CGCI researchers primarily use sequencing and, in some cases, other genome-based approaches to examine genomes and transcriptomes of tumors. With these in-depth analyses, they are able to detect cancer-associated alterations ranging from genomic rearrangements and copy number alterations in gene expression to single nucleotide insertion or deletion of small nucleotide mutations. By uncovering the full spectrum of alterations in tumors, CGCI researchers aim to elucidate which physiological pathways are disrupted in cancer. Finding the underlying molecular causes of cancer will, in some cases, inform better treatment strategies.

Read below to learn about CGCI’s genomic approaches and the type of genetic information they provide:

Next-generation Sequencing Methods

  • Whole Genome Sequencing
    • Provides the DNA sequence of the entire genome
    • Is used to identify structural alterations, such as translocations and inversions, as well as insertion and deletions (indels) and single point mutations
  • Transcriptome Sequencing 
    • Provides sequence from transcribed genes and non-coding RNAs (RNA-seq) and/or from small regulatory RNAs known as microRNAs (miRNA-seq)
    • Identifies mutations in the protein-coding regions of the genome, non-coding or regulatory RNAs, and a variety of alterations, including novel gene fusions, alternatively spliced isoforms, and variations in gene expression

Epigenetic Characterization Methods

  • Illumina Infinium MethylationEPIC BeadChip
    • Provides high-throughput genome-wide DNA methylation data of 850,000 CpG islands
  • ChIP sequencing
    • Uses combinations of immunoprecipitation and sequencing to identify various histone modifications and the chromatin state
    • Provides sequences for the DNA bound proteins (e.g. transcription factors and histones) to identify their locations in the genome
Last updated: June 03, 2019