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
    • Helps 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

  • Microarray
    • Provides high-throughput screening for DNA methylation in genome-wide analyses
  • ChIP sequencing
    • Identifies DNA binding sites for proteins and transcription factors in a genome
    • Provides sequences for the DNA bound proteins and transcription factors for analyses of interactions between DNA and proteins
Last updated: April 16, 2019