Evan Boyle

Post-Doctoral Fellow

Cellular and Molecular Medicine

 

 

Summary

Evan fulfilled a double major in Biochemistry and Microbiology at the University of Washington in Seattle. As an undergraduate, he learned the fundamentals of molecular biology in the Biochemistry department before transitioning to the lab of Dr. Jay Shendure in the Department of Genome Sciences. There he worked on new methods for DNA sequencing by molecular inversion probes and, after graduating, on multiplex genome editing using CRISPR. During his graduate studies and under the co-supervision of Dr. Jonathan Pritchard and Dr. William Greenleaf, Evan characterized the polygenicity of complex traits, biases in high-throughput genetic screening data, and the DNA-binding specificity of Cas9. His work includes proposing the ‘omnigenic model’ for complex traits and adapting the radioactive filter binding assay to a nonradioactive, sequencing-based readout. While at Stanford, Evan also completed Stanford Medical School’s Masters of Medicine program, designed to expose PhD students to the field of medicine. As a postdoctoral researcher in the Yeo Lab, Evan is interested in linking RNA-binding proteins to functional targets and developing new technologies for perturbing RNA processing in human cells.

 

Education

Ph.D. Genetics, Stanford University, 2019

M.S. Medicine, Stanford University, 2019

B.S. Biochemistry, University of Washington, 2013

B.S. Microbiology, University of Washington, 2013

 

Contact

eboyle@ucsd.edu

Publications

§ denotes equal contribution; † denotes consortium authorship

  • Berg J. J.§, Harpak A.§, Sinnott-Armstrong N.§, Joergensen A. M., Mostafavi H., Field Y., Boyle E. A., Zhang X., Racimo F., Pritchard J. K., Coop G. Reduced signal for polygenic adaptation of height in UK Biobank. Elife. 2019 Mar 21;8. doi: 10.7554/eLife.39725. PubMed PMID: 30895923; PubMed Central PMCID: PMC6428572.

  • Boyle E. A., Pritchard J. K., Greenleaf W. J. High-resolution mapping of cancer cell networks using co-functional interactions.Mol Syst Biol. 2018 Dec 20;14(12):e8594. doi: 10.15252/msb.20188594. PubMed PMID: 30573688; PubMed Central PMCID: PMC6300813.

  • Haney M. S.§, Bohlen C. J.§, Morgens D. W., Ousey J. A., Barkal A. A., Tsui C. K., Ego B. K., Levin R., Kamber R. A., Collins H., Tucker A., Li A., Vorselen D., Labitigan L., Crane E., Boyle E. A., Jiang L., Chan J., Rincón E., Greenleaf W. J., Li B., Snyder M. P., Weissman I. L., Theriot J. A., Collins S. R., Barres B. A., Bassik M. C. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nat Genet. 2018 Dec;50(12):1716-1727. doi: 10.1038/s41588-018-0254-1. Epub 2018 Nov 5. PubMed PMID: 30397336.

  • Corces M. R.§, Granja J. M.§, Shams S., Louie B. H., Seoane J. A., Zhou W., Silva T. C., Groeneveld C., Wong C. K., Cho S. W., Satpathy A. T., Mumbach M. R., Hoadley K. A., Robertson A. G., Sheffield N. C., Felau I., Castro M. A. A., Berman B. P., Staudt L. M., Zenklusen J. C., Laird P. W., Curtis C., Greenleaf W. J., Chang H. Y.†. The chromatin accessibility landscape of primary human cancers. Science. 2018 Oct 26;362(6413). doi: 10.1126/science.aav1898. PubMed PMID: 30361341; PubMed Central PMCID: PMC6408149.

  • Aalipour A., Dudley J. C., Park S. M., Murty S., Chabon J. J., Boyle E. A., Diehn M., Gambhir S. S. Deactivated CRISPR Associated Protein 9 for Minor-Allele Enrichment in Cell-Free DNA. Clin Chem. 2018 Feb;64(2):307-316. doi: 10.1373/clinchem.2017.278911. Epub 2017 Oct 16. PubMed PMID: 29038154.

  • Mumbach M. R.§, Satpathy A. T.§, Boyle E. A.§, Dai C.§, Gowen B. G., Cho S. W., Nguyen M. L., Rubin A. J., Granja J. M., Kazane K. R., Wei Y., Nguyen T., Greenside P. G., Corces M. R., Tycko J., Simeonov D. R., Suliman N., Li R., Xu J., Flynn R. A., Kundaje A., Khavari P. A., Marson A., Corn J. E., Quertermous T., Greenleaf W. J., Chang H. Y. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet. 2017 Nov;49(11):1602-1612. doi: 10.1038/ng.3963. Epub 2017 Sep 25. PubMed PMID: 28945252; PubMed Central PMCID: PMC5805393.

  • Rehker J., Rodhe J., Nesbitt R. R., Boyle E. A., Martin B. K., Lord J., Karaca I., Naj A., Jessen F., Helisalmi S., Soininen H., Hiltunen M., Ramirez A., Scherer M., Farrer L. A., Haines J. L., Pericak-Vance M. A., Raskind W. H., Cruchaga C., Schellenberg G. D., Joseph B., Brkanac Z. Caspase-8, association with Alzheimer’s Disease and functional analysis of rare variants. PLoS One.2017;12(10):e0185777. doi: 10.1371/journal.pone.0185777. eCollection 2017. PubMed PMID: 28985224; PubMed Central PMCID: PMC5630132.

  • Boyle E. A., Li Y. I., Pritchard J. K. An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell. 2017 Jun 15;169(7):1177-1186. doi: 10.1016/j.cell.2017.05.038. Review. PubMed PMID: 28622505; PubMed Central PMCID: PMC5536862.

  • Boyle EA§, Andreasson JOL§, Chircus LM§, Sternberg SH, Wu MJ, Guegler CK, Doudna JA, Greenleaf WJ. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proc Natl Acad Sci U S A. 2017 May 23;114(21):5461-5466. doi: 10.1073/pnas.1700557114. Epub 2017 May 11. PubMed PMID: 28495970; PubMed Central PMCID: PMC5448226.

  • Morgens D. W.§, Wainberg M.§, Boyle E. A., Ursu O., Araya C. L., Tsui C. K., Haney M. S., Hess G. T., Han K., Jeng E. E., Li A., Snyder M. P., Greenleaf W. J., Kundaje A., Bassik M. C. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nat Commun. 2017 May 5;8:15178. doi: 10.1038/ncomms15178. PubMed PMID: 28474669; PubMed Central PMCID: PMC5424143.

  • Neveling K., Mensenkamp A. R., Derks R., Kwint M., Ouchene H., Steehouwer M., van Lier B., Bosgoed E., Rikken A., Tychon M., Zafeiropoulou D., Castelein S., Hehir-Kwa J., Tjwan Thung D., Hofste T., Lelieveld S. H., Bertens S. M., Adan I. B., Eijkelenboom A., Tops B. B., Yntema H,. Stokowy T., Knappskog P. M., Høberg-Vetti H., Steen V. M., Boyle E. A., Martin B., Ligtenberg M. J., Shendure J., Nelen M. R., Hoischen A. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clin Chem. 2017 Feb;63(2):503-512. doi: 10.1373/clinchem.2016.263897. Epub 2016 Dec 14. PubMed PMID: 27974384.

  • Field Y.§, Boyle E. A.§, Telis N.§, Gao Z., Gaulton K. J., Golan D., Yengo L., Rocheleau G., Froguel P., McCarthy M. I., Pritchard J. K.Detection of human adaptation during the past 2000 years. Science. 2016 Nov 11;354(6313):760-764. doi: 10.1126/science.aag0776. Epub 2016 Oct 13. PubMed PMID: 27738015; PubMed Central PMCID: PMC5182071.

  • Mirzaa G. M.§, Campbell C. D.§, Solovieff N., Goold C., Jansen L. A., Menon S., Timms A. E., Conti V., Biag J. D., Adams C., Boyle E. A., Collins S., Ishak G., Poliachik S., Girisha K. M., Yeung K. S., Chung B. H. Y., Rahikkala E., Gunter S. A., McDaniel S. S., Macmurdo C. F., Bernstein J. A., Martin B., Leary R., Mahan S., Liu S., Weaver M., Doerschner M., Jhangiani S., Muzny D. M., Boerwinkle E., Gibbs R. A., Lupski J. R., Shendure J., Saneto R. P., Novotny E. J., Wilson C. J., Sellers W. R., Morrissey M., Hevner R. F., Ojemann J. G., Guerrini R., Murphy L. O., Winckler W., Dobyns W. B. Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism. JAMA Neurol. 2016 Jul 1;73(7):836-845. doi: 10.1001/jamaneurol.2016.0363. PubMed PMID: 27159400; PubMed Central PMCID: PMC4979321.

  • Mirzaa G., Timms A. E., Conti V., Boyle E. A., Girisha K. M., Martin B., Kircher M., Olds C., Juusola J., Collins S., Park K., Carter M., Glass I., Krägeloh-Mann I., Chitayat D., Parikh A. S., Bradshaw R., Torti E., Braddock S., Burke L., Ghedia S., Stephan M., Stewart F., Prasad C., Napier M., Saitta S., Straussberg R., Gabbett M., O’Connor B. C., Keegan C. E., Yin L. J., Lai A. H. M., Martin N., McKinnon M., Addor M. C., Boccuto L., Schwartz C. E., Lanoel A., Conway R. L., Devriendt K., Tatton-Brown K., Pierpont M. E., Painter M., Worgan L., Reggin J., Hennekam R., Tsuchiya K., Pritchard C. C., Aracena M., Gripp K. W., Cordisco M., Van Esch H., Garavelli L., Curry C., Goriely A., Kayserilli H., Shendure J., Graham J. Jr., Guerrini R., Dobyns W. B. PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution. JCI Insight. 2016 Jun 16;1(9). doi: 10.1172/jci.insight.87623. PubMed PMID: 27631024; PubMed Central PMCID: PMC5019182.

  • Mirzaa G. M., Conti V., Timms A. E., Smyser C. D., Ahmed S., Carter M., Barnett S., Hufnagel R. B., Goldstein A., Narumi-Kishimoto Y., Olds C., Collins S., Johnston K., Deleuze J. F., Nitschké P., Friend K., Harris C., Goetsch A., Martin B., Boyle E. A., Parrini E., Mei D., Tattini L., Slavotinek A., Blair E., Barnett C., Shendure J., Chelly J., Dobyns W. B., Guerrini R. Characterisation of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next-generation sequencing study. Lancet Neurol. 2015 Dec;14(12):1182-95. doi: 10.1016/S1474-4422(15)00278-1. Epub 2015 Oct 29. PubMed PMID: 26520804; PubMed Central PMCID: PMC4672724.

  • Bachmann-Gagescu R., Phelps I. G., Dempsey J. C., Sharma V. A., Ishak G. E., Boyle E. A., Wilson M., Marques Lourenço C., Arslan M., Shendure J., Doherty D. KIAA0586 is Mutated in Joubert Syndrome. Hum Mutat. 2015 Sep;36(9):831-5. doi: 10.1002/humu.22821. Epub 2015 Jul 2. PubMed PMID: 26096313; PubMed Central PMCID: PMC4537327.

  • Wheway G.§, Schmidts M.§, Mans D. A.§, Szymanska K.§, Nguyen T. T.§, Racher H., Phelps I. G., Toedt G., Kennedy J., Wunderlich K. A., Sorusch N., Abdelhamed Z. A., Natarajan S., Herridge W., van Reeuwijk J., Horn N., Boldt K., Parry D. A., Letteboer S. J. F., Roosing S., Adams M., Bell S. M., Bond J., Higgins J., Morrison E. E., Tomlinson D. C., Slaats G. G., van Dam T. J. P., Huang L., Kessler K., Giessl A., Logan C. V., Boyle E. A., Shendure J., Anazi S., Aldahmesh M., Al Hazzaa S., Hegele R. A., Ober C., Frosk P., Mhanni A. A., Chodirker B. N., Chudley A. E., Lamont R., Bernier F. P., Beaulieu C. L., Gordon P., Pon R. T., Donahue C., Barkovich A. J., Wolf L., Toomes C., Thiel C. T., Boycott K. M., McKibbin M., Inglehearn C. F., Stewart F., Omran H., Huynen M. A., Sergouniotis P. I., Alkuraya F. S., Parboosingh J. S., Innes A. M., Willoughby C. E., Giles R. H., Webster A. R., Ueffing M., Blacque O., Gleeson J. G., Wolfrum U., Beales P. L., Gibson T., Doherty D., Mitchison H. M., Roepman R., Johnson C. A. An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. Nat Cell Biol. 2015 Aug;17(8):1074-1087. doi: 10.1038/ncb3201. Epub 2015 Jul 13. PubMed PMID: 26167768; PubMed Central PMCID: PMC4536769.

  • Bachmann-Gagescu R., Dempsey J. C., Phelps I. G., O’Roak B. J., Knutzen D. M., Rue T. C., Ishak G. E., Isabella C. R., Gorden N., Adkins J., Boyle E. A., de Lacy N., O’Day D., Alswaid A., Ramadevi A. R., Lingappa L., Lourenço C., Martorell L., Garcia-Cazorla À., Ozyürek H., Haliloğlu G., Tuysuz B., Topçu M., Chance P., Parisi M. A., Glass I. A., Shendure J., Doherty D. Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity. J Med Genet. 2015 Aug;52(8):514-22. doi: 10.1136/jmedgenet-2015-103087. Epub 2015 Jun 19. PubMed PMID: 26092869; PubMed Central PMCID: PMC5082428.

  • Weren R. D., Ligtenberg M. J., Kets C. M., de Voer R. M., Verwiel E. T., Spruijt L., van Zelst-Stams W. A., Jongmans M. C., Gilissen C., Hehir-Kwa J. Y., Hoischen A., Shendure J., Boyle E. A., Kamping E. J., Nagtegaal I. D., Tops B. B., Nagengast F. M., Geurts van Kessel A., van Krieken J. H., Kuiper R. P.§, Hoogerbrugge N.§. A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer. Nat Genet. 2015 Jun;47(6):668-71. doi: 10.1038/ng.3287. Epub 2015 May 4. PubMed PMID: 25938944.

  • D’Gama A. M., Geng Y., Couto J. A., Martin B., Boyle E. A., LaCoursiere C. M., Hossain A., Hatem N. E., Barry B. J., Kwiatkowski D. J., Vinters H. V., Barkovich A. J., Shendure J., Mathern G. W., Walsh C. A.§, Poduri A.§. Mammalian target of rapamycin pathway mutations cause hemimegalencephaly and focal cortical dysplasia. Ann Neurol. 2015 Apr;77(4):720-5. doi: 10.1002/ana.24357. Epub 2015 Feb 26. PubMed PMID: 25599672; PubMed Central PMCID: PMC4471336.

  • Chong J. X., McMillin M. J., Shively K. M., Beck A. E., Marvin C. T., Armenteros J. R., Buckingham K. J., Nkinsi N. T., Boyle E. A., Berry M. N., Bocian M., Foulds N., Uzielli M. L., Haldeman-Englert C., Hennekam R. C., Kaplan P., Kline A. D., Mercer C. L., Nowaczyk M. J., Klein Wassink-Ruiter J. S., McPherson E. W., Moreno R. A., Scheuerle A. E., Shashi V., Stevens C. A., Carey J. C., Monteil A., Lory P., Tabor H. K., Smith J. D., Shendure J., Nickerson D. A., Bamshad M. J. De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay. Am J Hum Genet. 2015 Mar 5;96(3):462-73. doi: 10.1016/j.ajhg.2015.01.003. Epub 2015 Feb 12. PubMed PMID: 25683120; PubMed Central PMCID: PMC4375444.

  • Kumar A., Boyle E. A., Tokita M., Mikheev A. M., Sanger M. C., Girard E., Silber J. R., Gonzalez-Cuyar L. F., Hiatt J. B., Adey A., Lee C., Kitzman J. O., Born D. E., Silbergeld D. L., Olson J. M., Rostomily R. C., Shendure J. Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biol. 2014 Dec 3;15(12):530. doi: 10.1186/s13059-014-0530-z. PubMed PMID: 25608559; PubMed Central PMCID: PMC4272528.

  • O’Roak B. J.§, Stessman H. A.§, Boyle E. A., Witherspoon K. T., Martin B., Lee C., Vives L., Baker C., Hiatt J. B., Nickerson D. A., Bernier R., Shendure J., Eichler E. E.. Recurrent de novo mutations implicate novel genes underlying simplex autism risk. Nat Commun. 2014 Nov 24;5:5595. doi: 10.1038/ncomms6595. PubMed PMID: 25418537; PubMed Central PMCID: PMC4249945.

  • Boyle E. A., O’Roak B. J., Martin B. K., Kumar A., Shendure J. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. Bioinformatics. 2014 Sep 15;30(18):2670-2. doi: 10.1093/bioinformatics/btu353. Epub 2014 May 26. PubMed PMID: 24867941; PubMed Central PMCID: PMC4155255.

  • Findlay G. M.§, Boyle E. A.§, Hause R. J., Klein J. C., Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nature. 2014 Sep 4;513(7516):120-3. doi: 10.1038/nature13695. PubMed PMID: 25141179; PubMed Central PMCID: PMC4156553.

  • FitzGerald L. M., Kumar A., Boyle E. A., Zhang Y., McIntosh L. M., Kolb S., Stott-Miller M., Smith T., Karyadi D. M., Ostrander E. A., Hsu L., Shendure J., Stanford J. L. Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility. Cancer Epidemiology Biomarkers & Prevention. 2013 July; 22(9):1520-1528. doi: 10.1158/1055-9965.EPI-13-0345.