Genetic Analysis of the COVID Virus and Other Pathogens
In this eBook, I summarize to the best of my knowledge our current understanding of COVID-19 and the virus SARS-Cov-2 causing it. Most of the papers that I used to prepare this eBook were published since the beginning of this year. The body of knowledge is quickly expanding and evolving. Next-Generation Sequencing (NGS) can deliver significant insights in this process. This eBook outlines how NGS can be used and how Golden Helix software solutions can be utilized in the process.
Cyber Security Strategies for NGS Testing Labs
In this eBook, I review historic data breaches and discuss common cyber threats. This is mainly to explain the complexity we are dealing with both from a software vendor perspective and from a customer point of view implementing a state-of-the-art diagnostic pipeline. Moreover, I review how Golden Helix is able to provide a solution that can be utilized entirely internet independent behind a firewall.
Clinical Variant Analysis: Applying ACMG Guidelines to Analyze Germline Variants
In this eBook, I summarize the key concepts of the ACMG Guidelines, including what defines a pathogenic and respectively a benign variant; scoring mechanisms that allow us to classify a variant clinically, and a few interesting cases of variants and their classifications. This eBook is designed to show how we are able to support this equally complex and tedious process with our clinical interpretation solution VSClinical.
Clinical Variant Analysis for Cancer: Applying AMP Guidelines to Analyze Somatic Variants
The clinical utilization of Next-Gen Sequencing data to diagnose cancer has taken off. Along with it, the need arose to standardize the interpretation and reporting of observed genomic variations. This eBook gives an overview of how the clinical diagnostic process is designed. In this context, I also explain how our products support clinicians in their decision making in concordance with the guidelines issued by the College of American Pathologists (AMP).
Genetic Testing for Cancer
In this eBook, I cover lung cancer as an example for genomic testing; conducting a gene panel base cancer diagnosis; how a Tumor/Normal analysis can be conducted; how Copy Number Variations (CNVs) can be used in the diagnostics process; and a practical case-study of how VarSeq is deployed in leading institutions such as the University of Iowa.
NGS-Based Clinical Testing
This eBook discusses our best understanding of how this revolution in clinical diagnostics will unfold and the critical success factors for the clinical adoption of next-gen sequencing technology. I also cover how to implement, vet and maintain various parts of a clinical pipeline.
Secondary Analysis: Calling Single Nucleotide and Copy Number Variants in Next-Gen Sequencing Data
Golden Helix spearheaded the development of commercial-grade algorithms and methods that allow the analysis of CNVs in gene panels, clinical becomes, and whole genomes side by side with the standard SNP analysis. This eBook captures the most important concepts in this field, while at the same time providing insight into an integrated analysis applied in practice.
Through a collaborative effort between clinicians, pharma companies, scientists, and regulatory agencies, we are working on a new framework for standard care on a global basis. This eBook covers tailoring diagnostic and therapeutic strategies; regulatory issues; adoption by patients and health care professionals; the educational challenge; and a bioinformatics pipeline and system infrastructure.
Genetic Data Warehousing
In this eBook, I explain the concept of data warehousing and discuss the use cases for this technology vis-a-vis the upcoming requirements in clinical labs that are implementing Precision Medicine.
Genome Wide Association Study
This eBook explains the fundamental steps and concepts for completing a GWAS and how they’re implemented in SVS. I start with an introduction to GWAS – exploring its biology and origins, as well as the practical use of GWAS. Then, readers get an explanation on how to perform a GWAS in SVS, discussing quality control, including sample statistics, heterozygosity, LD pruning, population stratification and identity by descent. Additionally, this eBook explains how to impute data within SVS, genotype association testing, and how to conduct a meta-analysis.
Genomic Prediction in Agriculture
In the field of plant and animal research, genomic prediction is a key focus area. This eBook covers building predictive systems, predictive algorithms, Bayesian methods, and gBLUP with practical examples using Golden Helix software.
Teaching Bioinformatics: Concepts and Practical Skills
This eBook gives an introduction to the educational challenge at hand and a practical example from the University of Illinois Urbana-Champaign. I demonstrate how to learn clinical and research workflows and offer readers a teaching methodology.