Cancer tumor profiling

What is genomic profiling of cancer and tumor samples?

Cancer and tumor profiling, also known as genomic or molecular cancer profiling, uses next generation sequencing (NGS) to identify mutations in solid tumors or other samples, such as cell-free DNA (cfDNA) from liquid sources. This approach provides valuable molecular and genomic data beyond traditional microscopy and morphology-based techniques. Cancer and tumor profiling can help researchers by targeting specific sets of cancer-associated genes or genomic regions for more precise tumor classification.

Next generation sequencing for profiling tumors

Cancer researchers face multiple challenges when performing molecular profiling of tumor samples; however, advances in targeted NGS technologies can address many of these issues.

What are the challenges of molecular tumor profiling?

• Tumor heterogeneity—the genetic profile of cells within the same tumor, or across different tumors within the same individual, can be highly dissimilar
• FFPE samples—formalin-fixed paraffin-embedded (FFPE) tumor samples often contain low quality, degraded DNA which can make library preparation difficult
• Low allele frequency identification and monitoring—variants that are found in a small portion of tumor cells can play an outsized role in driving cancer progression

How can targeted NGS approaches help researchers profile tumors?

Targeted NGS focuses on specific regions of interest in a genome, allowing researchers to gain deeper sequencing coverage than other sequencing methods (e.g., whole genome sequencing, Sanger). Targeted sequencing is an especially powerful method for identifying variants and mutations, including rare variants within heterogeneous cell populations, which is critical for tumor profiling applications. Multiple targeted NGS approaches are available depending on tumor sample type and specific research goals.

Target enrichment methods

• Amplicon sequencing—a fast, low-cost method of enriching target regions by PCR amplification, well-suited for highly-targeted, smaller panels
• Hybridization capture—target enrichment via hybridization of long, biotinylated oligonucleotide baits (probes) with near unlimited multiplex capacity, well-suited for large target ranges, such as multi-kb length or whole exome

Targeted NGS solutions from IDT

• Panels designed to target cancer related genes—IDT offers predesigned panels targeting genomic regions associated with specific tumor types and known driver mutations. We can also help design custom panels to interrogate genomic targets relevant to your cancer research program. Both amplicon sequencing and hybridization capture methods of target enrichment are available in our predesigned and custom panel portfolio.
• Library preparation from challenging samples—both amplicon and hybridization capture technology can handle cell free DNA (cfDNA) and formalin-fixed paraffin embedded (FFPE) tumor samples. Amplicon sequencing panels using cfDNA or FFPE tumor samples are often designed with a max amplicon size of 150 bp to accommodate DNA crosslinks and short fragments. Hybridization capture workflows using cfDNA or FFPE samples can benefit from our xGen™ cfDNA & FFPE DNA Library Prep Kit, which enables usable sequencing data even with highly degraded research samples.
• Adapters with unique dual indexes (UDIs) and unique molecular identifiers (UMIs)—IDT offers a wide range of adapters that can identify duplicates that can mask true rare variants in a sample.