Chris Miller, Ph.D.,  McDonnell Genome Institute

Dr. Chris Miller leads a team that develops and applies computational tools to give us insight into the origins and progression of cancer. His research interests include:

  • Studying the evolutionary pressures driving tumorigenesis
  • Using integrative analysis to combine disparate sources of genomic data and place aberrations into a functional context
  • Determining structural changes in the human genome and their contributions to disease
  • Developing open-source software for integrating, mining, and visualizing genomic data
  • Utilizing online technologies to drive science communication and collaboration

Dr. Miller received Bachelor degrees in Biology and Computer Science from Truman State University, and his PhD in Computational Biology from Baylor College of Medicine.

Publications

title citation publication date
TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes. N Engl J Med. 2016 Nov 24;375(21):2023-2036. 1970-08-22
Integrated genomic characterization of oesophageal carcinoma. Nature. 2017 Jan 12;541(7636):169-175. doi: 10.1038/nature20805. Epub 2017 Jan 4. 1970-08-22
Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Jan 23. doi: 10.1038/nature21386. [Epub ahead of print] 1970-08-22
Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473-483. doi: 10.1182/blood-2016-07-729954. Epub 2016 Nov 14. 1970-08-22
Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases PLoS Med. 2016 Dec 6;13(12):e1002174. doi: 10.1371/journal.pmed.1002174. eCollection 2016. 1970-08-22
Endogenous Neoantigen-specific CD8 T Cells Identified in Two Glioblastoma Models Using a Cancer Immunogenomics Approach. Cancer Immunol Res. 2016 Oct 31. pii: canimm.0156.2016. [Epub ahead of print] 2016-10-31
Impact of mutational profiles on response of primary oestrogen receptor-positive breast cancers to oestrogen deprivation. Nat Commun. 2016 Nov 9;7:13294. doi: 10.1038/ncomms13294. 2016-11-09
Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy. Leukemia. 2016 Oct 14. doi: 10.1038/leu.2016.282. [Epub ahead of print] 2016-10-24
Visualizing tumor evolution with the fishplot package for R BMC Genomics. 2016 Nov 7;17(1):880 1970-08-22
Immunogenomics of Hypermutated Glioblastoma: a Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy. Cancer Discov. 2016 Sep 28. pii: CD-16-0575. [Epub ahead of print] 1970-08-22
Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas. Cell Rep. 2016 Sep 27;17(1):249-60. doi: 10.1016/j.celrep.2016.08.076. 1970-08-22
Targeted sequencing informs the evaluation of normal karyotype cytopenic patients for low-grade myelodysplastic syndrome Leukemia. 2016 Aug 30. doi: 10.1038/leu.2016.247. [Epub ahead of print] 1970-08-22
ATRX in diffuse gliomas with its mosaic/heterogeneous expression in a subset Brain Pathol. 2016 Feb 2. doi: 10.1111/bpa.12364. [Epub ahead of print] 2016-02-02
A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia Cold Spring Harb Mol Case Stud. 2016 Jan;2(1):a000687. doi: 10.1101/mcs.a000687 2015-01-01
Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia Exp Hematol. 2016 Jul;44(7):603-13. doi: 10.1016/j.exphem.2016.04.011. Epub 2016 May 13 2016-07-01
143 Identification of Neoantigen-specific CD8+ T Cells in Two Murine Orthotopic Glioblastoma Models Using Cancer Immunogenomics Neurosurgery. 2016 Aug;63 Suppl 1:158. doi: 10.1227/01.neu.0000489713.52326.9a 2016-08-01
Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers Nat Commun. 2016 Aug 9;7:12498. doi: 10.1038/ncomms12498 2016-08-09
A genomic analysis of Philadelphia chromosome-negative AML arising in patients with CML Blood Cancer J. 2016 Apr 8;6:e413. doi: 10.1038/bcj.2016.18 2016-04-08
Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun. 2015 Dec 22;6:10086. doi: 10.1038/ncomms10086. 2015-12-15
Optimizing cancer genome sequencing and analysis. Cell Syst. 2015 Sep 23;1(3):210-223. 2015-09-23
Rapid expansion of pre-existing non-leukemic hematopoietic clones frequently follows induction therapy for de novo AML. Blood. 2015 Dec 2. pii: blood-2015-10-677021. [Epub ahead of print] 2015-12-02
Genomic analysis of germline and somatic variants in familial myelodysplasia/acute myeloid leukemia. Blood. 2015 Oct 22. pii: blood-2015-04-641100. [Epub ahead of print] 2015-10-22
Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA. 2015 Aug 25;314(8):811-22. doi: 10.1001/jama.2015.9643. 2015-08-25
Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015. 2015-07-09
Genetic heterogeneity of induced pluripotent stem cells: results from 24 clones derived from a single C57BL/6 mouse. PLoS One. 2015 Mar 23;10(3):e0120585. doi: 10.1371/journal.pone.0120585. eCollection 2015. 2015-03-23
Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells. Leukemia. 2015 Jan 20. doi: 10.1038/leu.2015.6. [Epub ahead of print] 2015-02-17
Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia. Nature. 2014 Dec 8. doi: 10.1038/nature13968. [Epub ahead of print] 2014-12-08
Clonal architectures and driver mutations in metastatic melanomas. PLoS One. 2014 Nov 13;9(11):e111153. doi: 10.1371/journal.pone.0111153. eCollection 2014. 2014-11-13
Caspase 9 is required for normal hematopoietic development and protection from alkylator-induced DNA damage in mice. Blood. 2014 Oct 27. pii: blood-2014-06-582551. [Epub ahead of print] 2014-10-27
Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nat Med. 2014 Oct 19. doi: 10.1038/nm.3733. [Epub ahead of print] 2014-10-19
Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia. Leukemia. 2014 Sep 25. doi: 10.1038/leu.2014.289. [Epub ahead of print] 2014-09-24
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. PLoS Comput Biol. 2014 Aug 7;10(8):e1003665. doi: 10.1371/journal.pcbi.1003665. eCollection 2014. 2014-08-07
Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. 2014-07-09
Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. PLoS Genet. 2014 Jul 10;10(7):e1004462. doi: 10.1371/journal.pgen.1004462. eCollection 2014. 2014-07-10
The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers. Cancer Cell. 2014 Apr 14;25(4):442-54. doi: 10.1016/j.ccr.2014.02.010. Epub 2014 Mar 20 2014-04-14
Functional heterogeneity of genetically defined subclones in acute myeloid leukemia. Cancer Cell. 2014 Mar 17;25(3):379-92. doi: 10.1016/j.ccr.2014.01.031. Epub 2014 Mar 6. 2014-03-17
Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun. 2014 Jan 22;5:3156. doi: 10.1038/ncomms4156. 2014-01-22
Genomic landscapes and clonality of de novo AML. N Engl J Med. 2013 Oct 10;369(15):1473. doi: 10.1056/NEJMc1308782. 2013-10-10
Mutational landscape and significance across 12 major cancer types. Nature. 2013 Oct 17;502(7471):333-9. doi: 10.1038/nature12634. 2013-10-17
DGIdb: mining the druggable genome. Nat Methods. 2013 Oct 13. doi: 10.1038/nmeth.2689. [Epub ahead of print] 2013-10-13
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Sep 26;45(10):1113-20. doi: 10.1038/ng.2764. 2013-09-26
Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts. Cell Rep. 2013 Sep 18. pii: S2211-1247(13)00463-4. doi: 10.1016/j.celrep.2013.08.022. [Epub ahead of print] 2013-09-18
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. N Engl J Med. 2013 May 1. [Epub ahead of print] 2013-05-01
Clonal diversity of recurrently mutated genes in myelodysplastic syndromes. Leukemia. 2013 Feb 27. doi: 10.1038/leu.2013.58. [Epub ahead of print] 2013-02-27
Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res. 2012 Dec 5. [Epub ahead of print] 2012-12-05
Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012 Jun 10;486(7403):353-60. doi: 10.1038/nature11143. 2012-06-10
The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012 Jul 20;150(2):264-78. 2012-07-20
Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells. Cell Stem Cell. 2012 Apr 26. [Epub ahead of print] 2012-04-26
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012 Feb 2. [Epub ahead of print] 2012-02-12
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012 Jan 11. doi: 10.1038/nature10738. [Epub ahead of print] 2012-01-11
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8. Epub 2008 Sep 4. 2008-10-23