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
    • Molecular and Medical Genetics Graduate Program School of Medicine
    • Program in Molecular and Cellular Biosciences 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

  • "Comprehensive single-cell transcriptional profiling of a multicellular organism." Science  In: , Vol. 357, No. 6352, 18.08.2017, p. 661-667.
  • "Sequencing thousands of single-cell genomes with combinatorial indexing." Nature Methods  In: , Vol. 14, No. 3, 28.02.2017, p. 302-308.
  • "Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma." Genes Chromosomes and Cancer  In: , Vol. 55, No. 3, 01.03.2016, p. 278-287.
  • "Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing." Science  In: , Vol. 348, No. 6237, 22.05.2015, p. 910-914.
  • "Haplotype-resolved genome sequencing : Experimental methods and applications." Nature Reviews Genetics  In: , Vol. 16, No. 6, 18.05.2015, p. 344-358.
  • "Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing." Nature Genetics In: , Vol. 46, No. 12, 11.12.2014, p. 1343-1349.
  • "Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes." Genome Biology  In: , Vol. 15, No. 12, 530, 03.12.2014.
  • "In vitro, long-range sequence information for de novo genome assembly via transposase contiguity." Genome Research  In: , Vol. 24, No. 12, 01.12.2014, p. 2041-2049.
  • "MegaTALs : A rare-cleaving nuclease architecture for therapeutic genome engineering." Nucleic Acids Research In: , Vol. 42, No. 4, 02.2014, p. 2591-2601.
  • "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  In: , Vol. 16, No. 1, 01.2014, p. 56-67.
  • "Decoding long nanopore sequencing reads of natural DNA." Nature Biotechnology In: , Vol. 32, No. 8, 2014, p. 829-833.
  • "Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions." Nature Biotechnology  In: , Vol. 31, No. 12, 12.2013, p. 1119-1125.
  • "Tagmentation-based whole-genome bisulfite sequencing." Nature Protocols  In: , Vol. 8, No. 10, 10.2013, p. 2022-2032.
  • "The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line." Nature  In: , Vol. 500, No. 7461, 2013, p. 207-211.
  • "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  In: , Vol. 109, No. 46, 13.11.2012, p. 18749-18754.
  • "Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing." Genome Research  In: , Vol. 22, No. 6, 06.2012, p. 1139-1143.
  • "Erratum : Haplotype-resolved genome sequencing of a Gujarati Indian individual (Nature Biotechnology (2011) 29 (59-63))." Nature Biotechnology  In: , Vol. 29, No. 5, 05.2011, p. 459.
  • "Haplotype-resolved genome sequencing of a Gujarati Indian individual." Nature Biotechnology  In: , Vol. 29, No. 1, 01.2011, p. 59-64.
  • "Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition." Genome Biology  In: , Vol. 11, No. 12, R119, 08.12.2010.

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