Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

Massively parallel sequencing directly detects tumor-derived chromosomal alterations in plasma DNA from cancer patients. Getting Harder to Hide It might be challenging, but game players can usually answer the question: “Where’s Waldo? ” After all, we’ve met the traveler before and can comb the baroque illustrations for his characteristic striped ensemble and walking stick. But if we didn’t know what Waldo looked like, it would take a powerful detective and at least a clue or two to find him in a crowd. Now, Leary et al. use a well-characterized clue—the universal nature of chromosomal alterations in human cancer—along with powerful DNA sequencing technology to pinpoint tumor-specific chromosomal aberrations in the circulation of patients without knowing, in advance, precisely what the edited DNA looks like. The authors compared circulating cell-free DNA from 10 late-stage colorectal and breast cancer patients and 10 healthy individuals using massively parallel whole-genome sequencing (WGS) and detected chromosomal aberrations—copy number changes and rearrangements—present only in plasma DNA from patients. Two known cancer driver genes were amplified in the patients: ERBB2, which encodes HER2/Neu, the protein target of the anticancer drug trastuzumab, and a cell-cycle regulatory gene, CDK6. For three colorectal cancer cases where both tumor and blood samples were analyzed by WGS, the copy number patterns observed in blood samples resembled those of the resected tumor. The authors quantified the ability of their approach to discriminate between cancer patients and healthy subjects by analyzing simulated mixtures of varying concentrations of tumor and control DNA. Under certain defined conditions, tumor DNA concentrations of ≥0.75% could be detected in the circulation of breast and colorectal cancer patients with a sensitivity >90% and a specificity >99%. Leary et al. outline several current limitations of their method. For example, the patients studied were all in the late stages of cancer progression, and the sensitivity and specificity parameters were dependent on the amount of sequence data obtained. As the cost of WGS falls, this new approach may provide a powerful way to detect cancers in a noninvasive and unbiased manner even without prior knowledge of disease. Clinical management of cancer patients could be improved through the development of noninvasive approaches for the detection of incipient, residual, and recurrent tumors. We describe an approach to directly identify tumor-derived chromosomal alterations through analysis of circulating cell-free DNA from cancer patients. Whole-genome analyses of DNA from the plasma of 10 colorectal and breast cancer patients and 10 healthy individuals with massively parallel sequencing identified, in all patients, structural alterations that were not present in plasma DNA from healthy subjects. Detected alterations comprised chromosomal copy number changes and rearrangements, including amplification of cancer driver genes such as ERBB2 and CDK6. The level of circulating tumor DNA in the cancer patients ranged from 1.4 to 47.9%. The sensitivity and specificity of this approach are dependent on the amount of sequence data obtained and are derived from the fact that most cancers harbor multiple chromosomal alterations, each of which is unlikely to be present in normal cells. Given that chromosomal abnormalities are present in nearly all human cancers, this approach represents a useful method for the noninvasive detection of human tumors that is not dependent on the availability of tumor biopsies.