With the 2014 American Association for Cancer Research annual meeting right here in San Diego, we were very excited to host a Discovery Symposium focusing on advances being made in understanding and monitoring cancer made possible through next-generation sequencing technologies. A stellar lineup of researchers presented the latest findings and discussed their experiences with bringing NGS into their labs. All eight talks were excellent (some so good they’ve been featured before), and I have summarized three of these in this post. For more, check out a quick highlight video from featured speakers here!
Clonal Stasis and Diversity in Breast Cancer Revealed by Single-Cell Genome Sequencing
Dr. Nick Navin from the Department of Genetics at the MD Anderson Cancer Center presented results on the genomic and clonal evolution of two types of breast cancer: luminal A (ER+/PR+/HER2-) and the dreaded “triple negative” (ER-/PR-/HER2-). Dr. Navin highlighted issues of intratumor cellular heterogeneity, a complexity common to many cancers in which the genetics of cells in a tumor sample can be completely different. However, these mutations that accumulate within cell populations can also serve as a permanent mutation record which can delineate clones and sometimes, help predict the behaviors of certain subpopulations of cells. To understand the behavior of these cells, Navin’s group is using single-cell exome sequencing to achieve 80-90% genome coverage with base pair resolution. With a deep single-cell exome approach, very rare mutations can be uncovered that may have an impact on cell behavior, and mutation rates can be modeled on these data. Interestingly, they have noted that as a group, point mutations seem to accumulate over time gradually, whereas copy number changes appear as discrete bursts. Examining the evolution of luminal A and triple negative cancers, the rate of random mutation was elevated in triple negative breast cancers, while the luminal A type was similar to normal cells. Accurately modeling and understanding these patterns and rates of mutations has important implications for targeted therapies and diagnostic capabilities.
Identifying Prognostic Markers from Archival Samples in Clinical Cancer Populations
Asking the fundamental question of what genetic aberrations are associated with advanced-stage cancer, Dr. Hanlee Ji from the Stanford Genome Technology Center spoke on the need for being able to identify prognostic markers in individual samples. Highlighting the clinical immediacy around late stage/metastatic cancer, Dr. Ji emphasized that genetic events themselves can have predictive/prognostic significance, but more often a collection of multiple genomic features, such as those from The Cancer Genome Atlas (TCGA), are more informative. If a more comprehensive picture of the cancer emerges, interventions to reduce the risk of developing metastatic disease may ultimately be developed.
On a technical level, the question Dr. Ji’s group is tackling may be, is RNA too difficult to work with in a clinical context? In retrospective validation studies using a new RNA-Seq method optimized for small input quantities and tolerant of degraded or small fragment size (TruSeq RNA Access), they were able to produce libraries from 50% of FFPE samples, generating >20M aligned reads. Combined with clinical outcome information, they used this method to make a predictive analysis of driver and targetable mutations in a 30-year old colon cancer sample. FFPE samples offer a wealth of information that has been historically difficult to access, and the ability to prepare samples in an automated fashion and perform robust RNA-Seq is enabling them to consider larger clinical studies, and hopefully accelerate the adoption of RNA-based translational projects in the future.
Clinical Validation for Comprehensive Somatic Profiling to Support Genomics-Enabled Medicine Trials
Dr. John Carpten, the Director of Integrated Cancer Genomics at Phoenix’s Translational Genomics Research Institute (TGen), echoed the theme above, asking whether NGS profiling of late stage/metastatic cancer could possibly increase patient treatment options. Emphasizing the utility of NGS technology to assay point mutations, patterns of copy number variance, genomic structural rearrangements, and transcriptional profiling, Dr. Carpten gave an overview of how the TGen CLIA lab has developed an extensive analytical validation plan for detecting somatic events using Illumina sequencers. These included many variables of quality assessment, LIMS management, and data interpretation. Their methodology includes a genome-wide sequencing approach, with focused dives into regions of the exome, dubbed the “strexome”, meaning interrogating structural events within the exome. Using a metastatic melanoma tumor/normal cell line pair to model a truth dataset, Carpten’s group found that they reliably had 80% power to detect a variant down to 5% at 400x coverage. Other methods in use include RNA-Seq, differential gene expression, and allele-specific expression, and examining synthetic fusion detection with various algorithms and chemistries. An exciting project in their lab includes working on validation plans for a Stand Up 2 Cancer (SU2C) clinical trial for melanoma.
Dr. Carpten ended his talk with three clinical vignettes, or inspiring little stores of patients with triple negative breast cancer, cholangiocarcinoma, and pediatric glioblastoma, wherein the direct knowledge of the genomic profiles and/or expression of particular gene isoforms were highly therapeutically relevant.
Transforming the Future of Oncology with Genomics
Wrapping up the day, Illumina’s Chief Medical Officer Dr. Rick Klausner communicated his vision of becoming an enabling force in the global cancer community through upholding standards, answering definitive questions critical to making next-generation technologies for oncology routine, and helping standardize clinical trials.To paraphrase his words, oncology is the tip of the spear as we continue to use genomics to transform medicine for people at risk for, and living with disease.
Thanks to all speakers and participants for making the third AACR Discovery Symposium a big success!