Comparison of ultrasonography and pathology features between children and adolescents with papillary thyroid carcinoma

Objective

To compare the ultrasonography and pathology features between children and adolescents with papillary thyroid carcinoma (PTC).

Methods

A total of 53 patients who were surgically diagnosed with childhood or adolescent PTC between 2017 and 2022 were included in this study. The pre-operative ultrasonography, post-operative histology, and molecular and clinical characteristics were retrospectively analyzed.

Results

No differences were observed in composition, echogenicity, and shape using ultrasonography. Moreover, there was a significantly higher rate of extrathyroidal extension, punctate echogenic foci, and lymph node metastases in children compared to adolescents. The molecular analysis showed that BRAF^V600E mutations are the most prevalent abnormality in adolescent PTC (12/20, 60.0%). However, they are less in childhood PTC (7/23, 30.4%). In addition, using next-generation sequencing, three cases with oncogenic fusion (one TRIM33-RET case, one CCDC6-RET case, and one STRN-ALK case) were identified in childhood PTC.

Conclusion

The frequency of extrathyroidal extension, punctate echogenic foci, and lymph node metastases were higher in childhood PTC, while BRAF^V600E mutations were higher in adolescent PTC.

NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data

Background

The study of microbial communities and their applications have been leveraged by advances in sequencing techniques and bioinformatics tools. The Oxford Nanopore Technologies long-read sequencing by nanopores provides a portable and cost-efficient platform for sequencing assays. While this opens the possibility of sequencing applications outside specialized environments and real-time analysis of data, complementing the existing efficient library preparation protocols with streamlined bioinformatic workflows is required.

Results

Here we present NanoRTax, a Nextflow pipeline for nanopore 16S rRNA gene amplicon data that features state-of-the-art taxonomic classification tools and real-time capability. The pipeline is paired with a web-based visual interface to enable user-friendly inspections of the experiment in progress. NanoRTax workflow and a simulated real-time analysis were used to validate the prediction of adult Intensive Care Unit patient mortality based on full-length 16S rRNA sequencing data from respiratory microbiome samples.

Conclusions

This constitutes a proof-of-concept simulation study of how real-time bioinformatic workflows could be used to shorten the turnaround times in critical care settings and provides an instrument for future research on early-response strategies for sepsis.

Development and performance evaluation of whole-genome sequencing with paired-end and mate-pair strategies in molecular characterization of GM crops: One GM rice 114-7-2 line as an example

Basic data for the safety assessment of transgenic line involves the molecular characterization of the integration site of exogenous DNA, flanking sequences, copy number, and unintended plasmid backbone residues. However, performing a full molecular characterization remains challenging, especially for GMOs that possess complex exogenous DNA integrations. We established two whole-genome sequencing strategies: paired-end and mate-pair, to characterize the exogenous DNA integration of a human serum albumin gene into rice line 114-7-2, and evaluated the performance of these two strategies in the molecular characterization of transgenic line. The results showed the existence of two exogenous DNA insertion loci (Chr 01 and Chr 04) and their corresponding flanking sequences, five copies of the exogenous rHSA gene, and the presence of unintended residual plasmid backbone sequences. However, the WGS-MP strategy demonstrated higher efficiency, lower cost, and lower background noise compared with the WGS-PE analysis, especially for identification of the exogenous DNA integration site.

NGS allele counts versus called genotypes for testing genetic association

RNA sequence data are commonly summarized as read counts. By contrast, so far there is no alternative to genotype calling for investigating the relationship between genetic variants determined by next-generation sequencing (NGS) and a phenotype of interest. Here we propose and evaluate the direct analysis of allele counts for genetic association tests. Specifically, we assess the potential advantage of the ratio of alternative allele counts to the total number of reads aligned at a specific position of the genome (coverage) over called genotypes. We simulated association studies based on NGS data from HapMap individuals. Genotype quality scores and allele counts were simulated using NGS data from the Personal Genome Project. Real data from the 1000 Genomes Project was also used to compare the two competing approaches. The average proportions of probability values lower or equal to 0.05 amounted to 0.0496 for called genotypes and 0.0485 for the ratio of alternative allele counts to coverage in the null scenario, and to 0.69 for called genotypes and 0.75 for the ratio of alternative allele counts to coverage in the alternative scenario (9% power increase). The advantage in statistical power of the novel approach increased with decreasing coverage, with decreasing genotype quality and with decreasing allele frequency – 124% power increase for variants with a minor allele frequency lower than 0.05. We provide computer code in R to implement the novel approach, which does not preclude the use of complementary data quality filters before or after identification of the most promising association signals.

Author summary

Genetic association tests usually rely on called genotypes. We postulate here that the direct analysis of allele counts from sequence data improves the quality of statistical inference. To evaluate this hypothesis, we investigate simulated and real data using distinct statistical approaches. We demonstrate that association tests based on allele counts rather than called genotypes achieve higher statistical power with controlled type I error rates.

Living-Donor Liver Transplantation for Late-Onset Lysosomal Acid Lipase Deficiency

Late-onset liposomal acid lipase deficiency (LAL deficiency), previously known as Cholesteryl ester storage disease (CESD) is a rare genetic lysosomal storage disorder caused by deficiency of lysosomal acid lipase (LAL) due to mutations in the LIPA gene. LAL deficiency is a systemic disease that leads to the accumulation of fat and inflammation in the liver, premature atherosclerosis and gastrointestinal disease. Most of the patients require liver transplantation due to decompensated cirrhosis. Enzyme replacement therapy has been approved and is available in many countries. Here we describe a 16-year-old patient who was diagnosed to have late-onset LAL deficiency when he presented to us with ESLD. Subsequently, he underwent a living-donor liver transplant (LDLT) successfully. We discuss the ethical dilemmas in considering LDLT for LAL deficiency.

A novel variant m.8561C>T in the overlapping region of MT-ATP6 and MT-ATP8 in a child with early-onset severe neurological signs

Among mitochondrial diseases, isolated complex V (CV) deficiency represents a rare cause of respiratory chain (RC) dysfunction. In mammalian mitochondrial DNA (mtDNA), MT-ATP6 partly overlaps with MT-ATP8 making double mutations possible, yet extremely rarely reported principally in patients with cardiomyopathy. Here, we report a novel m.8561 C>T substitution in the overlapping region of MT-ATP6 and MT-ATP8 in a child with early-onset ataxia, psychomotor delay and microcephaly, enlarging the clinical manifestations spectrum associated with CV deficiency.

Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens

Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.