amplification and sequencing of the internal transcribed spacer region.

Analysis of molecular structures and mechanisms for toxins derived from venomous animals

As predominant component in the venom of many dangerous animal species, toxins have been thoroughly investigated for drug design or as pharmacologic tools. The present study demonstrated the use of size and hydrophobicity of amino acid residues for the purposes of quantifying the valuable sequence-structure relationship and performing further analysis of interactional mechanisms in secondary structure elements (SSEs) for toxin native conformations. First, we showed that the presence of large and hydrophobic residues varying in availability in the primary sequences correspondingly affects the amount of these residues being used in the SSEs in accordance with linear behavioral patterns from empirical assessments of experimentally derived toxins and non-toxins. Subsequent derivation of prediction rules was established with the aim of analyzing molecular structures and mechanisms by means of 114 residue compositions for venom toxins. The obtained results concerning the linear behavioral patterns demonstrated the nature of the information transfer occurring from the primary to secondary structures. A dual action mechanism was established, taking into account steric and hydrophobic interactions. Finally, a new residue composition prediction method for SSEs of toxins was suggested.

A conditional predictive p-value to compare a multinomial with an overdispersed multinomial in the analysis of T-cell populations

Immunological experiments that record primary molecular sequences of T-cell receptors produce moderate to high-dimensional categorical data, some of which may be subject to extra-multinomial variation caused by technical constraints of cell-based assays. Motivated by such experiments in melanoma research, we develop a statistical procedure for testing the equality of two discrete populations, where one population delivers multinomial data and the other is subject to a specific form of overdispersion. The procedure computes a conditional-predictive p-value by splitting the data set into two, obtaining a predictive distribution for one piece given the other, and using the observed predictive ordinate to generate a p-value. The procedure has a simple interpretation, requires fewer modeling assumptions than would be required of a fully Bayesian analysis, and has reasonable operating characteristics as evidenced empirically and by asymptotic analysis.