Cancer Genomics Research
Cancer Genomics Research Clinical Cancer Research Cancer Companion Diagnostics NGS in Oncology
Cancer Genomics Research
Cancer Genomics Research Clinical Cancer Research Cancer Companion Diagnostics NGS in Oncology

Cancer sequencing methods to unlock genomic insights

Combine next-generation sequencing methods for a deeper understanding of cancer

Male scientist holding an 8 lane pipette in one hand and a library tube in the other; tubes are filled with clear liquid; lab equipment in the foreground and background.

Using 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, advancements in NGS-based cancer sequencing methods 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

Targeted vs untargeted NGS methods for cancer research

Both targeted and untargeted approaches play crucial roles in cancer research. Targeted studies contain some bias since specific, preconceived pathways and 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.

Female scientist, front view, holding tube and pipetting clear liquid, NextSeq 1000/2000 in background

Key cancer sequencing methods

Method

Description and use
Genomics
Cancer whole-genome sequencing Identifies a comprehensive list of cancer-driving genetic events
Cancer whole-exome sequencing Identifies cancer-driving genes within the coding region of the genome and is a cost-effective and efficient sequencing method to compared to whole-genome sequencing
ctDNA sequencing Detects cell-free circulating tumor DNA (ctDNA), which can act as a noninvasive cancer biomarker and is used as a potential alternative to invasive tissue biopsies
Targeted NGS cancer panels Targets known DNA and/or RNA variants from the same FFPE sample
Epigenomics
Methylome sequencing Provides insight into methylation patterns at the single nucleotide level for both genome-wide analysis and targeted approaches
Cancer epigenetics Identifies cellular biomarkers associated with regulation of cancer genes or drug resistance
Assay for transposase-accessible chromatin with sequencing (ATAC-Seq) Determines chromatin accessibility across the genome without prior knowledge of regulatory elements
Transcriptomics
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 intact tissue 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 measure proteins and RNA simultaneously in single cells. This combined proteomics plus 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 resource with simple, comprehensive workflows for a broad range of cancer research applications. This guide discusses single-cell sequencing, spatial sequencing, methylation profiling, multiomics, cell-free RNA sequencing, and more.

Applications of cancer research

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

See cancer research applications

Sequencing workflow resources

Innovative Illumina 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.

Intuitive 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.

Side view of female scientist touching the start screen, instrument and wet and dry cartridges on lab bench, gradient background.

MiSeq i100 Series

Interrogate a focused selection of genes associated with specific cancer types or pathways using the fastest, simplest Illumina benchtop sequencer.

Meet the MiSeq i100 Series

Additional cancer research resources

Multiomics methods guide

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

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 topics in NGS as well as challenges and achievements in cancer research. They also detail how multiomics can be used to improve insights into this complex disease.

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.

Speak to a specialist

Interested in getting more information on cancer sequencing methods?