ACE Cancer Services

Analysis and Annotation

High accuracy alignment and variant calling for both germline and somatic variants

ACE Cancer Analysis and Annotation 2017-04-03T13:41:33+00:00

ACE Cancer Analysis and Annotation Pipeline

DNA Analysis

The Personalis DNA Analysis Pipeline for Cancer performs high accuracy alignment and variant calling for both germline and somatic variants. Somatic variants can be identified in either Tumor / Normal, or from Tumor-only data sets. Somatic variant types including single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variants (CNVs) are reported. Loss of heterozygosity is also reported. All of these variants are annotated against databases of known variants and cancer information and collated into reports. In addition, filtered and refined reports are generated for ease of use. Finally, QC reports delineating sequencing metrics as well as somatic analysis summary statistics are included in html format (see Data Deliverables table below).

DNA Analysis Pipeline

FIGURE 1: Personalis DNA Pipeline for Cancer

RNA Analysis

rna_pipeline

FIGURE 2: Personalis RNA Pipeline for Cancer

The Personalis RNA Analysis Pipeline for Cancer performs a high accuracy gapped alignment and variant calling. Personalis’ pipeline is capable of detecting a wide variety of important cancer related events from RNA sequencing data, including SNVs, Indels, and gene fusion events. Comparison of variants identified in RNA vs DNA, from the same sample, makes it clear which DNA variants are actually expressed, and at what level, in the tumor. RNA read depths can also be used to digitally quantify relative gene expression. To further empower researchers, our pipeline thoroughly annotates variants using a wide variety of sources, including information covering many important cancer features. As with the DNA analysis, detailed reports are provided for each variant class, easing accessibility (see Data Deliverables table below).

Comprehensive Annotation

We have created a comprehensive annotation engine that utilizes industry standard cancer databases (e.g., COSMIC, Cancer Gene Census, HGMD, etc.), pathway databases, drug-gene interaction databases (e.g., Drugbank), and hand-curated cancer gene annotations from the literature to generate annotated cancer variant reports for both somatic and germline variants. We also include pharmacogenomics annotations through our exclusively licensed, manually curated database, PharmGKB™.

 

Personalis® ACE Cancer Data Analysis Deliverables

Cancer DNA Analysis Cancer RNA Analysis
RAW data files: FASTQ, BAM files RAW data files: FASTQ, BAM files
Sample-level variant calling: VCF files Variant (SNV, indel) analysis
Sample-level variant calling: VAR file Variant (SNV, indel) annotation report
Somatic variant calling: VCF file Cancer gene associated variant (SNV/indel) analysis and report
Somatic variant annotation: VAR file Fusion gene analysis and report
Filtering and annotation of variants by cancer relevance and frequency: VAR file Gene based expression report
Somatic CNV report and plots QC report
Somatic LOH reports and plots
QC report