Using cutting-edge high-throughput profiling methods to discover diagnostic and treatment biomarkers of various human diseases. Clinical whole-genome sequencing analysis and interpretation for personalized precision medicine.


Dr. Sek Won Kong is an Assistant Professor at Harvard Medical School, and a faculty member in the Computational Health Informatics Program at Boston Children’s Hospital.

Dr. Sek Won Kong received a MD from Seoul National University College of Medicine in Seoul, South Korea. Dr. Kong is a psychiatrist by training and completed his clinical training at Seoul National University Hospital in Seoul, South Korea. Dr. Kong studied brain imaging and molecular medicine during his postdoctoral time and joined CHIP as a faculty member. His research interests include biomarker discovery using diverse genetics and genomics techniques as well as developing tools for computational biology and bioinformatics. Dr. Kong pioneered the discovery of molecular biomarkers for autism spectrum disorder for which he continues to dissect the sources and impacts of genetic and environmental risk factors. Dr. Kong has been leading precision medicine efforts in a network of pediatric hospitals, clinical implementation of whole-genome sequencing and polygenic risk score, and cell replacement therapy using reprogrammed autologous cells.


Publications powered by Harvard Catalyst Profiles

  1. Lee IH, Lee JW, Kong SW. A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations. Infect Genet Evol. 2020 Aug 26; 85:104507. View abstract
  2. Schweitzer JS, Song B, Herrington TM, Park TY, Lee N, Ko S, Jeon J, Cha Y, Kim K, Li Q, Henchcliffe C, Kaplitt M, Neff C, Rapalino O, Seo H, Lee IH, Kim J, Kim T, Petsko GA, Ritz J, Cohen BM, Kong SW, Leblanc P, Carter BS, Kim KS. Personalized iPSC-Derived Dopamine Progenitor Cells for Parkinson's Disease. N Engl J Med. 2020 05 14; 382(20):1926-1932. View abstract
  3. Gutiérrez-Sacristán A, De Niz C, Kothari C, Kong SW, Mandl KD, Avillach P. GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets. Brief Bioinform. 2020 04 06. View abstract
  4. Song B, Cha Y, Ko S, Jeon J, Lee N, Seo H, Park KJ, Lee IH, Lopes C, Feitosa M, Luna MJ, Jung JH, Kim J, Hwang D, Cohen BM, Teicher MH, Leblanc P, Carter BS, Kordower JH, Bolshakov VY, Kong SW, Schweitzer JS, Kim KS. Human autologous iPSC-derived dopaminergic progenitors restore motor function in Parkinson's disease models. J Clin Invest. 2020 02 03; 130(2):904-920. View abstract
  5. Mandl KD, Glauser T, Krantz ID, Avillach P, Bartels A, Beggs AH, Biswas S, Bourgeois FT, Corsmo J, Dauber A, Devkota B, Fleisher GR, Heath AP, Helbig I, Hirschhorn JN, Kilbourn J, Kong SW, Kornetsky S, Majzoub JA, Marsolo K, Martin LJ, Nix J, Schwarzhoff A, Stedman J, Strauss A, Sund KL, Taylor DM, White PS, Marsh E, Grimberg A, Hawkes C. Correction: The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system. Genet Med. 2020 Feb; 22(2):449. View abstract
  6. Kong SW, Hernandez-Ferrer C. Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020; 25:587-598. View abstract
  7. Lee IH, Negron JA, Hernandez-Ferrer C, Alvarez WJ, Mandl KD, Kong SW. The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Hum Mutat. 2020 Feb; 41(2):387-396. View abstract
  8. Palmer NP, Silvester JA, Lee JJ, Beam AL, Fried I, Valtchinov VI, Rahimov F, Kong SW, Ghodoussipour S, Hood HC, Bousvaros A, Grand RJ, Kunkel LM, Kohane IS. Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. PLoS One. 2019; 14(10):e0222952. View abstract
  9. Wedel J, Stack MP, Seto T, Sheehan MM, Flynn EA, Stillman IE, Kong SW, Liu K, Briscoe DM. T Cell-Specific Adaptor Protein Regulates Mitochondrial Function and CD4+ T Regulatory Cell Activity In Vivo following Transplantation. J Immunol. 2019 10 15; 203(8):2328-2338. View abstract
  10. Mandl KD, Glauser T, Krantz ID, Avillach P, Bartels A, Beggs AH, Biswas S, Bourgeois FT, Corsmo J, Dauber A, Devkota B, Fleisher GR, Heath AP, Helbig I, Hirschhorn JN, Kilbourn J, Kong SW, Kornetsky S, Majzoub JA, Marsolo K, Martin LJ, Nix J, Schwarzhoff A, Stedman J, Strauss A, Sund KL, Taylor DM, White PS, Marsh E, Grimberg A, Hawkes C. The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system. Genet Med. 2020 02; 22(2):371-380. View abstract
  11. Greenberg SA, Pinkus JL, Kong SW, Baecher-Allan C, Amato AA, Dorfman DM. Highly differentiated cytotoxic T cells in inclusion body myositis. Brain. 2019 09 01; 142(9):2590-2604. View abstract
  12. Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bönnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell. 2019 04 08; 49(1):10-29. View abstract
  13. Hwang KB, Lee IH, Li H, Won DG, Hernandez-Ferrer C, Negron JA, Kong SW. Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings. Sci Rep. 2019 03 01; 9(1):3219. View abstract
  14. Greenberg SA, Kong SW, Thompson E, Gulla SV. Co-inhibitory T cell receptor KLRG1: human cancer expression and efficacy of neutralization in murine cancer models. Oncotarget. 2019 Feb 15; 10(14):1399-1406. View abstract
  15. Lee SC, Quinn TP, Lai J, Kong SW, Hertz-Picciotto I, Glatt SJ, Crowley TM, Venkatesh S, Nguyen T. Solving for X: Evidence for sex-specific autism biomarkers across multiple transcriptomic studies. Am J Med Genet B Neuropsychiatr Genet. 2019 09; 180(6):377-389. View abstract
  16. Wedel J, Bruneau S, Liu K, Kong SW, Sage PT, Sabatini DM, Laplante M, Briscoe DM. DEPTOR modulates activation responses in CD4+ T cells and enhances immunoregulation following transplantation. Am J Transplant. 2019 01; 19(1):77-88. View abstract
  17. Kong SW, Lee IH, Liu X, Hirschhorn JN, Mandl KD. Measuring coverage and accuracy of whole-exome sequencing in clinical context. Genet Med. 2018 12; 20(12):1617-1626. View abstract
  18. Sonntag KC, Song B, Lee N, Jung JH, Cha Y, Leblanc P, Neff C, Kong SW, Carter BS, Schweitzer J, Kim KS. Pluripotent stem cell-based therapy for Parkinson's disease: Current status and future prospects. Prog Neurobiol. 2018 09; 168:1-20. View abstract
  19. Bourgeois FT, Avillach P, Kong SW, Heinz MM, Tran TA, Chakrabarty R, Bickel J, Sliz P, Borglund EM, Kornetsky S, Mandl KD. Development of the Precision Link Biobank at Boston Children's Hospital: Challenges and Opportunities. J Pers Med. 2017 Dec 15; 7(4). View abstract
  20. Feiglin A, Allen BK, Kohane IS, Kong SW. Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders. Cell Syst. 2017 08 23; 5(2):140-148.e2. View abstract
  21. Ong MS, Mullen MP, Austin ED, Szolovits P, Natter MD, Geva A, Cai T, Kong SW, Mandl KD. Learning a Comorbidity-Driven Taxonomy of Pediatric Pulmonary Hypertension. Circ Res. 2017 Aug 04; 121(4):341-353. View abstract
  22. Tylee DS, Hess JL, Quinn TP, Barve R, Huang H, Zhang-James Y, Chang J, Stamova BS, Sharp FR, Hertz-Picciotto I, Faraone SV, Kong SW, Glatt SJ. Blood transcriptomic comparison of individuals with and without autism spectrum disorder: A combined-samples mega-analysis. Am J Med Genet B Neuropsychiatr Genet. 2017 Apr; 174(3):181-201. View abstract
  23. Somekh J, Peleg M, Eran A, Koren I, Feiglin A, Demishtein A, Shiloh R, Heiner M, Kong SW, Elazar Z, Kohane I. A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease. J Biomed Inform. 2016 10; 63:366-378. View abstract
  24. Brown AS, Kong SW, Kohane IS, Patel CJ. ksRepo: a generalized platform for computational drug repositioning. BMC Bioinformatics. 2016 Feb 09; 17:78. View abstract
  25. Prilutsky D, Kho AT, Palmer NP, Bhakar AL, Smedemark-Margulies N, Kong SW, Margulies DM, Bear MF, Kohane IS. Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures. Mol Autism. 2015; 6:66. View abstract
  26. Park JH, Cho B, Kwon H, Prilutsky D, Yun JM, Choi HC, Hwang KB, Lee IH, Kim JI, Kong SW. I148M variant in PNPLA3 reduces central adiposity and metabolic disease risks while increasing nonalcoholic fatty liver disease. Liver Int. 2015 Dec; 35(12):2537-46. View abstract
  27. Seok HS, Song T, Kong SW, Hwang KB. An Efficient Search Algorithm for Finding Genomic-Range Overlaps Based on the Maximum Range Length. IEEE/ACM Trans Comput Biol Bioinform. 2015 Jul-Aug; 12(4):778-84. View abstract
  28. Zhang T, Zhou Q, Ogmundsdottir MH, Möller K, Siddaway R, Larue L, Hsing M, Kong SW, Goding CR, Palsson A, Steingrimsson E, Pignoni F. Mitf is a master regulator of the v-ATPase, forming a control module for cellular homeostasis with v-ATPase and TORC1. J Cell Sci. 2015 Aug 01; 128(15):2938-50. View abstract
  29. Kong SW, Lee IH, Leshchiner I, Krier J, Kraft P, Rehm HL, Green RC, Kohane IS, MacRae CA. Summarizing polygenic risks for complex diseases in a clinical whole-genome report. Genet Med. 2015 Jul; 17(7):536-44. View abstract
  30. Hwang KB, Lee IH, Park JH, Hambuch T, Choe Y, Kim M, Lee K, Song T, Neu MB, Gupta N, Kohane IS, Green RC, Kong SW. Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods. Hum Mutat. 2014 Aug; 35(8):936-44. View abstract
  31. Vassy JL, Lautenbach DM, McLaughlin HM, Kong SW, Christensen KD, Krier J, Kohane IS, Feuerman LZ, Blumenthal-Barby J, Roberts JS, Lehmann LS, Ho CY, Ubel PA, MacRae CA, Seidman CE, Murray MF, McGuire AL, Rehm HL, Green RC. The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine. Trials. 2014 Mar 20; 15:85. View abstract
  32. Lee IH, Lee K, Hsing M, Choe Y, Park JH, Kim SH, Bohn JM, Neu MB, Hwang KB, Green RC, Kohane IS, Kong SW. Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. Hum Mutat. 2014 May; 35(5):537-47. View abstract
  33. Kong SW, Sahin M, Collins CD, Wertz MH, Campbell MG, Leech JD, Krueger D, Bear MF, Kunkel LM, Kohane IS. Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis. Mol Autism. 2014 Feb 24; 5(1):16. View abstract
  34. Campbell MG, Kohane IS, Kong SW. Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome. BMC Med Genomics. 2013 Sep 24; 6:34. View abstract
  35. Larman HB, Salajegheh M, Nazareno R, Lam T, Sauld J, Steen H, Kong SW, Pinkus JL, Amato AA, Elledge SJ, Greenberg SA. Cytosolic 5'-nucleotidase 1A autoimmunity in sporadic inclusion body myositis. Ann Neurol. 2013 Mar; 73(3):408-18. View abstract
  36. Kong SW, Collins CD, Shimizu-Motohashi Y, Holm IA, Campbell MG, Lee IH, Brewster SJ, Hanson E, Harris HK, Lowe KR, Saada A, Mora A, Madison K, Hundley R, Egan J, McCarthy J, Eran A, Galdzicki M, Rappaport L, Kunkel LM, Kohane IS. Characteristics and predictive value of blood transcriptome signature in males with autism spectrum disorders. PLoS One. 2012; 7(12):e49475. View abstract
  37. Song T, Hwang KB, Hsing M, Lee K, Bohn J, Kong SW. gSearch: a fast and flexible general search tool for whole-genome sequencing. Bioinformatics. 2012 Aug 15; 28(16):2176-7. View abstract
  38. Kohane IS, Hsing M, Kong SW. Taxonomizing, sizing, and overcoming the incidentalome. Genet Med. 2012 Apr; 14(4):399-404. View abstract
  39. He A, Ma Q, Cao J, von Gise A, Zhou P, Xie H, Zhang B, Hsing M, Christodoulou DC, Cahan P, Daley GQ, Kong SW, Orkin SH, Seidman CE, Seidman JG, Pu WT. Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res. 2012 Feb 03; 110(3):406-15. View abstract
  40. Greenberg SA, Higgs BW, Morehouse C, Walsh RJ, Kong SW, Brohawn P, Zhu W, Amato A, Salajegheh M, White B, Kiener PA, Jallal B, Yao Y. Relationship between disease activity and type 1 interferon- and other cytokine-inducible gene expression in blood in dermatomyositis and polymyositis. Genes Immun. 2012 Apr; 13(3):207-13. View abstract
  41. He A, Kong SW, Ma Q, Pu WT. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A. 2011 Apr 05; 108(14):5632-7. View abstract
  42. Kuttippurathu L, Hsing M, Liu Y, Schmidt B, Maskell DL, Lee K, He A, Pu WT, Kong SW. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics. 2011 Mar 01; 27(5):715-7. View abstract
  43. Kong SW, Hu YW, Ho JW, Ikeda S, Polster S, John R, Hall JL, Bisping E, Pieske B, dos Remedios CG, Pu WT. Heart failure-associated changes in RNA splicing of sarcomere genes. Circ Cardiovasc Genet. 2010 Apr; 3(2):138-46. View abstract
  44. Salajegheh M, Kong SW, Pinkus JL, Walsh RJ, Liao A, Nazareno R, Amato AA, Krastins B, Morehouse C, Higgs BW, Jallal B, Yao Y, Sarracino DA, Parker KC, Greenberg SA. Interferon-stimulated gene 15 (ISG15) conjugates proteins in dermatomyositis muscle with perifascicular atrophy. Ann Neurol. 2010 Jan; 67(1):53-63. View abstract
  45. Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics. 2009 Dec 01; 25(23):3121-7. View abstract
  46. Parker KC, Kong SW, Walsh RJ, Salajegheh M, Moghadaszadeh B, Amato AA, Nazareno R, Lin YY, Krastins B, Sarracino DA, Beggs AH, Pinkus JL, Greenberg SA. Fast-twitch sarcomeric and glycolytic enzyme protein loss in inclusion body myositis. Muscle Nerve. 2009 Jun; 39(6):739-53. View abstract
  47. Zhou B, Ma Q, Kong SW, Hu Y, Campbell PH, McGowan FX, Ackerman KG, Wu B, Zhou B, Tevosian SG, Pu WT. Fog2 is critical for cardiac function and maintenance of coronary vasculature in the adult mouse heart. J Clin Invest. 2009 Jun; 119(6):1462-76. View abstract
  48. Ikeda S, He A, Kong SW, Lu J, Bejar R, Bodyak N, Lee KH, Ma Q, Kang PM, Golub TR, Pu WT. MicroRNA-1 negatively regulates expression of the hypertrophy-associated calmodulin and Mef2a genes. Mol Cell Biol. 2009 Apr; 29(8):2193-204. View abstract
  49. Rojas A, Kong SW, Agarwal P, Gilliss B, Pu WT, Black BL. GATA4 is a direct transcriptional activator of cyclin D2 and Cdk4 and is required for cardiomyocyte proliferation in anterior heart field-derived myocardium. Mol Cell Biol. 2008 Sep; 28(17):5420-31. View abstract
  50. Lee H, Kong SW, Park PJ. Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinformatics. 2008 Apr 01; 24(7):889-96. View abstract
  51. Ranade SS, Yang-Zhou D, Kong SW, McDonald EC, Cook TA, Pignoni F. Analysis of the Otd-dependent transcriptome supports the evolutionary conservation of CRX/OTX/OTD functions in flies and vertebrates. Dev Biol. 2008 Mar 15; 315(2):521-34. View abstract
  52. Walsh RJ, Kong SW, Yao Y, Jallal B, Kiener PA, Pinkus JL, Beggs AH, Amato AA, Greenberg SA. Type I interferon-inducible gene expression in blood is present and reflects disease activity in dermatomyositis and polymyositis. Arthritis Rheum. 2007 Nov; 56(11):3784-92. View abstract
  53. Ikeda S, Kong SW, Lu J, Bisping E, Zhang H, Allen PD, Golub TR, Pieske B, Pu WT. Altered microRNA expression in human heart disease. Physiol Genomics. 2007 Nov 14; 31(3):367-73. View abstract
  54. Sangster TA, Bahrami A, Wilczek A, Watanabe E, Schellenberg K, McLellan C, Kelley A, Kong SW, Queitsch C, Lindquist S. Phenotypic diversity and altered environmental plasticity in Arabidopsis thaliana with reduced Hsp90 levels. PLoS One. 2007 Jul 25; 2(7):e648. View abstract
  55. Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007 Jun; 3(6):e96. View abstract
  56. Kong SW. Statistical methods in cardiac gene expression profiling: from image to function. Methods Mol Biol. 2007; 366:75-105. View abstract
  57. Bisping E, Ikeda S, Kong SW, Tarnavski O, Bodyak N, McMullen JR, Rajagopal S, Son JK, Ma Q, Springer Z, Kang PM, Izumo S, Pu WT. Gata4 is required for maintenance of postnatal cardiac function and protection from pressure overload-induced heart failure. Proc Natl Acad Sci U S A. 2006 Sep 26; 103(39):14471-6. View abstract
  58. Rivera-Feliciano J, Lee KH, Kong SW, Rajagopal S, Ma Q, Springer Z, Izumo S, Tabin CJ, Pu WT. Development of heart valves requires Gata4 expression in endothelial-derived cells. Development. 2006 Sep; 133(18):3607-18. View abstract
  59. Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics. 2006 Oct 01; 22(19):2373-80. View abstract
  60. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13544-9. View abstract
  61. Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJ. CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinformatics. 2005 May 01; 21(9):2116-7. View abstract
  62. Kong SW, Bodyak N, Yue P, Liu Z, Brown J, Izumo S, Kang PM. Genetic expression profiles during physiological and pathological cardiac hypertrophy and heart failure in rats. Physiol Genomics. 2005 Mar 21; 21(1):34-42. View abstract
  63. Hwang KB, Kong SW, Greenberg SA, Park PJ. Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics. 2004 Oct 25; 5:159. View abstract
  64. Tarnavski O, McMullen JR, Schinke M, Nie Q, Kong S, Izumo S. Mouse cardiac surgery: comprehensive techniques for the generation of mouse models of human diseases and their application for genomic studies. Physiol Genomics. 2004 Feb 13; 16(3):349-60. View abstract
  65. McMullen JR, Shioi T, Huang WY, Zhang L, Tarnavski O, Bisping E, Schinke M, Kong S, Sherwood MC, Brown J, Riggi L, Kang PM, Izumo S. The insulin-like growth factor 1 receptor induces physiological heart growth via the phosphoinositide 3-kinase(p110alpha) pathway. J Biol Chem. 2004 Feb 06; 279(6):4782-93. View abstract
  66. Lyoo IK, Kong SW, Sung SM, Hirashima F, Parow A, Hennen J, Cohen BM, Renshaw PF. Multinuclear magnetic resonance spectroscopy of high-energy phosphate metabolites in human brain following oral supplementation of creatine-monohydrate. Psychiatry Res. 2003 Jun 30; 123(2):87-100. View abstract
  67. Ha KS, Youn T, Kong SW, Park HJ, Ha TH, Kim MS, Kwon JS. Optimized individual mismatch negativity source localization using a realistic head model and the Talairach coordinate system. Brain Topogr. 2003; 15(4):233-8. View abstract
  68. Lyoo IK, Lee DW, Kim YS, Kong SW, Kwon JS. Patterns of temperament and character in subjects with obsessive-compulsive disorder. J Clin Psychiatry. 2001 Aug; 62(8):637-41. View abstract