Katherine E. Varley, PhD

Research Interests

  • Breast Cancer
  • Epigenetics
  • Gene Expression Regulation
  • Medical Diagnosis and Prognosis Using Biomarkers

Labs

Lab Website

Languages

  • English

Academic Information

  • Departments: Oncological Sciences - Assistant Professor
  • Cancer Center Programs: Nuclear Control of Cell Growth & Differentiation

Academic Office Information

  • 801-213-5661
  • Huntsman Cancer Institute
    Oncological Sciences
    2000 Circle of Hope, Room: 3719
    Salt Lake City, UT 84112

Academic Bio

Katherine (K-T) Varley, PhD, is an investigator at Huntsman Cancer Institute and an assistant professor in the Department of Oncological Sciences at the University of Utah. She is a member of the Nuclear Control of Cell Growth and Differentiation Program and her laboratory studies epigenetic gene regulation in breast cancer.

Genomic technology has revolutionized the ability to detect the molecular defects that occur in cancer. Dr. Varley’s research focuses on using next-generation sequencing assays and computational analysis to study the gene expression, transcription factor binding and DNA methylation patterns in breast cancer. Her goals are to answer fundamental questions about how epigenetic gene regulation is disrupted in cancer cells as well as to discover drug targets and biomarkers that may have a more immediate impact on breast cancer treatment. Research in her lab involves the development of new molecular methods and bioinformatics approaches to explore the cancer genome and to translate discoveries into clinical tools that improve patient care.

Dr. Varley received her BS in Biology with a concentration in Computational Biology from Cornell University in 2003. She received her PhD in Computational Biology in 2009 from Washington University School of Medicine where Dr. Robi Mitra was her thesis advisor. Her postdoctoral studies were conducted in Dr. Richard M. Myers’ laboratory at the HudsonAlpha Institute for Biotechnology and included collaborative studies with the ENCODE Project Consortium and researchers at the University of Alabama at Birmingham Comprehensive Cancer Center.

Education History

Type School Degree
Postdoctoral Fellowship HudsonAlpha Institute for Biotechnology
Genomics
Postdoctoral Fellow
Doctoral Training Washington University School of Medicine
Computational Biology
Ph.D.
Undergraduate Cornell University
Biology, Computational Biology
B.S.

Selected Publications

Journal Article

  1. Stewart RL, Updike KL, Factor RE, Henry NL, Boucher KM, Bernard PS, Varley KE (2019). A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer. Cancer Res, 79(13), 3466-3478.
  2. Giraddi RR, Chung CY, Heinz RE, Balcioglu O, Novotny M, Trejo CL, Dravis C, Hagos BM, Mehrabad EM, Rodewald LW, Hwang JY, Fan C, Lasken R, Varley KE, Perou CM, Wahl GM, Spike BT (2018). Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development. Cell Rep, 24(6), 1653-1666.e7.
  3. Zabriskie MS, Antelope O, Verma AR, Draper LR, Eide CA, Pomicter AD, Tran TH, Druker BJ, Tyner JW, Miles RR, Graham JM, Hwang JY, Varley KE, Toydemir RM, Deininger MW, Raetz EA, OHare T (2017). A novel AGGF1-PDGFRb fusion in pediatric T-cell acute lymphoblastic leukemia. Haematologica, 103(2), e87-e91.
  4. McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, Boone B, Levy SE, Oliver PG, Sexton KC, Grizzle WE, Forero A, Buchsbaum DJ, Cooper SJ, Myers RM (2017). Genomic regulation of invasion by STAT3 in triple negative breast cancer. Oncotarget, 8(5), 8226-8238.
  5. Forero A, Li Y, Chen D, Grizzle WE, Updike KL, Merz ND, Downs-Kelly E, Burwell TC, Vaklavas C, Buchsbaum DJ, Myers RM, LoBuglio AF, Varley KE (2016). Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes. Cancer Immunol Res, 4(5), 390-9.
  6. Forero-Torres A, Varley KE, Abramson VG, Li Y, Vaklavas C, Lin NU, Liu MC, Rugo HS, Nanda R, Storniolo AM, Traina TA, Patil S, Van Poznak CH, Nangia JR, Irvin WJ Jr, Krontiras H, De Los Santos JF, Haluska P, Grizzle W, Myers RM, Wolff AC (2015). TBCRC 019: A Phase II Trial of Nanoparticle Albumin-Bound Paclitaxel with or without the Anti-Death Receptor 5 Monoclonal Antibody Tigatuzumab in Patients with Triple-Negative Breast Cancer. Clin Cancer Res, 21(12), 2722-9.
  7. Varley KE, Gertz J, Roberts BS, Davis NS, Bowling KM, Kirby MK, Nesmith AS, Oliver PG, Grizzle WE, Forero A, Buchsbaum DJ, LoBuglio AF, Myers RM (2014). Recurrent read-through fusion transcripts in breast cancer. Breast Cancer Res Treat, 146(2), 287-97.
  8. Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM (2013). Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell, 52(1), 25-36.
  9. Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M (2013). Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics, 8(3), 317-32.
  10. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM (2013). Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res, 23(3), 555-67.
  11. Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q (2012). CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice. Proc Natl Acad Sci U S A, 109(51), 21081-6.
  12. Gertz J, Reddy TE, Varley KE, Garabedian MJ, Myers RM (2012). Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner. Genome Res, 22(11), 2153-62.
  13. Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA (2012). Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res, 22(9), 1680-8.
  14. Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM (2012). Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res, 22(5), 860-9.
  15. Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernandez-Neuta I, Samper S, Martin C, Garcia MJ, Ritacco V, Lopez L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P (2012). IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. BMC Genomics, 13, 249.
  16. Gertz J, Varley KE, Davis NS, Baas BJ, Goryshin IY, Vaidyanathan R, Kuersten S, Myers RM (2012). Transposase mediated construction of RNA-seq libraries. Genome Res, 22(1), 134-41.
  17. ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74.
  18. Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM (2011). Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet, 7(8), e1002228.
  19. ENCODE Project Consortium (2011). A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol, 9(4), e1001046.
  20. Varley KE, Mitra RD (2010). Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res, 20(9), 1279-87.
  21. Varley KE, Mutch DG, Edmonston TB, Goodfellow PJ, Mitra RD (2009). Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing. Nucleic Acids Res, 37(14), 4603-12.
  22. Varley KE, Mitra RD (2009). Nested Patch PCR for highly multiplexed amplification of genomic loci. Cold Spring Harb Protoc, 2009(7), pdb.prot5252.
  23. Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD (2009). Quantification of rare allelic variants from pooled genomic DNA. Nat Methods, 6(4), 263-5.
  24. Varley KE, Mitra RD (2008). Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Res, 18(11), 1844-50.

Patent

  1. Katherine E. Varley, Ryan H. Miller, Jeffrey Greenland (2019). Targeted sequencing to detect and quantify low levels of methylated DNA. In preparation.
  2. Katherine E. Varley, Rachel L. Stewart, Philip S. Bernard, and Katherine Updike (2019). Multigene assay to assess risk of recurrence of cancer. Provisional. U.S. Patent No. 62/829,440. Washington, D.C.:U.S. Patent and Trademark Office.
  3. Richard M. Myers, Albert F. Lobuglio, Katherine E. Varley, Andres Forero, Donald J. Buchsbaum (2014). Biomarkers for triple-negative breast cancer. U.S. Patent No. WO2016037009 A1. International Application Published Under the Patent Cooperation Treaty. World Intellectual Property Organization.. Washington, D.C.:U.S. Patent and Trademark Office.
  4. Katherine E. Varley, D. Troy Moore, Randall Bachmeyer, David Kloske (2014). Capture Methodologies for Circulating Cell Free DNA. U.S. Patent No. US 9,982,255 B2. Washington, D.C.:U.S. Patent and Trademark Office.
  5. Katherine E. Varley, Richard M. Myers, Brian S. Roberts, Jason Gertz, Donald J. Buchsbaum, Andres Forero-Torres, Albert F. LoBuglio (2012). Novel Read-Through Fusion Polynucleotides and Polypeptides and Uses Thereof. U.S. Patent No. 13/828,901. Publication No. US2017/0267733 A1. Washington, D.C.:U.S. Patent and Trademark Office.
  6. Robi M. Mitra, Katherine E. Varley (2008). Method for multiplexed nucleic acid patch polymerase chain reaction. U.S. Patent No. US 8,586,310 B2 and US 9,909,170 B2. Washington, D.C.:U.S. Patent and Trademark Office.

U of U Health News

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