Photo of Andrew C. Adey, Ph.D.

Andrew C. Adey Ph.D.

  • (503) 494-1004
    • Assistant Professor of Molecular and Medical Genetics School of Medicine
    • CEDAR Member OHSU Knight Cancer Institute School of Medicine
    • Molecular and Medical Genetics Graduate Program School of Medicine
    • Program in Molecular and Cellular Biosciences School of Medicine
    • Cancer Biology Graduate Program School of Medicine

Dr. Adey started out in biotechnology development at the University of Texas where he researched alternative applications of microarrays in the lab of Andrew D. Ellington, Ph.D. He later served as interim director of the UT microarray core facility and then helped set up the UT genome sequencing and analysis facility in the early days of next generation sequencing. He then completed his doctoral studies in the Molecular and Cellular Biology Program at the University of Washington in the lab of Jay Shendure, M.D., Ph.D. in the Genome Sciences Department.

Previous research highlights include pioneering a novel transposase-based method for rapid, low-input DNA sequencing library construction, which I extended to the genome-wide analysis of DNA methylation. I also applied long-range sequencing methods to produce the first haplotype resolved genome and epigenome of an aneuploid cell line, HeLa, where I investigated the role of haplotype and copy number on the epigenetic and transcriptional landscape. I plan to continue my focus on the development and implementation of novel strategies to investigate the epigenome with high precision. This includes single cell approaches to disambiguate epigenetic and transcriptional heterogeneity within populations of cells which is typically obscured by bulk preparation methods. This work will provide insight into the dynamic regulatory landscape of cells and may reveal functional and targetable subpopulations in the context of disease intervention.

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Areas of interest

  • Single Cell
  • Epigenetics
  • Development
  • Sequencing
  • Biotechnology

Education

  • B.S., University of Texas, Austin Texas 2008
  • Ph.D., University of Washington, Seattle Washington 2014

Honors and awards

  • University of Washington Distinguished Dissertation Award 2014
  • Harold M. Weintraub Graduate Student Award 2014

Memberships and associations

  • Member, American Society of Human Genetics
  • SAB, Phase Genomics

Publications

Selected publications

  • Adey A, Burton JN, Kitzman JO, Daza R, Patwardhan RP, Kumar A, et. al. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res. 2014 Oct. 19.

  •  Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, et. al. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature. 2013 Aug 8;500(7461):207-11.

  •  Adey A & Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res. 2012 Jun;22(6):1139-43.

  • Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, et. al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 2010;11(12):R119. Highly Accessed.

  •  Amini S, Pushkarev D, Christiansen L, Royce T, Turk C, Pignatelli N, Adey A, et. al. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet. 2014 Oct. 19:10.1038/ng.3119.

  • Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, et. al. Decoding long nanopore sequencing reads of natural DNA. Nat Biotech. 2014 Jun 26;10.1038/nbt.2950.

  • Boissel SJ,  Astrakhan A, Jarjour J, Adey A, Shendure J, Stoddard B, et. al. megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. Nucl Acid Res. 2013 Nov 26.

  • Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotech. 2013 Nov 3;10.1038/nbt.2727.

  • Schwartz JJ, Lee C, Hiatt JB, Adey A, Shendure J. Capturing native long-range contiguity by in situ library construction and optical sequencing. Proc Natl Acad Sci USA. 2012 Nov 13;109(46):18749-54.

  • Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, et. al. Haplotype resolved genome sequencing of a Gujarati Indian individual. Nat Biotech. 2011 Jan;29(1):59-63.

Publications

  • "Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes" Genome Biology December 3 2014
  • "Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing" Nature Genetics December 11 2014
  • "Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions" Biotechnology December 2013
  • "Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing" PCR Methods and Applications June 2012
  • "Erratum" Biotechnology May 2011
  • "Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing" Science May 22 2015
  • "Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition" Genome Biology December 8 2010
  • "Decoding long nanopore sequencing reads of natural DNA" Biotechnology  2014
  • "Capturing native long-range contiguity by in situ library construction and optical sequencing" Proceedings of the National Academy of Sciences of the United States of America November 13 2012
  • "Tagmentation-based whole-genome bisulfite sequencing" Nature Protocols October 2013
  • "Haplotype-resolved genome sequencing" Nature Reviews Genetics May 18 2015
  • "In vitro, long-range sequence information for de novo genome assembly via transposase contiguity" PCR Methods and Applications December 1 2014
  • "MegaTALs" Nucleic Acids Research February 2014
  • "Haplotype-resolved genome sequencing of a Gujarati Indian individual" Biotechnology January 2011
  • "Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens" Journal of Molecular Diagnostics January 2014
  • "The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line" Nature  2013
  • "Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma" Genes Chromosomes and Cancer March 1 2016
  • "Sequencing thousands of single-cell genomes with combinatorial indexing" PLoS Medicine February 28 2017
  • "Comprehensive single-cell transcriptional profiling of a multicellular organism" Science August 18 2017
  • "Haplotype resolution at the single-cell level" Proceedings of the National Academy of Sciences of the United States of America November 21 2017
  • "Tagmentation-based library preparation for low DNA input whole genome bisulfite sequencing"  January 1 2018
  • "Highly scalable generation of DNA methylation profiles in single cells" Biotechnology June 1 2018
  • "Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer" Nature Communications December 1 2018
  • "Joint profiling of chromatin accessibility and gene expression in thousands of single cells" Science September 28 2018
  • "Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals" Genes and Development November 1 2018
  • "Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data" Molecular Cell September 6 2018
  • "Joint profiling of chromatin accessibility and gene expression in thousands of single cells" Science January 1 2018
  • "Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion" PCR Methods and Applications March 1 2019
  • "The accessible chromatin landscape of the murine hippocampus at single-cell resolution" PCR Methods and Applications May 1 2019
  • "Integration of Single-Cell Genomics Datasets" Cell June 13 2019

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