Severe kerion Celsi caused by Trichophyton quinckeanum: Severe kerion Celsi due to Trichophyton quinckeanum

We report a severe case of kerion Celsi of the scalp in a previously healthy 13-year-old girl due to Trichophyton quinckeanum, an emerging dermatophyte species in Europe. The species was definitely identified by DNA sequencing and the patient was successfully treated by oral terbinafine for 6 weeks. Kerion Celsi is a severe inflammatory form of tinea capitis, which is characterised by a purulent discharge and alopecia [1]. It typically occurs in children infected with zoophilic dermatophytes, such as Trichophyton mentagrophytes, and an increasing number of cases caused by other Trichophyton species has recently been reported [2]. Herein we report a severe case of kerion Celsi of the scalp caused by the emerging species Trichophyton quinckeanum, which was successfully treated by oral antifungal.

A systematic review on machine learning approaches in the diagnosis and prognosis of rare genetic diseases

BACKGROUND

The diagnosis of rare genetic diseases is often challenging due to the complexity of the genetic underpinnings of these conditions and the limited availability of diagnostic tools. Machine learning (ML) algorithms have the potential to improve the accuracy and speed of diagnosis by analyzing large amounts of genomic data and identifying complex multiallelic patterns that may be associated with specific diseases. In this systematic review, we aimed to identify the methodological trends and the ML application areas in rare genetic diseases.

METHODS

We performed a systematic review of the literature following the PRISMA guidelines to search studies that used ML approaches to enhance the diagnosis of rare genetic diseases. Studies that used DNA-based sequencing data and a variety of ML algorithms were included, summarized, and analyzed using bibliometric methods, visualization tools, and a feature co-occurrence analysis.

FINDINGS

Our search identified 22 studies that met the inclusion criteria. We found that exome sequencing was the most frequently used sequencing technology (59%), and rare neoplastic diseases were the most prevalent disease scenario (59%). In rare neoplasms, the most frequent applications of ML models were the differential diagnosis or stratification of patients (38.5%) and the identification of somatic mutations (30.8%). In other rare diseases, the most frequent goals were the prioritization of rare variants or genes (55.5%) and the identification of biallelic or digenic inheritance (33.3%). The most employed method was the random forest algorithm (54.5%). In addition, the features of the datasets needed for training these algorithms were distinctive depending on the goal pursued, including the mutational load in each gene for the differential diagnosis of patients, or the combination of genotype features and sequence-derived features (such as GC-content) for the identification of somatic mutations.

CONCLUSIONS

ML algorithms based on sequencing data are mainly used for the diagnosis of rare neoplastic diseases, with random forest being the most common approach. We identified key features in the datasets used for training these ML models according to the objective pursued. These features can support the development of future ML models in the diagnosis of rare genetic diseases.

Genotyping and Phylogenetic Analysis of Human Papillomaviruses in Formalin Fixed Paraffin Embedded Sections from Cervical Lesions in Duhok-Iraq

OBJECTIVE

Human papillomavirus (HPV) has been identified as an important causative factor in cervical cancer development. Cervical cancer is the fourth most prevalent malignant tumor among women globally. The purpose of this study was to investigate the prevalence and genotyping sequences of HPV in formalin-fixed paraffin-embedded (FFPE) cervical tissue using conventional polymerase chain reaction (PCR), and HPV-DNA sequencing.

MATERIAL AND METHODS

Retrospective cross-sectional study. Forty (FFPE) blocks with different cervical lesions were taken; patients' ages ranged from 24 to 65 years. Detection and sequencing of HPV DNA were done by conventional PCR (L1 gene), which was achieved by universal PCR primers (MY09/11 oligonucleotides). Then sequencing and phylogenetic tree was constructed.

RESULTS

Nine samples were found positive and detected by conventional PCR, they were identified in CIN1 and SCC at 7.5% (n=3) for each, 5.0% (n=2) KA, and 2.5% (n=1) in CIN3 cases, after sequencing were submitted to GenBank and accession numbers were obtained. The phylogenetic tree was constructed and the aligned sequences showed high homology with the nucleotide sequence of the references from the Genbank database. HPV 11, 16, 18, 22, 33, 52, and 58 were found to have little nucleotide heterogeneity and thus no amino acid heterogeneity.  Conclusion: Sequencing and  phylogenetic analysis of circulating HPV types in Duhok provides very essential data about nucleotides and amino acid heterogeneity, to reveal genetic diversity with strains included in the vaccines that have not been introduced to Iraq yet.

Nannizzia incurvata as a rare cause of favus and tinea corporis in Cambodia and Vietnam

Nannizzia (N.) incurvata (formerly Microsporum incurvatum) represents a geophilic dermatophyte which has been previously classified as belonging to the species complex of N. gypsea (formerly Microsporum gypseum). A 42-year-old Vietnamese female from Saxony, Germany, suffered from tinea corporis of the right buttock after she returned from a 2-week-visit to her homeland Vietnam. From skin scrapings of lesions, N. incurvata grew on Sabouraud's dextrose agar. Treatment by ciclopirox olamine cream twice daily for 4 weeks was successful. A 6-year-old Cambodian boy living near river Mekong with contact history to chicken, dogs and cattle suffered from tinea faciei and capitis. Symptoms of the favus-like tinea capitis and tinea faciei were erythema and scaly patches with areas of alopecia. N. incurvata grew on Sabouraud's dextrose agar. The boy was treated with oral terbinafine 125 mg daily, topical miconazole cream and ketoconazole shampoo. The symptoms healed within 4 weeks of treatment. Cultivation of the samples revealed growth of N. incurvata. For confirmation of species identification, the isolates were subject to sequencing of ITS (internal transcribed spacer) region of the rDNA, and addition of the "translation elongation factor 1 α" (TEF 1 α) gene. Sequencing of the ITS region showed 100% accordance with the sequence of N. incurvata deposited at the NCBI database under the accession number MF415405. N. incurvata is a rare, or might be underdiagnosed geophilic dermatophyte described in Sri Lanka and Vietnam until now. This is the first isolation of N. incurvata in Cambodia, and the first description of favus in a child due to this dermatophyte.

Diagnosis, Phenotype, and Molecular Genetics of Congenital Analbuminemia

Congenital analbuminemia (CAA) is an inherited, autosomal recessive disorder with an incidence of 1:1,000,000 live birth. Affected individuals have a strongly decreased concentration, or complete absence, of serum albumin. The trait is usually detected by serum protein electrophoresis and immunochemistry techniques. However, due to the existence of other conditions in which the albumin concentrations are very low or null, analysis of the albumin (ALB) gene is necessary for the molecular diagnosis. CAA can lead to serious consequences in the prenatal period, because it can cause miscarriages and preterm birth, which often is due to oligohydramnios and placental abnormalities. Neonatally and in early childhood the trait is a risk factor that can lead to death, mainly from fluid retention and infections in the lower respiratory tract. By contrast, CAA is better tolerated in adulthood. Clinically, in addition to the low level of albumin, the patients almost always have hyperlipidemia, but they usually also have mild oedema, reduced blood pressure and fatigue. The fairly mild symptoms in adulthood are due to compensatory increment of other plasma proteins. The condition is rare; clinically, only about 90 cases have been detected worldwide. Among these, 53 have been studied by sequence analysis of the ALB gene, allowing the identification of 27 different loss of function (LoF) pathogenic variants. These include a variant in the start codon, frame-shift/insertions, frame-shift/deletions, nonsense variants, and variants affecting splicing. Most are unique, peculiar for each affected family, but one, a frame-shift deletion called Kayseri, has been found to cause about one third of the known cases allowing to presume a founder effect. This review provides an overview of the literature about CAA, about supportive and additional physiological and pharmacological information obtained from albumin-deficient mouse and rat models and a complete and up-to-date dataset of the pathogenic variants identified in the ALB gene.

Cryobiopsy with endobronchial ultrasonography using a guide sheath for peripheral pulmonary lesions and DNA analysis by next generation sequencing and rapid on-site evaluation

BACKGROUND

The purpose of this study was to evaluate the diagnostic accuracy of Cryo with endobronchial ultrasonography using a guide sheath (EBUS-GS) for peripheral pulmonary lesions (PPLs) to assess the volume of specimen, determine DNA sequencing analysis, and evaluate the utility of rapid on-site evaluation (ROSE).

METHODS

Out of 30 patients assessed for eligibility, 23 were enrolled in this prospective study. The histological diagnostic yield of Cryo was evaluated and the volume was compared to that of trans-bronchial biopsy (TBB). DNA analysis of Cryo was performed using next generation sequencing (NGS). ROSE was compared with the final diagnosis.

RESULTS

The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy rate was 85%, 100%, 100%, 50%, 87% for Cryo and 80%, 100%, 100%, 42.9%, 82.6% for TBB, respectively. The mean volume was 0.078 cm³ for Cryo and 0.003 cm³ for TBB (p < 0.0001). All Cryo specimens provided sufficient quantity and quality of DNA for analysis by NGS. ROSE had a high sensitivity (70%), specificity (100%), PPV (100%), and diagnostic accuracy (73.9%). There were no clinically serious adverse events except mild bleeding in 4 cases.

CONCLUSIONS

Cryo with EBUS-GS for PPLs is a safe and potentially useful diagnostic strategy. It has a high diagnostic yield, and provides significantly larger specimens than TBB. It also provides high quantity and quality of DNA for NGS and high concordance rate between ROSE and the final diagnosis.

Detection of Copy Number Variation Regions Using the DNA-Sequencing Data from Multiple Profiles with Correlated Structure

In this article, we investigate the problem of detecting boundaries of DNA copy number variation (CNV) regions using the DNA-sequencing data from multiple subject samples. Genomic features along the linear realization of the actual genome are correlated, especially within vicinity of a locus, so are the sequencing reads along the genome. It is then crucial to take the correlated structure of such high-throughput genomic data into consideration when modeling DNA-sequencing data for CNV detection from statistical and computational viewpoints. We use the framework of a fused Lasso latent feature model to solve the problem, and propose a modified information criterion for selecting the tuning parameter when search for common CNVs is shared by multiple subjects. Simulation studies and application on multiple subjects' next-generation sequencing data, downloaded from the 1000 Genome Project, showed that the proposed approach can effectively identify individual CNVs of a single subject profile and common CNVs shared by multiple subjects.

Robust in-silico identification of cancer cell lines based on next generation sequencing

Cancer cell lines (CCL) are important tools for cancer researchers world-wide. However, handling of cancer cell lines is error-prone, and critical errors such as misidentification and cross-contamination occur more often than acceptable. Based on the fact that CCL today very often are sequenced (partly or entirely) anyway as part of the studies performed, we developed Uniquorn, a computational method that reliably identifies CCL samples based on variant profiles derived from whole exome or whole genome sequencing. Notably, Uniquorn does neither require a particular sequencing technology nor downstream analysis pipeline but works robustly across different NGS platforms and analysis steps. We evaluated Uniquorn by comparing more than 1900 CCL profiles from three large CCL libraries, embracing 1585 duplicates, against each other. In this setting, our method achieves a sensitivity of 97% and specificity of 99%. Errors are strongly associated to low quality mutation profiles. The R-package Uniquorn is freely available as Bioconductor-package.

MPD: multiplex primer design for next-generation targeted sequencing

Background

Targeted resequencing offers a cost-effective alternative to whole-genome and whole-exome sequencing when investigating regions known to be associated with a trait or disease. There are a number of approaches to targeted resequencing, including microfluidic PCR amplification, which may be enhanced by multiplex PCR. Currently, there is no open-source software that can design next-generation multiplex PCR experiments that ensures primers are unique at a genome-level and efficiently pools compatible primers.

Results

We present MPD, a software package that automates the design of multiplex PCR primers for next-generation sequencing. The core of MPD is implemented in C for speed and uses a hashed genome to ensure primer uniqueness, avoids placing primers over sites of known variation, and efficiently pools compatible primers. A JavaScript web application (http://multiplexprimer.io) utilizing the MPD Perl package provides a convenient platform for users to make designs. Using a realistic set of genes identified by genome-wide association studies (GWAS), we achieve 90% coverage of all exonic regions using stringent design criteria. Using the first 47 primer pools for wet-lab validation, we sequenced ~25Kb at 99.7% completeness with a mean coverage of 300X among 313 samples simultaneously and identified 224 variants. The number and nature of variants we observe are consistent with high quality sequencing.

Conclusions

MPD can successfully design multiplex PCR experiments suitable for next-generation sequencing, and simplifies retooling targeted resequencing pipelines to focus on new targets as new genetic evidence emerges.

RAPD marker in grapevine (Vitis spp.) similar to plant retrotransposons

When assaying for sequence heterogeneity within monomorphic RAPD-PCR products in grapevines (Vitis spp.), we observed partial digestibility of a marker with the restriction enzyme MspI. The degree of digestion varied reproducibly between different cultivars. To study this phenomenon, two of the amplification products were cloned and sequenced. They show 91.7% similarity to each other. The DNA analysed was found to possess high similarity to retrotransposons from higher plants. This element seems repetitive and dispersed throughout the genome. To our knowledge, this is the first report of retrotransposon-like elements in woody plants.