Next-Generation Sequencing

Teach Me in 10

In this Teach Me in 10 episode, we are joined by Dr. Andrew Mtewa, senior lecturer in chemistry at the Malawi University of Science and Technology.

Mtewa discusses the properties that make a molecule a potential drug candidate worthy of pursuing, factors that help improve drug absorption and drug distribution in the body as well as the role of metabolism on drug action and rates.


Andrew Mtewa suggests the resources below for further reading:
•https://www.nature.com/articles/nrd1032
• https://www.sciencedirect.com/science/article/abs/pii/S1056871900001076?via%3Dihub
• https://www.sciencedirect.com/science/article/abs/pii/S1359644618303301
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350845/

ADMET in Drug Discovery With Dr. Andrew Mtewa

CD Genomics

RNA-Seq is the premier tool for mapping and quantifying transcriptomes by utilizing next-generation sequencing (NGS) technology. The transcriptome refers to the complete set of transcripts in a cell, which provides information on the transcript level for a specific developmental stage or physiological condition. Understanding the transcriptome is necessary for interpreting the functional elements of the genome and understanding development and disease. The key purpose of transcriptomics includes cataloging all species of transcripts; determining the transcriptional structure of genes; and quantifying the expression levels of each transcript under different conditions.

The Development and Workflow of RNA-seq, Learn more at https://www.cd-genomics.com/resourse-Bioinformatics-Workflow-of-RNA-Seq.html

Principle and Workflow of RNA Sequencing

16S rRNA gene sequencing is commonly used for identification, classification and quantitation of microbes within complex biological mixture. In brief, the hypervariable regions of 16s rDNA in prokaryote are amplified by PCR.  The CD genomics can provide microorganism quantification amplicon sequencing based on 16S external standard sequences to obtain absolute abundance data for species in the sample. The 16S amplicon library is constructed and sequenced by adding a synthetic sequence of known copy number to the sample DNA, and then a standard curve is drawn according to the number of amplicon reads and the absolute copy number of the external standard sequence.  https://www.cd-genomics.com/absolute-quantitative-16s-18s-its-amplicon-sequencing.html

What Is 16s rRNA sequencing？

CD genomics can help you analyze genetic variation efficiently to meet diverse research needs. By utilizing Affymetrix and Illumina array platforms, we support high-throughput and multiplex processing to meet diverse research needs, delivering high-quality data at a low per-sample cost. https://www.cd-genomics.com/SNP-Microarray.html

SNP Genotyping Technologies

Oncotarget

Dr. Robert Hsu from the Department of Internal Medicine, Division of Medical Oncology, Norris Comprehensive Cancer Center and Hospital, University of Southern California, describes a recent research paper he co-authored that was published by Oncotarget, entitled, “Molecular characterization of Kita-Kyushu lung cancer antigen (KK-LC-1) expressing carcinomas.”

DOI - https://doi.org/10.18632/oncotarget.28132

Correspondence to - Jorge J. Nieva - jorge.nieva@med.usc.edu

Abstract

Cancer/testis antigens (CTAs) are strongly expressed in some solid tumors but minimally expressed in normal tissue, making them appealing therapeutic targets. KK-LC-1 (CXorf61) has cytoplasmic expression in gastric, breast, and lung cancer. We characterized the molecular subtypes of non-small cell lung cancer (NSCLC) expressing KK-LC-1 to inform rational clinical trials of T-cell receptor therapy (TCR-T) targeting KK-LC-1. 9790 NSCLC tumors that underwent whole transcriptome sequencing (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES) at Caris Life Sciences (Phoenix, AZ) were analyzed. Tumors were split into quartiles based on KK-LC-1 expression and pathological and molecular differences were investigated. Adenocarcinoma had significantly higher KK-LC-1 expression than squamous cell carcinoma (median, 3.25 vs. 1.17 transcripts per million (TPM), p < 0.0001). Tumors with the highest quartile of KK-LC-1 expression had a greater proportion of tumors with high tumor mutation burden (TMB) (≥10 mutations per megabase; 44% vs. 28% in Q1, p < 0.001). Increased KK-LC-1 expression was associated with increased M1 macrophage abundance. Higher levels of KK-LC-1 expression were seen in pan-wild type and KRAS mutated tumors and associated with high TMB. TCR-T therapy directed against KK-LC-1 should be considered in patients whose clinical features reflect these characteristics.

Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.28132


Press release - https://www.oncotarget.com/news/pr/kita-kyushu-lung-cancer-antigen-kk-lc-1-expressing-carcinomas/

Keywords - lung cancer, tumor microenvironment, diagnostic biomarkers, biomarkers for immunotherapy, cancer testis antigen

About Oncotarget

Oncotarget is a peer-reviewed, open access biomedical journal covering research on all aspects of oncology.

To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us:

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Oncotarget is published by Impact Journals, LLC: https://www.ImpactJournals.com

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Behind the Study: Molecular Characterization of Lung Carcinomas Expressing KK-LC-1

To support the increasing research interest in small RNA, CD Genomics is offering the qualified small RNA sequencing service that covers novel small RNA discovery, mutation characterization, and expression profiling of small RNAs by leveraging of advanced NGS technologies and data analysis pipeline.	https://www.cd-genomics.com/Small-RNA.html

Small RNA Sequencing: Challengs and Workflow

CD Genomics has been providing the accurate and affordable whole genome sequencing service for couple of years. We combine both Illumina (short reads) and PacBio (long reads) platforms to achieve whole genome de novo assemblies and re-sequencing for viruses, microbes, plants, animals and humans.	https://www.cd-genomics.com/Whole-Genome-Sequencing.html

Methods and Workflow of Whole Genome Sequencing

CD Genomics has extensive experience in providing support for the selection and design of microsatellite markers for a wide range of plant and animal species. Besides microsatellite genotyping, we also provide genotyping by sequencing (GBS) method, which saves time and resources.  https://www.cd-genomics.com/Microsatellite-Genotyping-Service.html

Microsatellite Genotyping Service  at CD Genomics

Highly integrated single-base resolution DNA methylation patterning; Providing insights into gene cell-fate commitment and reprogramming, as well as gene regulation; Identifying novel epigenetic markers and targets for disease· Unable to distinguish between 5mC and 5hmC.
More information at https://www.cd-genomics.com/5mc-5hmc-sequencing-1.html

Next-Generation Sequencing

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