CGCI Molecular Characterization Platforms

The following next-generation sequencing methods are used for all Burkitt Lymphoma Genome Sequencing Project and HIV+ Tumor Molecular Characterization Project cases.

Whole Genome Sequencing

• performed on both tumor and matching normal (if available) samples
• provides the DNA sequence of the entire genome
• used to identify structural alterations, such as translocations and inversions, as well as insertion and deletions (indels) and single point mutations

Transcriptome Sequencing

• performed on tumor samples only
• 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

Targeted Sequencing

• custom hybridization-based DNA capture protocols were used to capture and sequence targeted genes
• targeted sequencing libraries that featured exons of recurrently mutated genes, exons of several known diffuse large B-cell lymphoma and Burkitt lymphoma genes were used for the pediatric Burkitt Lymphoma Genome Sequencing Project manuscript

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