This morning I released a new version of my eBook “Clinical Variant Analysis – Second Edition.” The clinical interpretation of variants in Next-Gen Sequencing is a quickly evolving field. While the body of knowledge is growing exponentially, experts have to derive sound, clinical decisions leveraging an ever-expanding set of specialty databases, clinical publications, and algorithms that are designed to predict the… Read more »
I am pleased to share with you the official release of my updated eBook, “Precision Medicine“. Almost 2,500 years ago, Hippocrates captured one of the key principles underlying precision medicine. In the 21st century, we take an understanding of the individual characteristics of a person to a new level. By leveraging information about an individual’s genome, we are able to… Read more »
This morning I released a new version of my eBook “Genetic Data Warehousing – Second Edition.” As Next-Generation Sequencing is taking off in the clinic, it creates a significant data management issue for clinicians, scientists, and IT professionals alike. How can we retain the massive amounts of data coming out of clinical pipelines in a way that enables labs to… Read more »
This morning I released a new version of my eBook “Clinical Variant Analysis for Cancer – Second Edition.” The clinical utilization of Next-Generation Sequencing data to diagnose cancer has taken off, resulting in the need to standardize the interpretation and reporting of observed genomic variations. This eBook explores the entire clinical diagnostic process. It demonstrates how Golden Helix software can support clinicians with their… Read more »
Next-Generation Sequencing (NGS) technology has decreased the price of nucleotide sequencing exponentially in the last 10 years. The clinical applications are broad, from diagnosis of rare diseases, to carrier screening and hereditary disease risk, and finally, for the personalized treatment of cancer with molecular profiling of tumors for therapeutic, diagnostic, and prognostic genomic biomarkers. Discovery and Sharing of the Reference Genome for SARS-CoV-2 With… Read more »
*The following text is only a preview of our new eBook “Genetic Analysis of the COVID-19 Virus and Other Pathogens”. Request a free copy to access the full version.* Next-Gen Sequencing (NGS) of the novel virus can make a tremendous contribution in enhancing our understanding of the underlying pathways in which it impacts humans. In a short period of time… Read more »
*The following text is only a preview of our new eBook “Genetic Analysis of the COVID-19 Virus and Other Pathogens”. Request a free copy to access the full version.* SARS-CoV-2 has just been recently discovered. The knowledge about this virus is fairly new and certain aspects of it are still under review or in-flux entirely as we learn more about… Read more »
*The following text is only a preview of our new eBook “Genetic Analysis of the COVID-19 Virus and Other Pathogens”. Request a free copy to access the full version.* At the end of 2019, a virus appeared somewhere in the Chinese city of Wuhan. It caused cold and flu-like symptoms in most, but also pneumonia and death in a few…. Read more »
This morning I released a new eBook titled “Genetic Analysis of the COVID-19 Virus and Other Pathogens“. The COVID-19 pandemic is reaching historic proportions. We are dealing with an infectious disease that is caused by a novel coronavirus we discovered just a few months ago. Since then, it has brought healthcare systems to the brink, it altered how we work,… Read more »
Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Detecting cancer at an early stage can make it much more treatable. Developing tests and making them clinically actionable is crucial to beat this disease. This eBook covers the state-of-the-art gene panel tests for cancer. Of course, there is more that can be done. The field is… Read more »
Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Somatic variants can manifest in different ways: Single Nucleotide Variants Indels Fusions and Copy Number Variations There is a difference between the interpretation of germline and somatic variants. The former is exclusively focused on establishing the level of pathogenicity vis a vis a particular disease. In contrast… Read more »
Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants As described in my eBook “Genetic Testing for Cancer,” any bioinformatic pipeline for cancer ultimately calls variants based on the aligned reads that the sequencer generated. Variant calling is the process of reviewing a sequence alignment, typically in the form of a BAM file, to identify loci… Read more »
Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Analogous to the ACMG guidelines for germline mutations, the Association for Molecular Pathologists (AMP) has issued guidelines to assess and report on somatic variants. The key paper in this area was published by Li et. al (2017) with the title “Standards and Guidelines for the Interpretation and… Read more »
Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Precision Medicine uses genetic information from individual patients. This may include the following areas: Diagnosis Treatment Prevention Specifically, in the cancer space, data derived from Next-Gen Sequencing (NGS) is used to diagnose and prognose diseases, select a targeted therapy and potentially evaluate the suitability of a patient… Read more »
Applying AMP Guidelines to Analyze Somatic Variants Today, I am thrilled to share with you the launch of a brand new eBook titled “Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants”. We would happy to send you a complimentary copy which can be requested on our website here. The clinical utilization of Next-Gen Sequencing data… Read more »
Yesterday, I released a new version of my eBook, “Genetic Testing for Cancer – Third Edition”. We would be happy to send you one! To download a complimentary copy, please submit a request on our site here. In 1914, the German cytologist Theodor Boveri coined the phrase “Cancer is a disease of the genome.” At this time, his ideas were… Read more »
We have released a new version of my eBook, “Secondary Analysis 3.0”. To download a complimentary copy, I encourage you to do so here. Next-Generation Sequencing (NGS) promises to be the ultimate paradigm when it comes to genetic research and clinical testing since it contains the complete genetic information. When it comes to the current reality in testing labs, there… Read more »
With a properly defined wet-lab and bioinformatics process, we are able to zero in on clinically relevant variants. How does a lab report on the outcome of their analysis? We find that most laboratories conduct their variant classification based on the guidelines formulated by the American College of Medical Genetics (ACMG) for inherited diseases. The ACMG guidelines for variant classification… Read more »
Any validated bioinformatics pipeline must be continuously monitored. Quality management in clinical testing labs ensures that any divergence from predefined quality metrics during the analysis of clinical samples is investigated. For example: There is an insufficient number of sequence reads that passed the predefined base quality score threshold The number of variants identified in a data set may deviate substantially… Read more »
After the Wet Lab process has been completed, the bioinformatics analysis of the sequencing data work begins. The next three blogs will focus on three aspects of this process. The building blocks of a bioinformatics pipeline, documentation and validation (today’s topic) Quality Management Clinical Reporting The Building Blocks of an NGS PipelineThe bioinformatics process to analyze NGS data occurs in three… Read more »
