Set-Wise Differential Interaction Between Copy Number Alterations and Gene Expressions of Lower-Grade Glioma Reveals Prognosis-Associated Pathways

From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research

Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.

Entropy analysis and grey cluster analysis of multiple indexes of 5 kinds of genuine medicinal materials

5 kinds of genuine medicinal materials, including Diding (Latin name: Corydalis bungeana Turcz), Purslane (Latin name: Portulaca oleracea L.), straw sandal board (Latin name: Hoya carnosa (L.f.) R. Br), June snow (Latin name: Serissa japonica (Thunb.) Thunb.), pine vine rattan (Latin name: Lycopodiastrum casuarinoides (Spring) Holub. [Lycopodium casuarinoides Spring]), were selected as the research objects. The combustion heat, thermo gravimetric parameters, and fat content, calcium content, trace element content, ash content of 5 kinds of genuine medicinal materials were measured. The combustion heat, differential thermal gravimetric analysis, fat content, calcium content, trace elements content, and ash content of 5 kinds of genuine medicinal materials were used to build a systematic multi-index evaluation system by gray pattern recognition and grey correlation coefficient cluster analysis, which can make up for the gaps in this area and provide scientific basis and research significance for the study of genuine medicinal materials quality. The results showed that the order of combustion heat of 5 kinds of genuine medicinal materials, including Diding, Purslane, straw sandal board, June snow, pine vine rattan, was Diding > June snow > straw sandal board > Purslane > pine vine rattan, the order of fat content (%) of 5 kinds of genuine medicinal materials was straw sandal board > Diding > pine vine rattan > June snow > Purslane, the order of calcium content (%) was pine vine rattan > June snow > Purslane > straw sandal board > Diding, the order of ash content was June snow > Purslane > straw sandal board > pine vine rattan > Diding. From the analysis of thermogravimetric analysis results and thermogravimetric combustion stability, the order of combustion stability of 5 kinds of genuine medicinal materials was June snow > pine Vine rattan > straw sandal board > Diding > Portulaca oleracea. The order of the content of 12 trace elements in 5 kinds of genuine medicinal materials, in terms of trace element content, June snow contains the highest trace elements in all samples. According to combustion heat, combustibility (combustion stability of genuine medicinal materials), fat, calcium, ash, trace element content, the comprehensive evaluation results of multi-index analysis constructed by gray correlation degree, gray correlation coefficient factor analysis, and gray hierarchical cluster analysis showed that the comprehensive evaluation multi-index order of 5 genuine medicinal materials, including Diding, Purslane, straw sandal board, June snow and pine vine rattan, was June snow > straw sandal board > Diding > Purslane > pine vine rattan. Therefore, the comprehensive evaluation results of the quality of genuine medicinal materials selected in this study were June snow the best, followed by straw sandal board. This research has important theoretical and practical significance for the multi-index measurement and comprehensive evaluation of genuine medicinal materials, and can provide scientific basis and research significance for the research of multi-index quality control of genuine medicinal material.