Recent technological advances allow single-cell DNA sequencing analysis at the genomic, transcriptomic, and proteomic levels. These powerful sequencing tools have already provided key insight into cell-specific genetic networks, cellular development and demise, and tissue composition. On Tuesday morning, Jay Shendure, MD, PhD delivered an innovative plenary presentation, “Beyond Sequencing: New Frontiers in Genomics.”
Shendure gave an in depth look at massively parallel DNA sequencing techniques, new technologies on the horizon, and the applications of these techniques in clinical medicine. His laboratory, a member of the Howard Hughes Medical Institute, located at the University of Washington in Seattle, focuses on exploiting next-generation DNA sequencing to measure biological phenomena in six areas: new molecular methods, genomic approaches to developmental biology, massively parallel functional genomics, translating genomics to the clinic, the genetic basis of human disease, and genome sequencing technologies.
He gave a step-by-step review of massively parallel sequencing. “The power of this approach comes from the sheer parallelism,” Shendure said. He asked the audience to ponder what a sequence instrument is and why it is we sequence. “Try to think of DNA sequencing as—yes, a device for discovering variations in individual genomes—but potentially more importantly, as simply a molecular counting device,” he said.
Shendure took the audience on a brief historical journey highlighting scientific methods including gels (analog molecular measurement), Sanger sequencing (digital molecular measurement), microarray (analog parallel molecular measurement), and next-generation sequencing (digital and parallel molecular measurement).
He then explained how single-cell sequencing techniques can identify cell-specific gene expression. This data can be used to construct system biology models that help researchers understand cell-specific development.
Single-cell analysis has several significant advantages, according to Shendure. For example, it avoids the problem of traditional experiments that average gene changes across a heterogeneous cell population, which can cloud significant, cell-specific gene expression. Single-cell analysis also preserves key data that have the potential to lead to disease-specific therapeutics.
The limitations of current technology include experimental variability and the fact that cell behavior such as gene expression may not be detected due to experimental “noise.” However, with the advent of commercially available algorithms, robust analysis is possible. Single-cell RNA sequencing has the potential to avoid problems that plague other sequencing protocols, which find many varients of unknown significance, Shendure noted.
Shendure also revealed that studies from his laboratory demonstrate that massively parallel sequencing identifies circulating tumor DNA from normal cell-free DNA. The ability to accurately discriminate malignant cells from healthy cells via fragment length size may have a significant impact on personalized medicine—from early cancer detection to targeted treatment and predicting of reoccurrence. Deep sequencing of cell-free DNA can be used to determine a cancer’s tissue of origin, relying on nucleosome transcription factor information. This has promise in determining the pathogenesis and behavior of malignancies.
Furthermore, his group has reported that massively parallel assays can generate prediction models to aid in the interpretation of BRCA1 variants in breast cancer.
Shendure also explained how his lab identified within their own intensive care unit population novel microbiota, multiple unrelated lineages of bacteria, and possible crytic transmission of bacteria using microbial whole genome sequencing.
“Single cell sequencing technologies are evolving very rapidly,” Shendure said. It is imperative that laboratorians and other healthcare professionals receive training in these new technologies to ensure that basic research findings are appropriately translated into clinical practice.