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Lauge Farnaes, MD, PhD



  • BS, biochemistry, UCSD 1999
  • BA, anthropology, UCSD 1999
  • MS, Biology, UCSD 2000
  • PHD Oceanography, Scripps Institution of Oceanography 2009
  • MD, UCSD 2011
  • Residency in Pediatrics, UCSD 2014
  • Fellowship in Pediatric Hematology, Oncology and Infectious Disease 2018

Currently my work at the Rady Children’s Institute for Genomic Medicine (RCIGM) focuses on helping to create the clinical evidence which will allow all children to have access to the benefits of clinical advances in next generation sequencing. With the group at the RCIGM we are using rapid whole genome sequencing to aid in the care of critically ill infants. We use both whole genome sequencing, transcriptomics and pathogen sequencing to better define the disease process in the critically ill child. We are expanding our clinical work and actively developing clinical trials to test various uses for this technology. By creating evidence for the application of rapid sequencing techniques we are working to change the standard of care for children. Our work is largely clinical/implementation science with a focus on practical application including clinical utility and health economics.
  • Clark MM, Hildreth A, Batalov S, Ding Y, Chowdhury S, Watkins K, Ellsworth K, Camp B, Kint CI, Yacoubian C, Farnaes L, Bainbridge MN, Beebe C, Braun JJA, Bray M, Carroll J, Cakici JA, Caylor SA, Clarke C, Creed MP, Friedman J, Frith A, Gain R, Gaughran M, George S, Gilmer S, Gleeson J, Gore J, Grunenwald H, Hovey RL, Janes ML, Lin K, McDonagh PD, McBride K, Mulrooney P, Nahas S, Oh D, Oriol A, Puckett L, Rady Z, Reese MG, Ryu J, Salz L, Sanford E, Stewart L, Sweeney N, Tokita M, Van Der Kraan L, White S, Wigby K, Williams B, Wong T, Wright MS, Yamada C, Schols P, Reynders J, Hall K, Dimmock D, Veeraraghavan N, Defay T, Kingsmore SF. Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation. Sci Transl Med. 2019 Apr 24;11(489). pii: eaat6177. doi: 10.1126/scitranslmed.aat6177.
  • Farnaes L, Coufal NG, Spector SA. Vaccine Strain Varicella Infection in an Infant With Previously Undiagnosed Perinatal Human Immunodeficiency Type-1 Infection. Pediatr Infect Dis J. 2019 Apr;38(4):413-415. doi: 10.1097/INF.0000000000002183.
  • Farnaes L, Wilke J, Ryan Loker K, Bradley JS, Cannavino CR, Hong DK, Pong A, Foley J, Coufal NG. Community-acquired pneumonia in children: cell-free plasma sequencing for diagnosis and management. Diagn Microbiol Infect Dis. 2019 Feb 2. pii: S0732-8893(18)30508-X. doi: 10.1016/j.diagmicrobio.2018.12.016.
  • Sanford E, Farnaes L, Batalov S, Bainbridge M, Laubach S, Worthen HM, Tokita M, Kingsmore SF, Bradley J. Concomitant diagnosis of immune deficiency and Pseudomonas sepsis in a 19 month old with ecthyma gangrenosum by host whole-genome sequencing. Cold Spring Harb Mol Case Stud. 2018 Dec 17;4(6). pii: a003244. doi: 10.1101/mcs.a003244. Print 2018 Dec.
  • Briggs B, James K, Chowdhury S, Thornburg C, Farnaes L, Dimmock D, Kingsmore S. Novel Factor XIII variant identified through whole genome sequencing in a child with intracranial hemorrhage. Cold Spring Harb Mol Case Stud. 2018 Nov 7. pii: mcs.a003525. doi: 10.1101/mcs.a003525. [Epub ahead of print] PubMed PMID:30404926.
  • Yu JC, Shliakhtsitsava K, Wang YM, Paul M, Farnaes L, Wong V, Kim J, Thornburg CD. Hematologic Manifestations of Nutritional Deficiencies: Early Recognition is Essential to Prevent Serious Complications. J Pediatr Hematol Oncol. 2018 Oct 18. doi: 10.1097/MPH.0000000000001338. [Epub ahead of print] PubMed PMID: 30339653.
  • Farnaes L, Coufal N, Spector SA. Vaccine Strain Varicella Infection in an Infant with Previously Undiagnosed Perinatal Human Immunodeficiency Type-1 Infection. Pediatr Infect Dis J. 2018 Sep 7. doi: 10.1097/INF.0000000000002183. [Epub ahead of print] PubMed PMID: 30199479.
  • Chen DY, Chowdhury S, Farnaes L, Friedman JR, Honold J, Dimmock DP, Gold OBOTRIJJ. Rapid Diagnosis of KCNQ2-Associated Early Infantile Epileptic
  • Encephalopathy Improved Outcome. Pediatr Neurol. 2018 Sep;86:69-70. doi: 10.1016/j.pediatrneurol.2018.06.002. Epub 2018 Jul 10. PubMed PMID: 30107960.
  • Grosse SD, Farnaes L. Genomic sequencing in acutely ill infants: what will it take to demonstrate clinical value? Genet Med. 2018 Aug 13. doi:10.1038/s41436-018-0124-3. [Epub ahead of print] PubMed PMID: 30100610.
  • Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genom Med. 2018 Jul 9;3:16. doi: 10.1038/s41525-018-0053-8.eCollection 2018. PubMed PMID: 30002876; PubMed Central PMCID: PMC6037748.
  • Farnaes L, Hildreth A, Sweeney NM, Clark MM, Chowdhury S, Nahas S, Cakici JA, Benson W, Kaplan RH, Kronick R, Bainbridge MN, Friedman J, Gold JJ, Ding Y, Veeraraghavan N, Dimmock D, Kingsmore SF. Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization. NPJ Genom Med. 2018 Apr 4;3:10. doi: 10.1038/s41525-018-0049-4. eCollection 2018.
  • Sanford E, Watkins K, Nahas S, Gottschalk M, Coufal N, Farnaes L, Dimmock D, Kingsmore S, Investigators R.: Rapid whole genome sequencing identifies a novel AIRE variant associated with Autoimmune Polyendocrine Syndrome Type 1. Cold Spring Harb Mol Case Stud. 2018 Feb 1. pii: mcs.a002485. doi: 10.1101/mcs.a002485
  • Farnaes L, Schiff D, McElroy AK, Coufal NG, Crawford JR, Cannavino C.: Encephalitis and Thalamic Injury From Neuroinvasive West Nile Virus in Children on Treatment for Acute Lymphoblastic Leukemia. Pediatr Neurol. 2017 Dec 2. pii: S0887-8994(17)30463-0. doi: 10.1016/j.pediatrneurol.2017.11.013
  • Farnaes L, .Nahas SA, Chowdhury S, Nelson J, Batalov S, Dimmock D, Kingsmore SF, Investigators R: Rapid whole genome sequencing identifies a novel GABRA1 variant associated with West syndrome. Cold Spring Harb Mol Case Stud. 2017 Sep 1;3(5). pii: a001776. doi: 10.1101/mcs.a001776.
  • Gallo RL, Hultschb T, Farnaes L: Recognizing that the microbiome is part of the human immune system will advance treatment of both cancer and infections. Journal of the American Academy of Dermatology March 7, 2016
  • Thornton SL, Farnaes L, Minns A: Prolonged Antimuscarinic Delirium in a Child Due to Benztropine Exposure Treated with Multiple Doses of Physostigmine. Pediatric Emergency Care 9/2015
  • Farnaes L, Coufal NG, Kauffman CA, Rheingold AL, Dipasquale AG, Jensen PR, Fenical W: Napyradiomycin Derivatives, Produced by a Marine-Derived Actinomycete, Illustrate Cytotoxicity by Induction of Apoptosis. Journal of Natural Products 12/2013;
  • Farnaes L, La Clair JJ, Fenical W: Napyradiomycins CNQ525.510B and A80915C target the Hsp90 paralogue Grp94.. Organic & Biomolecular Chemistry 11/2013;
  • Haste NM, Farnaes L, Perera VR, Fenical W, Nizet V, Hensler ME: Bactericidal kinetics of marine-derived napyradiomycins against contemporary methicillin-resistant Staphylococcus aureus.. Marine Drugs 01/2011; 9(4):680-9.
  • Koefoed K, Farnaes L, Wang M, Svejgaard A, Burton DR, Ditzel HJ: Molecular characterization of the circulating anti-HIV-1 gp120-specific B cell repertoire using antibody phage display libraries generated from pre-selected HIV-1 gp120 binding PBLs.. Journal of Immunological Methods 03/2005; 297(1-2):187-201.
  • Farnaes L, Ditzel HJ: Dissecting the cellular functions of annexin XI using recombinant human annexin XI-specific autoantibodies cloned by phage display.. Journal of Biological Chemistry 09/2003; 278(35):33120-6.
  • Gao C, Mao S, Ditzel HJ, Farnaes L, Wirsching P, Lerner RA, Janda KD: A cell-penetrating peptide from a novel pVII-pIX phage-displayed random peptide library.. Bioorganic & Medicinal Chemistry 01/2003; 10(12):4057-65.
  • Ditzel HJ, Masaki Y, Nielsen H, Farnaes L, Burton DR: Cloning and expression of a novel human antibody-antigen pair associated with Felty's syndrome.. Proceedings of the National Academy of Sciences 09/2000; 97(16):9234-9.