Processing
Cancer Genome Sequencing
Overview
Whole genome sequencing (WGS) is a method of next generation sequencing that can provide comprehensive genomic data. Sequencing a cancer patient's whole genome may help researchers better understand the genetic components of cancer pathogenesis, including heritability and the identification of cancer driver genes.
Benefits of cancer whole genome sequencing
Targeted next generation sequencing can be a cost-effective, faster alternative to whole genome sequencing if researchers already know what regions of the genome will provide helpful data. However, many cancers have an unknown genetic background, so sequencing the whole genome gives researchers the opportunity to link cancer phenotypes to genotypes. Whole genome sequencing is the best approach for discovery science or data mining which can help identify new variants. It also provides a comparison of tumor DNA profiles to that of normal DNA samples to determine novel cancer variants in both coding and non-coding regions of the genome.
Cancer molecular profiling
Research in the discovery and identification of new, targetable biomarkers is driven by comprehensive tumor profiling using NGS. However, converting tissue samples into NGS libraries is often challenging due to the low quantity and quality of DNA in such samples. Download this application note to explore how low-frequency variants were identified using this application.
Tumor-normal sequencing
Whole genome sequencing can be used to compare the whole genomes of tumor tissues to normal tissues to find point mutations and other aberrations. Tumor-normal sequencing compares the sequence of tumor tissues to healthy tissues using next generation sequencing data. The comparison can identify:
- Oncogenes—genes that have the potential to transform normal cells to cancer cells
- Somatic mutations—mutations that are accumulated due to environmental exposure and are passed down to cells of the same type
- Driver mutations—mutations that may increase tumor growth
Identify DNA methylation signatures
Performing comprehensive methylation profiling, such as whole genome bisulfite sequencing, is a commonly utilized approach for target discovery. Once target methylation signatures are known, a more cost-effective approach can be applied to increase the number of samples analyzed. Download this application note to explore the targeted methyl-seq approach used to identify DNA methylation in low-input samples consistent with WGBS.
Whole genome sequencing workflow
Whole genome sequencing is a type of next generation sequencing. After genomic material is extracted from the sample, libraries must be prepared. Library prep involves the addition of adapters to identify the samples or molecules in the sample and help the DNA adhere to the sequencing apparatus.
Extraction
LIBRARY PREP
Library prep kits
-
xGen DNA Library Prep Kit EZ (16 or 96 rxn)
for high-quality DNA samples
Indexing primers
- UDI primers (16 rxn)
-
UDI Normalase primers (96 rxn)
Normalization
xGen Normalase Module (96 rxn)
Sequencing & analysis
Tips for designing spike-in controls for next generation sequencing analysis
Every experiment needs controls to guarantee results. The performance of your next generation sequencing experiments can be tracked using synthetic DNA fragments. Read about the applications of gBlocks Gene Fragments as sequencing controls.
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