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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

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