Cancer Sequencing Methods

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Utilizing next-generation sequencing in cancer research

NGS-based cancer sequencing methods have expanded our understanding of cancer development, regulation, and progression to unlock new pathways for research. These techniques help detect changes in the cancer genome and identify their impact on the transcriptome, epigenome, and proteome.

Unlike other methods, such as PCR and Sanger sequencing, NGS has the ability to assess thousands of targets at once, greatly amplifying the discovery potential per sample. NGS can also detect low-frequency molecular events associated with carcinogenesis, cancer growth, and metastasis that could be missed using traditional molecular methods. Together, these advancements are paving the future towards improving translational medicine and therapies.

General NGS approaches to cancer research

Researchers can leverage several approaches when studying biological “omes”: bulk-cell analysis, single-cell analysis, spatial analysis, and metagenomic analysis. Each method studies cancer at a different level of biological resolution and has a distinct use case depending on the research goals and objectives.

Bulk-cell analysis: Bulk-cell analysis allows scientists to study pooled cell populations, tissue sections, or biopsies.

Single-cell analysis: Single-cell analysis studies a given “ome” at the resolution of a single cell.

Spatial analysis (also called spatial genomics): Spatial analysis captures “omic” information at the cellular level within an intact tissue sample to link structure and activity.

Metagenomic analysis: Metagenomic analysis sequences every gene in every organism of a complex microbial community present within a tissue, organ, or tumor.

Multiomics in cancer research

Multiomics (multiple omics) integrates data across genomics, transcriptomics, epigenetics, and proteomics to make insights into complex diseases such as cancer. This comprehensive approach aids researchers in understanding molecular changes driving normal development, cellular responses, and diseases.

Learn more about multiomics

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Targeted vs. untargeted NGS methods for cancer research

Both targeted and untargeted approaches play crucial roles in research. Targeted research contains some bias since specific, preconceived pathways/targets are assessed. Although this approach may be more efficient and cost-effective in limited cases, untargeted approaches can maximize novel discoveries as they are not dependent on prior knowledge of sequence information. To achieve untargeted sequencing, NGS offers a comprehensive selection of methods to analyze complex cancer samples.

Key cancer sequencing methods

Method Description and Use
Cancer whole-genome sequencing Identifies a comprehensive list of cancer-driving genetic events.
Cancer whole-exome sequencing A cost-effective and efficient sequencing method to find cancer-driving genes within the coding region of the genome compared to whole-genome sequencing.
ctDNA sequencing Used as a potential alternative to invasive tissue biopsies to detect cell-free circulating tumor DNA (ctDNA), which can act as a noninvasive cancer biomarker.
Targeted NGS cancer panels Targets known DNA and/or RNA variants from the same FFPE sample.
Methylome sequencing Both genome-wide analysis and targeted approaches can provide insight into methylation patterns at the single nucleotide level.
Cancer epigenetics Identifies cellular biomarkers associated with regulation of cancer genes or drug resistance.
ATAC-Seq Determines chromatin accessibility across the genome without prior knowledge of regulatory elements.
Cancer RNA-Seq Measures the average RNA expression and transcriptome changes in cancer samples.
Spatial transcriptomics Analyzes gene expression within the natural tumor microenvironment and architecture.
Single-cell RNA-Seq Measures gene expression and explores the distinct biology of individual cancer cells in complex tissues.
Proteomics + Transcriptomics
Cellular indexing of transcriptomes and epitopes (CITE-Seq) Uses oligonucleotide-labeled antibodies to simultaneously measure proteins and RNA in single cells. This combined proteomics/transcriptomics approach links RNA expression to cancer phenotypes.
cancer research methods guide

Cancer Research Methods Guide

The Cancer Research Methods Guide is a 40+ page comprehensive resource with simple, comprehensive workflows for a broad range of cancer research applications. This guide includes single-cell sequencing, spatial sequencing, methylation profiling, multiomics, cell-free RNA sequencing, and more.

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Cancer research applications

Cancer research applications

Learn about specific cancer research applications and explore resources covering research developments, guides, products, and more.

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Sequencing workflow resources

Sequencing platforms

Our innovative platforms deliver exceptional data quality and accuracy at a massive scale. View sequencer comparison tables and find tools designed to help you choose the right platform for your needs.

Cancer research products

View NGS and microarray products supporting multiple cancer research applications, including tools for analyzing DNA, RNA, epigenetics, and more.

Sequencing data analysis

User-friendly Illumina tools ease the process of analyzing sequencing data so you can spend more time doing research and less time configuring workflows.

Additional cancer research resources

Multiomics Methods Guide eBook

This Methods Guide provides examples of multiomic research from recent literature and detailed, end-to-end workflows. Includes recommendations for sample isolation, library prep, sequencing depth, data analysis, and more.

Liquid Biopsy Methods Guide eBook

This 20+ page eBook provides published, comprehensive workflows to thoroughly characterize liquid biopsy samples using NGS and microarrays.

Redefining NGS in cancer research

In this webinar, experts cover essential background topics in NGS, achievements, challenges, and how an integrated multiomics approach can be used in cancer diagnosis and treatment.

Advancing cancer research with multiomics

Learn how researchers at the Ontario Institute for Cancer Research and United Health Network are linking the causes and consequences of complex phenotypes through multiomics to enable discoveries that weren’t possible before.

NGS for beginners

Learn the basics of next-generation sequencing and find tips for getting started.