CAPP-Seq, or cancer personalized profiling by deep sequencing, is an advanced method that quantifies circulating tumor DNA (ctDNA). These ctDNA fragments are released into the bloodstream from dead tumor cells. Introduced in 2014 by researchers at Stanford University, CAPP-Seq measures these cell-free tumor DNA fragments, marking a significant step in non-invasive cancer diagnostics.
The Unique Strengths of CAPP-Seq
CAPP-Seq distinguishes itself through several advancements. It is highly sensitive, detecting very low concentrations of tumor DNA. CAPP-Seq can identify a single mutant DNA molecule among 10,000 healthy DNA molecules, providing a detailed view of subtle cancer changes. This precision benefits early detection or monitoring minimal disease.
It offers a broader genetic survey in a single run compared to techniques like digital polymerase chain reaction (dPCR) or amplicon sequencing. While dPCR targets only a few mutations, CAPP-Seq examines numerous genetic locations simultaneously. This reduces the sample material needed, which is advantageous when patient samples are limited.
CAPP-Seq also detects various types of genetic alterations within tumor DNA. It can identify point mutations, insertions and deletions (indels), and larger structural variations like translocations or inversions. It also identifies copy number variations. This broad spectrum provides a more complete genetic profile of the tumor.
Compared to more extensive sequencing approaches like whole exome sequencing (WES) or whole genome sequencing (WGS), CAPP-Seq is more cost-effective. Its targeted approach focuses on recurrently mutated regions of interest in the cancer genome. By concentrating on relevant areas, it avoids the expense and complexity of sequencing the entire genome, while providing meaningful clinical insights.
Understanding How CAPP-Seq Works
The CAPP-Seq process begins with the collection of peripheral blood from the patient. From this blood sample, the plasma component is separated, and circulating tumor DNA (ctDNA) is isolated. These ctDNA fragments, released from dying tumor cells, are the material for analysis.
Following ctDNA isolation, a specialized component known as a “selector” is designed. This selector consists of a panel of biotinylated DNA oligonucleotide probes. These probes are designed to target and bind to recurrently mutated regions associated with the specific type of cancer being investigated.
The selector is then used in hybridization capture. In this step, both tumor DNA and the isolated ctDNA from the plasma are mixed with the selector probes. The probes bind to complementary DNA sequences, capturing targeted tumor-derived DNA fragments from the larger pool of healthy DNA.
After capture, the selected DNA fragments undergo deep sequencing. This sequencing generates millions of DNA reads. Computational algorithms analyze these sequences, comparing them against reference genomes and known cancer mutations. This analysis identifies and quantifies patient-specific mutations in the ctDNA.
The data provides a molecular fingerprint of the tumor, revealing specific mutations and their abundance. This information tracks the tumor, assesses treatment effectiveness, and guides therapeutic decisions.
CAPP-Seq’s Role in Cancer Management
CAPP-Seq is a significant tool in cancer management, extending beyond traditional diagnostic methods. One primary application is monitoring tumor burden, assessing disease progression or regression. CtDNA levels correlate with tumor volume, making it a reliable indicator.
This correlation allows clinicians to assess treatment response earlier than conventional imaging techniques. While imaging shows changes after weeks or months, ctDNA levels can change within days or weeks of treatment. This early insight enables faster therapy adjustments, potentially improving outcomes.
CAPP-Seq also functions as a prognostic indicator in various cancer types. Detecting ctDNA after treatment, even at low levels, predicts disease relapse. For example, persistent ctDNA post-surgery often signals a higher risk of recurrence.
This allows for personalized follow-up, identifying patients who might benefit from additional therapy to prevent recurrence. This information helps stratify patients into risk groups, guiding decisions on treatments or surveillance.
CAPP-Seq facilitates biopsy-free tumor genotyping, addressing limitations of traditional tissue biopsies. A conventional biopsy is invasive and carries risks. CAPP-Seq eliminates invasive procedures, requiring only a blood draw, making it safer and more patient-friendly.
Beyond being less invasive, CAPP-Seq liquid biopsies provide a more comprehensive genetic overview of the tumor. A single tissue biopsy samples only a small portion, which might not fully represent the tumor’s genetic makeup due to heterogeneity. CtDNA, however, is shed from various parts, offering a broader genetic snapshot.
This also extends to tracking tumor evolution. Tumors acquire new mutations as they progress or in response to treatment, leading to drug resistance. Repeated CAPP-Seq blood draws monitor these genetic changes non-invasively, allowing clinicians to identify emerging resistance and adjust treatment. This supports adaptive and personalized treatment planning, ensuring therapies remain effective as the tumor evolves.