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Whole genome sequencing for cancer research
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 assess patients’ prognoses and tailor treatment plans based on their molecular profile, an approach called precision medicine.
Benefits of WGS for cancer research
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. Many cancers have 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.
Discovery
AgBio
Environmental Sustainability
Next generation sequencing in the clinic
Dr Elaine Mardis' lab focuses on NGS in relation to cancer care. She shares her views on the current uses of NGS, the challenges that NGS technologies face, and what can be expected in the future.
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. Identifying differences gives researchers information about how to potentially treat the tumor without damaging healthy tissue. 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 cause cancer
- 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
Combining NGS technologies for biomarker identification and confirmation research application note
IDT has developed 2 unique, high-performing targeted NGS approaches to maximize researchers’ ability to confidently identify and confirm biomarkers in germline and somatic mutations. Here, we describe the benefits and caveats of using either hybridization capture or amplicon sequencing to identify mutations in normal tissue, formalin-fixed, paraffin-embedded (FFPE) tumor, and cell-free DNA (cfDNA).
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 includes the addition of adapters to identify the samples or molecules in the sample and to help the DNA adhere to the sequencing apparatus.
Extraction
- Beckman Coulter Life Sciences Genomics Reagents
Sequencing
- Illumina
- Pacific Biosciences
- Oxford Nanopore Technologies
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.
Get started with WGS solutions for cancer research
Working in an area that would benefit from sequencing? Just starting? See how you can easily improve your workflows and results.
Lotus DNA Library Prep Kit
The Lotus DNA Library Prep Kit enables streamlined preparation of high-quality next generation sequencing (NGS) libraries from double-stranded DNA (dsDNA)—generate libraries suitable for PCR-free, PCR-amplified, and targeted sequencing applications on Illumina platforms.
xGen Stubby Adapter and Unique Dual Index Primer Pairs
Ensure maximum accuracy in your NGS reads with xGen Stubby Adapter and Unique Dual Indexing (UDI) Primer Pairs. A convenient indexing option for a variety of applications from whole-genome to targeted sequencing, the kit provides adapters and unique i5 and i7 primer pairs that can be used with TruSeq™-compatible library prep for sequencing on Illumina instruments.
NGS Discovery Pools
NGS Discovery Pools allow you to build custom panels quickly at a fraction of the cost of conventional custom panels.
gBlocks™ & gBlocks HiFi Gene Fragments
gBlocks and gBlocks HiFi Gene Fragments are dsDNA fragments of 125–3000 bp in length. They are designed for affordable and easy gene construction or modification, qPCR/NGS controls, and more.