Katherine E. Varley, Ph.D.

Research Interests

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

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: 4363
    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. Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes.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.
  2. 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.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.
  3. Recurrent read-through fusion transcripts in breast cancer.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.
  4. Dynamic DNA methylation across diverse human cell lines and tissues.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.
  5. ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74.
  6. Transposase mediated construction of RNA-seq libraries.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.
  7. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.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.
  8. Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.Varley KE, Mitra RD (2010). Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res, 20(9), 1279-87.
  9. Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing.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.
  10. Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes.Varley KE, Mitra RD (2008). Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Res, 18(11), 1844-50.

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