GenomeWebinars

This webinar provides a comparison of several next-generation sequencing (NGS) approaches — including short-read 16S, whole-genome sequencing (WGS), and synthetic long-read sequencing technology — for use in microbiome research studies.

NGS is a powerful method for characterizing complex microbial mixtures, but both short-read 16S and WGS methods have their shortcomings. While short-read 16S data is inexpensive, it only enables family- or genus-level identification, is not comparable across different variable regions, and provides poor relative abundance estimation. WGS, meanwhile, offers more accurate relative abundance estimation and greater specificity, but at increased cost and complexity.

Another approach, LoopSeq synthetic long-read sequencing technology from Loop Genomics, offers an intermediate solution by providing species-level identification and significantly improved relative abundance estimation over short-read 16S data. LoopSeq uses unique molecular identifiers to generate synthetic long reads on short-read Illumina sequencing instruments. 

In this webinar, Nick Greenfield of One Codex discusses a comparison study of short-read 16S, WGS, and LoopSeq data for four samples – two known composition-positive controls, including a 20-organism bacterial mixture from ATCC, and two complex microbiome samples.

He shares details from this comparison as well as demonstrate how to analyze these datasets on the One Codex software platform.

This webinar is the first Loop Genomics GenomeWebinar on the topic of long-read versus short-read sequencing approaches. Part 2 will provide a comparison of (NGS) approaches for human transcriptome sequencing, including short-read Illumina sequencing and synthetic long-read sequencing technology. Register Here - Part 2.

Rhythm Pharmaceuticals and Genomenon will discuss their efforts to assemble a database of mutations associated with rare genetic disorders of obesity, and how this was optimized to facilitate a deep understanding of the variant landscape of melanocortin-4 receptor (MC4R)-pathway genes. This database may help identify MC4R-pathway deficient individuals who might benefit from future precision therapies.

WHY ATTEND? Developing an evidence-based view of the genetic contributors to human disease can help improve the diagnosis of rare disorders and drive important advances in precision drug development. Learn how Rhythm Pharmaceuticals partnered with Genomenon to inform their understanding of rare genetic disorders of obesity and help identify patients who might be appropriate for participation in clinical trials.

DETAILS: By indexing over 6 million full-text genomic articles using the Mastermind Genomic Search Engine, 120 genes and over 10,000 variants were identified as being associated with obesity in the medical literature. Each individual variant was interpreted using the evidence assembled through an automated technical process. This novel semi-automated approach to variant identification and annotation was accomplished via the Mastermind genomic database and vetted using American College of Medical Genetics and Genomics (ACMG) guidelines.

Join Alastair Garfield, PhD, Vice President, Translational Research & Development (TRAD) at Rhythm Pharmaceuticals and Dr. Mark Kiel, Founder and Chief Science Officer at Genomenon, as they share how a database of genes and variants associated with obesity was developed in less than 60 days, including scientific evidence complete with literature citations and ACMG interpretations for each mutation. The machine-learning driven process replaced several years of manual research of the scientific literature to find obesity-related mutations.

You will learn:

• The importance of published genetic evidence in ensuring the success of a drug candidate
• How to rapidly assemble a comprehensive biomarker database of this genetic evidence using data available in Mastermind
• Why automated approaches are required for such disease-variant projects

This webinar will demonstrate how a research team at the National Institutes of Health evaluated a novel in situ hybridization approach and applied it to study splice variants related to schizophrenia.

The neurotrophic factor neuregulin-1, as well as its neuronal receptor ErbB4, are risk factors for schizophrenia. Distinct ErbB4 isoforms are generated by alternative splicing, and the levels of specific receptor isoforms are altered in postmortem brains of patients.

Because of these splice variants differ functionally, it is important to identify the cells that express distinct isoforms. However, traditional molecular analysis tools such as qRT-PCR and RNA sequencing require the disruption of dissected tissue to isolate RNA. To investigate in different cell types the relative amounts of the four ErbB4 variants in morphologically conserved brain tissue, the NIH team used the BaseScope in situ hybridization system with specific oligonucleotides targeting single exon/exon boundaries and fluorescence signal amplification.

This webinar will outline how the NIH researchers first determined the specificity and sensitivity of the BaseScope system and then used it to identify regional and cell-type specific expression of ErbB4 isoforms in the brain. The presentation will also explain how the NIH team quantified both the BaseScope and RNAscope assay signals using the freeware CellProfiler combined with an in-house analysis pipeline.

With the Next Generation Sequencing (NGS), genome sequencing has been democratized over the last decades with the detection of genomic alterations.

This webinar will discuss the different steps taken by the CHU de Dijon to move from a non-NGS lab to an experienced NGS lab and how Sophia Genetics has successfully accompanied the lab to use different diagnostic molecular applications to address their clinical needs in a short turnaround time using Sophia artificial intelligence (AI).

In the first part of the webinar, Dr. Caroline Chapusot will cover the set-up program used to implement the Solid Tumor Solution by Sophia Genetics in the lab and the advantages of this solution over previous lab’s tests.

Then, Dr. Chapusot will discuss two specific clinical cases addressed using STS and Sophia DDM platform for the analysis and the interpretation of the data.

Finally, Dr. Chapusot will discuss the vision of the CHU de Dijon over the NGS applications used for clinical and research purposes and their impact on the reimbursement system.

In the last part of the webinar, Dr. Shirine Benhenda of Sophia Genetics will briefly introduce a solution that will soon be launched to detect gene fusions, beside SNVs, Indels, MSI and gene amplifications in FFPE samples from various solid tumors.

The Solid Tumor Solution by Sophia Genetics is a molecular application that bundles a capture-based target enrichment kit with the analytical power of Sophia AI with and full access to Sophia DDM platform. The application is designed to accurately characterize the complex mutational landscape of solid cancers associated with lung, colorectal, skin and brain cancers using FFPE samples.

This webinar will address a range of methods for optimizing small RNA library preparation.

Anitha Jayaprakash, co-founder of T-cell receptor sequencing firm Girihlet, will provide her perspectives on sequencing small RNAs and its utility in the study of various applications, including miRNA profiling in various systems and other small RNAs such as piRNAs in the germline.

Dr. Jayaprakash will discuss challenges and complications that can occur during small RNA-seq library prep and ways to avoid them. She will review the various steps in small RNA-seq library construction and discuss how protocol optimization can improve results and increase user friendliness. She will also discuss the 4N sequencing method, which uses randomized adapters to reduce the ligation bias associated with small RNA sequencing.