Tag Archives: Somatic Variants

Somatic Variant Calling with Sentieon: Customizations

         December 10, 2019
Sentieon

The first two blogs in this series covered Sentieon’s somatic variant calling from Tumor with Normal (Part I) and Tumor without Normal (Part II). In addition to providing multiple somatic variant calling processes, users also have access to high-sensitivity scripts and full support for the GRCh38 reference assembly. Without going into excessive detail, this final blog of the series will… Read more »

Somatic Variant Calling with Sentieon: Tumor-Only Workflow

         November 19, 2019
Sentieon

To recap what we have covered in this blog series thus far, Sentieon allows users to call somatic variants against a matched normal sample and a tumor-only analysis. Part I of this series covered the variant calling workflow for tumors with matching normal samples. However, a common situation would be to call variants for a tumor sample without the normal…. Read more »

Somatic Variant Calling with Sentieon: Tumor-Normal Workflow

         October 31, 2019
Sentieon

As I mentioned in the first part of this series, Sentieon allows users to call somatic variants against a matched normal sample and a tumor-only analysis. Utilization of a Tumor-Normal Workflow In addition to the fundamental process of alignment and variant calling, there are a few more steps that will improve the quality of your secondary analysis. Figure 1 (below)… Read more »

Somatic Variant Calling with Sentieon

         October 7, 2019
Sentieon

Sentieon has become well known for the dramatic improvements it supplies in speed and accuracy for secondary analysis. Luckily, these improvements are not only available for DNAseq germline based variants but also for TNSeq somatic investigation. Sentieon has proven the capability by leading in awards such as the ICGC-TCGA DREAM Challenge for SNVs, Indel, and structural variants. This value not… Read more »

Clinical Variant Analysis for Cancer: Part V

         July 2, 2019

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: Part IV

         June 25, 2019

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: Part III

         June 18, 2019

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: Part II

         June 13, 2019

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: Part I

         June 11, 2019

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 »