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Semiconductor-based DNA sequencing of histone modification states

Author

Listed:
  • Christine S. Cheng

    (Broad Institute of MIT and Harvard)

  • Kunal Rai

    (University of Texas MD Anderson Cancer Center)

  • Manuel Garber

    (Broad Institute of MIT and Harvard
    Bioinformatics and Integrative Biology, University of Massachusetts Medical School)

  • Andrew Hollinger

    (Broad Institute of MIT and Harvard)

  • Dana Robbins

    (Broad Institute of MIT and Harvard)

  • Scott Anderson

    (Broad Institute of MIT and Harvard)

  • Alyssa Macbeth

    (Broad Institute of MIT and Harvard)

  • Austin Tzou

    (Broad Institute of MIT and Harvard)

  • Mauricio O. Carneiro

    (Broad Institute of MIT and Harvard)

  • Raktima Raychowdhury

    (Broad Institute of MIT and Harvard)

  • Carsten Russ

    (Broad Institute of MIT and Harvard)

  • Nir Hacohen

    (Broad Institute of MIT and Harvard
    Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital
    Harvard Medical School)

  • Jeffrey E. Gershenwald

    (University of Texas MD Anderson Cancer Center)

  • Niall Lennon

    (Broad Institute of MIT and Harvard)

  • Chad Nusbaum

    (Broad Institute of MIT and Harvard)

  • Lynda Chin

    (University of Texas MD Anderson Cancer Center)

  • Aviv Regev

    (Broad Institute of MIT and Harvard
    Howard Hughes Medical Institute, Massachusetts Institute of Technology)

  • Ido Amit

    (Broad Institute of MIT and Harvard
    Weizmann Institute)

Abstract

The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumour tissues.

Suggested Citation

  • Christine S. Cheng & Kunal Rai & Manuel Garber & Andrew Hollinger & Dana Robbins & Scott Anderson & Alyssa Macbeth & Austin Tzou & Mauricio O. Carneiro & Raktima Raychowdhury & Carsten Russ & Nir Haco, 2013. "Semiconductor-based DNA sequencing of histone modification states," Nature Communications, Nature, vol. 4(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3672
    DOI: 10.1038/ncomms3672
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