As more diverse genetic links are established with cancer, the utility of one-gene-one-test diagnostics is diminished. In addition, biopsies are mixed populations of tumor and normal tissue, requiring deconvolution of tumor and non-tumor genoptypes to accurately understand disease etiology and inform treatment decisions. The next generation of cancer diagnostics must therefore achieve two goals: 1) identify genetic variation in a high number of cancer-associated genes and 2) do so in a sample containing a mixed cellular population. Deep sequencing, using the so-called next generation sequencing (NGS) platforms represents a powerful and unique approach to address these challenges. Various capture methods exist, to isolate specific regions of the genome for sequencing on NGS platforms. Tumor and nontumor genotypes can then be discerned through bioinformatic analysis of the resulting sequencing data. To better enable deep sequencing of tumor biopsies, Advanced Liquid Logic (ALL) will apply its proprietary digital microfluidic liquid handling technology to automate the diagnostic cancer panel assay developed by Foundation Medicine. The resulting prototype system will automate the complex upstream sample preparation system required for NGS analysis of DNA extracted from crude tumor biopsies. ALL will develop a digital microfluidic cartridge capable of DNA purification/concentration, library preparation and targeted enrichment of the cancer-associated genes included in Foundation's panel. By processing these samples in sub-microliter volumes, the ALL platform will also enable analysis of very small biopsy samples, reducing DNA input requirements by 100-1000 fold. In addition to the reliability and labor savings associated with automation, ALL's platform offers cost-effectiveness for non- PCR based sequence capture methods ahead of NGS.
Public Health Relevance Statement: Public Health Relevance: As high throughput DNA sequencing is beginning to move into clinical applications, the arduous sample preparation that is required is likely to become a significant bottleneck. A microfluidic system which automates these processes within an inexpensive cartridge will be developed.
Project Terms: Address; Automation; base; Base Sequence; Bioinformatics; Biological Assay; Biopsy; Biopsy Specimen; Businesses; Cancer Diagnostics; Cells; Clinical; clinical application; Collaborations; commercialization; Complex; cost effective; cost effectiveness; Crude Extracts; Data; deep sequencing; design; Development; Diagnosis; Diagnostic; Diagnostic tests; digital; Disease; DNA; DNA Library; DNA purification; DNA Sequence; Doctor of Philosophy; Etiology; Evaluation; Foundations; Future; Generations; Genes; Genetic; Genetic Markers; Genetic Predisposition to Disease; genome sequencing; Genomics; Genotype; Goals; improved; instrument; Laboratories; Left; Libraries; Link; Liquid substance; Logic; Malignant Neoplasms; Manuals; Medicine; Methods; Microfluidics; Mixed Cellular Population; Molecular Biology; Monitor; next generation; next generation sequencing; Normal tissue morphology; novel; Phase; Population; Preparation; Process; programs; Protocols documentation; prototype; public health relevance; Reagent; Research; Research Personnel; research study; Sampling; Savings; Sequence Analysis; Series; skills; Speed (motion); System; Technology; Testing; tool; Translating; tumor; Tumor Tissue; Variant; Variation (Genetics)
