Cancer Genomics Technology Development

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

We have worked to extend the range of analyzable samples by developing protocols suitable for sample types including formalin fixed, paraffin embedded samples, flow sorted primary cells and fine needle aspirates. We have established that useful nucleic acid preparations can be obtained from these fixed tissues and are continuing to refine these methods to extend the analysis of this material for a wider range of genomic technologies, especially for sequencing. Our methods for handling FFPE samples have been adapted by academic and industrial laboratories. We have applied these methods to many FFPE samples from cancers and precancerous tissues from solid tumors and hematological malignancies (e.g. Gastrointestinal Stromal Tumor, Gliomas, Medullary Thyroid Cancer, Bladder, Breast, Prostate, and lung Cancers). We have extended this pre-analytical work to analyses of sequence based assays for DNA mutation, RNA expression, DNA methylation, and DNA copy number. We have optimized our approaches to targeted sequencing efforts to regions of interest such as the small proportion of the genome composed of genes, or subsets of genes of particular interest in order to be able to sequence thousands of genes in individual samples or in a complementary fashion, to sequence a few key genes in hundreds of samples. We are also developing efficient methods to target intergenic and intronic regions which are often the sites of important structural rearrangements in cancer. We continue to improve methods for the detection of genome rearrangements, mutations, and the measurement of chromatin modifications, DNaseI hypersensitive sites, and transcription factor binding. Recently we have developed and tested implementations of several new technologies for DNA and chromatin analyses. For chromatin studies, we have developed cut-and-run and related methods which are now supplanting traditional ChIP-Seq for many applications. Currently, we are also evaluating and implementing long read technologies for DNA and RNA sequencing. Although long read technologies are limited to samples that contain intact HMW DNA/RNA, long read sequencing presents exciting new opportunities to better determine cancer genome structures. A major part of this effort is the development and implementation of software tools needed to analyze the massive amount of sequence data which is generated by this work. Although this is a challenging process, it ultimately will yield a streamlined analysis pipeline in which multiple sequence-based assays will be easy to integrate and free of array platform specific artifacts. Specific goals of our computational efforts include the optimization of pipelines to process sequence data for chromatin analysis, chromosome rearrangements, gene expression, mutation detection, and epigenetic analyses. We make use of informative models as need to test our novel approaches to genome characterization.