Evan Boyle

Post-Doctoral Fellow
Cellular and Molecular Medicine
eboyle at ucsd.edu

Degrees

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

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 lab 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.

Publications

§ denotes equal contribution; † denotes consortium authorship

  1. Berg JJ§, Harpak A§, Sinnott-Armstrong N§, Joergensen AM, Mostafavi H, Field Y, Boyle EA, Zhang X, Racimo F, Pritchard JK, 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.

  2. Boyle EA, Pritchard JK, Greenleaf WJ. 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.

  3. Haney MS§, Bohlen CJ§, Morgens DW, Ousey JA, Barkal AA, Tsui CK, Ego BK, Levin R, Kamber RA, Collins H, Tucker A, Li A, Vorselen D, Labitigan L, Crane E,Boyle E, Jiang L, Chan J, Rincón E, Greenleaf WJ, Li B, Snyder MP, Weissman IL, Theriot JA, Collins SR, Barres BA, Bassik MC. 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.

  4. Corces MR§, Granja JM§, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY†. 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.

  5. Aalipour A, Dudley JC, Park SM, Murty S, Chabon JJ, Boyle EA, Diehn M, Gambhir SS. 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.

  6. Mumbach MR§, Satpathy AT§, Boyle EA§, Dai C§, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. 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.

  7. Rehker J, Rodhe J, Nesbitt RR, Boyle EA, Martin BK, Lord J, Karaca I, Naj A, Jessen F, Helisalmi S, Soininen H, Hiltunen M, Ramirez A, Scherer M, Farrer LA, Haines JL, Pericak-Vance MA, Raskind WH, Cruchaga C, Schellenberg GD, 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.

  8. Boyle EA, Li YI, Pritchard JK. 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.

  9. 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.

  10. Morgens DW§, Wainberg M§, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC. 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.

  11. Neveling K, Mensenkamp AR, 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 SH, Bertens SM, Adan IB, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM, Boyle E, Martin B, Ligtenberg MJ, Shendure J, Nelen MR, 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.

  12. Field Y§, Boyle EA§, Telis N§, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK.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.

  13. Mirzaa GM§, Campbell CD§, Solovieff N, Goold C, Jansen LA, Menon S, Timms AE, Conti V, Biag JD, Adams C, Boyle EA, Collins S, Ishak G, Poliachik S, Girisha KM, Yeung KS, Chung BHY, Rahikkala E, Gunter SA, McDaniel SS, Macmurdo CF, Bernstein JA, Martin B, Leary R, Mahan S, Liu S, Weaver M, Doerschner M, Jhangiani S, Muzny DM, Boerwinkle E, Gibbs RA, Lupski JR, Shendure J, Saneto RP, Novotny EJ, Wilson CJ, Sellers WR, Morrissey M, Hevner RF, Ojemann JG, Guerrini R, Murphy LO, Winckler W, Dobyns WB. 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.

  14. Mirzaa G, Timms AE, Conti V, Boyle EA, Girisha KM, Martin B, Kircher M, Olds C, Juusola J, Collins S, Park K, Carter M, Glass I, Krägeloh-Mann I, Chitayat D, Parikh AS, 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 BC, Keegan CE, Yin LJ, Lai AHM, Martin N, McKinnon M, Addor MC, Boccuto L, Schwartz CE, Lanoel A, Conway RL, Devriendt K, Tatton-Brown K, Pierpont ME, Painter M, Worgan L, Reggin J, Hennekam R, Tsuchiya K, Pritchard CC, Aracena M, Gripp KW, Cordisco M, Van Esch H, Garavelli L, Curry C, Goriely A, Kayserilli H, Shendure J, Graham J Jr, Guerrini R, Dobyns WB. 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.

  15. Mirzaa GM, Conti V, Timms AE, Smyser CD, Ahmed S, Carter M, Barnett S, Hufnagel RB, Goldstein A, Narumi-Kishimoto Y, Olds C, Collins S, Johnston K, Deleuze JF, Nitschké P, Friend K, Harris C, Goetsch A, Martin B, Boyle EA, Parrini E, Mei D, Tattini L, Slavotinek A, Blair E, Barnett C, Shendure J, Chelly J, Dobyns WB, 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.

  16. Bachmann-Gagescu R, Phelps IG, Dempsey JC, Sharma VA, Ishak GE, Boyle EA, 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.

  17. Wheway G§, Schmidts M§, Mans DA§, Szymanska K§, Nguyen TT§, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA, Sorusch N, Abdelhamed ZA, Natarajan S, Herridge W, van Reeuwijk J, Horn N, Boldt K, Parry DA, Letteboer SJF, Roosing S, Adams M, Bell SM, Bond J, Higgins J, Morrison EE, Tomlinson DC, Slaats GG, van Dam TJP, Huang L, Kessler K, Giessl A, Logan CV, Boyle EA, Shendure J, Anazi S, Aldahmesh M, Al Hazzaa S, Hegele RA, Ober C, Frosk P, Mhanni AA, Chodirker BN, Chudley AE, Lamont R, Bernier FP, Beaulieu CL, Gordon P, Pon RT, Donahue C, Barkovich AJ, Wolf L, Toomes C, Thiel CT, Boycott KM, McKibbin M, Inglehearn CF, Stewart F, Omran H, Huynen MA, Sergouniotis PI, Alkuraya FS, Parboosingh JS, Innes AM, Willoughby CE, Giles RH, Webster AR, Ueffing M, Blacque O, Gleeson JG, Wolfrum U, Beales PL, Gibson T, Doherty D, Mitchison HM, Roepman R, Johnson CA. 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.

  18. Bachmann-Gagescu R, Dempsey JC, Phelps IG, O’Roak BJ, Knutzen DM, Rue TC, Ishak GE, Isabella CR, Gorden N, Adkins J, Boyle EA, 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 MA, Glass IA, 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.

  19. Weren RD, Ligtenberg MJ, Kets CM, de Voer RM, Verwiel ET, Spruijt L, van Zelst-Stams WA, Jongmans MC, Gilissen C, Hehir-Kwa JY, Hoischen A, Shendure J, Boyle EA, Kamping EJ, Nagtegaal ID, Tops BB, Nagengast FM, Geurts van Kessel A, van Krieken JH, Kuiper RP§, 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.

  20. D’Gama AM, Geng Y, Couto JA, Martin B, Boyle EA, LaCoursiere CM, Hossain A, Hatem NE, Barry BJ, Kwiatkowski DJ, Vinters HV, Barkovich AJ, Shendure J, Mathern GW, Walsh CA§, 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.

  21. Chong JX, McMillin MJ, Shively KM, Beck AE, Marvin CT, Armenteros JR, Buckingham KJ, Nkinsi NT, Boyle EA, Berry MN, Bocian M, Foulds N, Uzielli ML, Haldeman-Englert C, Hennekam RC, Kaplan P, Kline AD, Mercer CL, Nowaczyk MJ, Klein Wassink-Ruiter JS, McPherson EW, Moreno RA, Scheuerle AE, Shashi V, Stevens CA, Carey JC, Monteil A, Lory P, Tabor HK, Smith JD, Shendure J, Nickerson DA, Bamshad MJ. 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.

  22. Kumar A, Boyle EA, Tokita M, Mikheev AM, Sanger MC, Girard E, Silber JR, Gonzalez-Cuyar LF, Hiatt JB, Adey A, Lee C, Kitzman JO, Born DE, Silbergeld DL, Olson JM, Rostomily RC, 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.

  23. O’Roak BJ§, Stessman HA§, Boyle EA, Witherspoon KT, Martin B, Lee C, Vives L, Baker C, Hiatt JB, Nickerson DA, Bernier R, Shendure J, Eichler EE. 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.

  24. Boyle EA, O’Roak BJ, Martin BK, 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.

  25. Findlay GM§, Boyle EA§, Hause RJ, Klein JC, 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.

  26. FitzGerald LM, Kumar A, Boyle EA, Zhang Y, McIntosh, LM, Kolb S, Stott-Miller M, Smith T, Karyadi DM, Ostrander EA, Hsu L, Shendure J, Stanford JL. 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.