David Carrell, PhD

David Carrell PhD

“My work uses computers to mine and analyze information about patients’ health from the millions of clinical notes Kaiser Permanente Washington doctors and nurses write about their patients in a typical year.”

David Carrell, PhD

Associate Investigator, Kaiser Permanente Washington Health Research Institute

Biography

David Carrell, PhD, is an assistant investigator who develops and applies technology for extracting rich information from unstructured clinical text, such as physician progress notes. This work uses state-of-the-art clinical natural language processing (NLP) technologies in single- and multi-site settings.

An example of this work is an NLP system to identify women who have been diagnosed with recurrent breast cancer. Despite being a common and consequential clinical diagnosis, recurrent breast cancer cannot be tracked reliably using standard medical codes found in a person’s chart. Supported by a grant from the National Cancer Institute, he and his colleagues used information from clinician progress notes, radiology reports, and pathology reports to classify women by breast cancer recurrence.

Working with teams of researchers inside and outside Kaiser Permanente Washington Health Research Institute, Dr. Carrell has applied similar precision phenotyping methods to identify evidence of carotid artery stenosis, colon polyps, problem use of prescription opioids, and colonoscopy quality.

Dr. Carrell’s current research projects are applying NLP and machine learning methods to improve medication safety surveillance (through the Food and Drug Administration Sentinel Initiative) and to evaluate the impact on drug use disorder diagnosis and treatment of Kaiser Permanente Washington patients screened for unhealthy cannabis and other drug use.  His ongoing work also includes development and application of automated algorithms based on electronic health record data to identify patients with particular health conditions (called “patient phenotypes”) for use in genetic and epidemiological research.

RESEARCH INTERESTS AND EXPERIENCE

  • Medication Use & Patient Safety

    Surveillance methods for adverse events associated with medication exposure, including problem use of prescription opioids

  • Health Informatics

    Methods for using structured and unstructured electronic health record data to identify patients with (or without) specific clinical conditions or phenotypes for large scale epidemiological and genomic studies

  • Cancer and Cancer Screening

    Identifying recurrent breast cancer using EHR text; Colonoscopy quality metrics

  • Clinical Natural Language Processing

    Recurrent breast cancer; Colonoscopy quality; Extracting information from clinical text; Automated de-identification of clinical text; Methods for applying NLP methods in multi-site research

  • Addictions

    Prevention and treatment

  • Substance Use Disorders

  • Mental Health

  • Pharmacoepidemiology

     

  • Clinical Text De-identification

Recent publications

Mehrotra A, Morris M, Gourevitch RA, Carrell DS, Leffler DA, Rose S, Greer JB, Crockett SD, Baer A, Schoen RE. Physician characteristics associated with higher adenoma detection rate. Gastrointest Endosc. 2017 Aug 30. pii: S0016-5107(17)32205-8. doi: 10.1016/j.gie.2017.08.023. [Epub ahead of print]. PubMed

Huhdanpaa HT, Tan WK, Rundell SD, Suri P, Chokshi FH, Comstock BA, Heagerty PJ, James KT, Avins AL, Nedeljkovic SS, Nerenz DR, Kallmes DF, Luetmer PH, Sherman KJ, Organ NL, Griffith B, Langlotz CP, Carrell D, Hassanpour S, Jarvik JG. Using natural language processing of free-text radiology reports to identify type 1 modic endplate changes. J Digit Imaging. 2017 Aug 14. doi: 10.1007/s10278-017-0013-3. [Epub ahead of print]. PubMed

Holzinger ER, Verma SS, Moore CB, Hall M, De R, Gilbert-Diamond D, Lanktree MB, Pankratz N, Amuzu A, Burt A, Dale C, Dudek S, Furlong CE, Gaunt TR, Kim DS, Riess H, Sivapalaratnam S, Tragante V, van Iperen EPA, Brautbar A, Carrell DS, Crosslin DR, Jarvik GP, Kuivaniemi H, Kullo IJ, Larson EB, Rasmussen-Torvik LJ, Tromp G, Baumert J, Cruickshanks KJ, Farrall M, Hingorani AD, Hovingh GK, Kleber ME, Klein BE, Klein R, Koenig W, Lange LA, M?rz W, North KE, Charlotte Onland-Moret N, Reiner AP, Talmud PJ, van der Schouw YT, Wilson JG, Kivimaki M, Kumari M, Moore JH, Drenos F, Asselbergs FW, Keating BJ, Ritchie MD. Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals. BioData Min. 2017 Jul 24;10:25. doi: 10.1186/s13040-017-0145-5. eCollection 2017. PubMed

Sims R, van der Lee SJ, Naj AC, Bellenguez C, Badarinarayan N, Jakobsdottir J, Kunkle BW, Boland A, Raybould R, Bis JC, Martin ER, Grenier-Boley B, Heilmann-Heimbach S, Chouraki V, Kuzma AB, Sleegers K, Vronskaya M, Ruiz A, Graham RR, Olaso R, Hoffmann P, Grove ML, Vardarajan BN, Hiltunen M, Nöthen MM, White CC, Hamilton-Nelson KL, Epelbaum J, Maier W, Choi SH, Beecham GW, Dulary C, Herms S, Smith AV, Funk CC, Derbois C, Forstner AJ, Ahmad S, Li H, Bacq D, Harold D, Satizabal CL, Valladares O, Squassina A, Thomas R, Brody JA, Qu L, Sánchez-Juan P, Morgan T, Wolters FJ, Zhao Y, Garcia FS, Denning N, Fornage M, Malamon J, Naranjo MCD, Majounie E, Mosley TH, Dombroski B, Wallon D, Lupton MK, Dupuis J, Whitehead P, Fratiglioni L, Medway C, Jian X, Mukherjee S, Keller L, Brown K, Lin H, Cantwell LB, Panza F, McGuinness B, Moreno-Grau S, Burgess JD, Solfrizzi V, Proitsi P, Adams HH, Allen M, Seripa D, Pastor P, Cupples LA, Price ND, Hannequin D, Frank-García A, Levy D, Chakrabarty P, Caffarra P, Giegling I, Beiser AS, Giedraitis V, Hampel H, Garcia ME, Wang X, Lannfelt L, Mecocci P, Eiriksdottir G, Crane PK, Pasquier F, Boccardi V, Henández I, Barber RC, Scherer M, Tarraga L, Adams PM, Leber M, Chen Y, Albert MS, Riedel-Heller S, Emilsson V, Beekly D, Braae A, Schmidt R, Blacker D, Masullo C, Schmidt H, Doody RS, Spalletta G, Jr WTL, Fairchild TJ, Bossù P, Lopez OL, Frosch MP, Sacchinelli E, Ghetti B, Yang Q, Huebinger RM, Jessen F, Li S, Kamboh MI, Morris J, Sotolongo-Grau O, Katz MJ, Corcoran C, Dunstan M, Braddel A, Thomas C, Meggy A, Marshall R, Gerrish A, Chapman J, Aguilar M, Taylor S, Hill M, Fairén MD, Hodges A, Vellas B, Soininen H, Kloszewska I, Daniilidou M, Uphill J, Patel Y, Hughes JT, Lord J, Turton J, Hartmann AM, Cecchetti R, Fenoglio C, Serpente M, Arcaro M, Caltagirone C, Orfei MD, Ciaramella A, Pichler S, Mayhaus M, Gu W, Lleó A, Fortea J, Blesa R, Barber IS, Brookes K, Cupidi C, Maletta RG, Carrell D, Sorbi S, Moebus S, Urbano M, Pilotto A, Kornhuber J, Bosco P, Todd S, Craig D, Johnston J, Gill M, Lawlor B, Lynch A, Fox NC, Hardy J; ARUK Consortium, Albin RL, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Baldwin CT, Barnes LL, Barral S, Beach TG, Becker JT, Bigio EH, Bird TD, Boeve BF, Bowen JD, Boxer A, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Carroll SL, Diaz CC, Chui HC, Clark DG, Cribbs DH, Crocco EA, DeCarli C, Dick M, Duara R, Evans DA, Faber KM, Fallon KB, Fardo DW, Farlow MR, Ferris S, Foroud TM, Galasko DR, Gearing M, Geschwind DH, Gilbert JR, Graff-Radford NR, Green RC, Growdon JH, Hamilton RL, Harrell LE, Honig LS, Huentelman MJ, Hulette CM, Hyman BT, Jarvik GP, Abner E, Jin LW, Jun G, Karydas A, Kaye JA, Kim R, Kowall NW, Kramer JH, LaFerla FM, Lah JJ, Leverenz JB, Levey AI, Li G, Lieberman AP, Lunetta KL, Lyketsos CG, Marson DC, Martiniuk F, Mash DC, Masliah E, McCormick WC, McCurry SM, McDavid AN, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Morris JC, Murrell JR, Myers AJ, O'Bryant S, Olichney JM, Pankratz VS, Parisi JE, Paulson HL, Perry W, Peskind E, Pierce A, Poon WW, Potter H, Quinn JF, Raj A, Raskind M, Reisberg B, Reitz C, Ringman JM, Roberson ED, Rogaeva E, Rosen HJ, Rosenberg RN, Sager MA, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Smith AG, Sonnen JA, Spina S, Stern RA, Swerdlow RH, Tanzi RE, Thornton-Wells TA, Trojanowski JQ, Troncoso JC, Van Deerlin VM, Van Eldik LJ, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Wilhelmsen KC, Williamson J, Wingo TS, Woltjer RL, Wright CB, Yu CE, Yu L, Garzia F, Golamaully F, Septier G, Engelborghs S, Vandenberghe R, De Deyn PP, Fernadez CM, Benito YA, Thonberg H, Forsell C, Lilius L, Kinhult-Stählbom A, Kilander L, Brundin R, Concari L, Helisalmi S, Koivisto AM, Haapasalo A, Dermecourt V, Fievet N, Hanon O, Dufouil C, Brice A, Ritchie K, Dubois B, Himali JJ, Keene CD, Tschanz J, Fitzpatrick AL, Kukull WA, Norton M, Aspelund T, Larson EB, Munger R, Rotter JI, Lipton RB, Bullido MJ, Hofman A, Montine TJ, Coto E, Boerwinkle E, Petersen RC, Alvarez V, Rivadeneira F, Reiman EM, Gallo M, O'Donnell CJ, Reisch JS, Bruni AC, Royall DR, Dichgans M, Sano M, Galimberti D, St George-Hyslop P, Scarpini E, Tsuang DW, Mancuso M, Bonuccelli U, Winslow AR, Daniele A, Wu CK; GERAD/PERADES, CHARGE, ADGC, EADI, Peters O, Nacmias B, Riemenschneider M, Heun R, Brayne C, Rubinsztein DC, Bras J, Guerreiro R, Al-Chalabi A, Shaw CE, Collinge J, Mann D, Tsolaki M, Clarimón J, Sussams R, Lovestone S, O'Donovan MC, Owen MJ, Behrens TW, Mead S, Goate AM, Uitterlinden AG, Holmes C, Cruchaga C, Ingelsson M, Bennett DA, Powell J, Golde TE, Graff C, De Jager PL, Morgan K, Ertekin-Taner N, Combarros O, Psaty BM, Passmore P, Younkin SG, Berr C, Gudnason V, Rujescu D, Dickson DW, Dartigues JF, DeStefano AL, Ortega-Cubero S, Hakonarson H, Campion D, Boada M, Kauwe JK, Farrer LA, Van Broeckhoven C, Ikram MA, Jones L, Haines JL, Tzourio C, Launer LJ, Escott-Price V, Mayeux R, Deleuze JF, Amin N, Holmans PA, Pericak-Vance MA, Amouyel P, van Duijn CM, Ramirez A, Wang LS, Lambert JC, Seshadri S, Williams J, Schellenberg GD. Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease. Nat Genet. 2017 Jul 17. doi: 10.1038/ng.3916. [Epub ahead of print]. PubMed

Carrell DS, Schoen RE, Leffler DA, Morris M, Rose S, Baer A, Crockett SD, Gourevitch RA, Dean KM, Mehrotra A. Challenges in adapting existing clinical natural language processing systems to multiple, diverse health care settings. JJ Am Med Inform Assoc. 2017 Sep 1;24(5):986-991. doi: 10.1093/jamia/ocx039. PubMed

Dumitrescu L, Ritchie MD, Denny JC, El Rouby NM, McDonough CW, Bradford Y, Ramirez AH, Bielinski SJ, Basford MA, Chai HS, Peissig P, Carrell D, Pathak J, Rasmussen LV, Wang X, Pacheco JA, Kho AN, Hayes MG, Matsumoto M, Smith ME, Li R, Cooper-DeHoff RM, Kullo IJ, Chute CG, Chisholm RL, Jarvik GP, Larson EB, Carey D, McCarty CA, Williams MS, Roden DM, Bottinger E, Johnson JA, de Andrade M, Crawford DC. Genome-wide study of resistant hypertension identified from electronic health records. PLoS One. 2017 Feb 21;12(2):e0171745. doi: 10.1371/journal.pone.0171745. eCollection 2017. PubMed

Almoguera B, Vazquez L, Mentch F, Connolly J, Pacheco JA, Sundaresan AS, Peissig PL, Linneman JG, McCarty CA, Crosslin D, Carrell DS, Lingren T, Namjou-Khales B, Harley JB, Larson E, Jarvik GP, Brilliant M, Williams MS, Kullo IJ, Hysinger EB, Sleiman PM, Hakonarson H. Identification of four novel loci in asthma in European American and African American populations. Am J Respir Crit Care Med. 2017;195(4):456-463. doi: 10.1164/rccm.201604-0861OC. PubMed

 

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