Technological Considerations for Clinical Cancer Genome Profiling: From FFPE to Liquid Biopsy
This review examines the technical variables at every stage of cancer genome profiling, from sample collection and preservation through to sequencing and variant calling, that impact analytical sensitivity and clinical utility. The authors compare FFPE tissue and liquid biopsy platforms, addressing challenges of sample degradation, low nucleic acid yields, and low variant allele fractions. The paper provides practical guidance on pre-analytical and analytical factors critical for laboratories implementing clinical-grade genomic testing.
The original study
Technological considerations for genome-guided diagnosis and management of cancer.
- Authors
- Lennon NJ, Adalsteinsson VA, Gabriel SB
- Journal
- Genome medicine
- Type
- Journal Article, Review
- PMID
- 27784341
Original abstract
Technological, methodological, and analytical advances continue to improve the resolution of our view into the cancer genome, even as we discover ways to carry out analyses at greater distances from the primary tumor sites. These advances are finally making the integration of cancer genomic profiling into clinical practice feasible. Formalin fixation and paraffin embedding, which has long been the default pathological biopsy medium, is now being supplemented with liquid biopsy as a means to profile the cancer genomes of patients. At each stage of the genomic data generation process-sample collection, preservation, storage, extraction, library construction, sequencing, and variant calling-there are variables that impact the sensitivity and specificity of the analytical result and the clinical utility of the test. These variables include sample degradation, low yields of nucleic acid, and low variant allele fractions (proportions of assayed molecules carrying variant allele(s)). We review here the most common pre-analytical and analytical factors relating to routine cancer patient genome profiling, some solutions to common challenges, and the major sample preparation and sequencing technology choices available today.