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Dr. Chen, Hung-Hsin

Assistant Research Fellow
Specialty:
  1. Human Genome
  2. Genetic Epidemiology
  3. RNA-sequencing
  4. Biobank analysis
  5. Longitudinal analysis
Education and Positions:

  • Ph.D. Vanderbilt University

    Postdoc. Vanderbilt University Medical Center

Large-scale genetic data with linked health records represent a major untapped resource for understanding genetic mechanisms of human health and disease. Our lab takes three general directions, each leveraging large-scale and longitudinal data to improve human health:

 

Genomic segments shared due to relatedness in large-scale biobanks provide an opportunity to identify novel disease genes.

 

Most biobanks contain a substantial amount of cryptic relatedness, which can introduce bias or reduce statistical power in traditional GWAS and is often considered as a nuisance variable. However, these patterns of relatedness can also be utilized for gene mapping. Since shared segments are inherited from the same ancestor, rare, pathogenic variants within a shared region are likely to be shared. Because of this, comparison of the distribution of shared segments within cases and controls can be used for gene mapping. We are focusing on developing and implementing shared segment approaches for identifying novel disease genes in large-scale biobank data.

 

Longitudinal, repeated measurements in the EHR allow us to investigate genetic effects on a phenotype’s trajectory over time.

 

Traditional epidemiological studies typically have cross-sectional measurements or measurements from study visits over a short follow-up time, while biobanks’ linked longitudinal health records can contain repeated measures spanning decades. Extracting optimal values for analysis (e.g., highly heritable or predictive of disease risk) is a major challenge in biobank studies. Longitudinal data can also be used to study phenotypic trajectories across the lifespan. As a result, my group's goal is to create algorithms that capture powerful features of repeated measurements and use them to further our understanding of disease genetic mechanisms.

 

Longitudinal multi-omic measures enable characterizations of the change in expression (or other omic measure) pattern associated with development of disease.

 

Gene expression and other omics are the product of complex interactions between genetic regulation and environmental stimuli. Analysis of these longitudinal measures will increase understanding of genetic effects and response to environmental changes during disease pathogenesis. My lab works with existing cohorts to develop multi-omic profiling approaches for studying correlations between omics patterns and disease incidence.

Journal 17 Book 0

  1. Walker JT, Saunders DC, Rai V, Chen HH, Orchard P, Dai C, Pettway YD, Hopkirk AL, Reihsmann CV, Tao Y, Fan S, Shrestha S, Varshney A, Petty LE, Wright JJ, Ventresca C, Agarwala S, Aramandla R, Poffenberger G, Jenkins R, Mei S, Hart NJ, Phillips S, Kang H, Greiner DL, Shultz LD, Bottino R, Liu J, Below JE, Parker SCJ, Powers AC, Brissova M Genetic risk converges on regulatory networks mediating early type 2 diabetes. Nature 624(7992), 621-629 (2023) [JCR] [WOS]
  2. Zhu W, (Chen HH), Petty AS, Petty LE, Polikowsky HG, Gamazon ER, Below JE, Highland HM IMMerge: merging imputation data at scale. Bioinformatics (Oxford, England) 39(1), btac750-btac750 (2023) [JCR] [WOS]
  3. Kim D, Memili A, (Chen HH), Highland HM, Polikowsky HG, Anwar MY, Laing ST, Lee M, McCormick JB, Fisher-Hoch SP, Below JE, North KE, Gutierrez AD Sex-specific associations between adipokine profiles and carotid-intima media thickness in the Cameron County Hispanic Cohort (CCHC). Cardiovascular diabetology 22(1), 231 (2023) [JCR] [WOS]
  4. Anwar MY, Baldassari AR, Polikowsky HG, Sitlani CM, Highland HM, Chami N, (Chen HH), Graff M, Howard AG, Jung SY, Petty LE, Wang Z, Zhu W, Buyske S, Cheng I, Kaplan R, Kooperberg C, Loos RJF, Peters U, McCormick JB, Fisher-Hoch SP, Avery CL, Taylor KC, Below JE, North KE Genetic pleiotropy underpinning adiposity and inflammation in self-identified Hispanic/Latino populations. BMC medical genomics 15(1), 192 (2022) [JCR] [WOS]
  5. Bellenguez C, Kucukali F, Jansen IE, Kleineidam L, Moreno-Grau S, Amin N, Naj AC, Campos-Martin R, Grenier-Boley B, Andrade V, Holmans PA, Boland A, Damotte V, van der Lee SJ, Costa MR, Kuulasmaa T, Yang Q, de Rojas I, Bis JC, Yaqub A, Prokic I, Chapuis J, Ahmad S, Giedraitis V, Aarsland D, Garcia-Gonzalez P, Abdelnour C, Alarcon-Martin E, Alcolea D, Alegret M, Alvarez I, Alvarez V, Armstrong NJ, Tsolaki A, Antunez C, Appollonio I, Arcaro M, Archetti S, Pastor AA, Arosio B, Athanasiu L, Bailly H, Banaj N, Baquero M, Barral S, Beiser A, Pastor AB, Below JE, Benchek P, Benussi L, Berr C, Besse C, Bessi V, Binetti G, Bizarro A, Blesa R, Boada M, Boerwinkle E, Borroni B, Boschi S, Bossu P, Brathen G, Bressler J, Bresner C, Brodaty H, Brookes KJ, Brusco LI, Buiza-Rueda D, Burger K, Burholt V, Bush WS, Calero M, Cantwell LB, Chene G, Chung J, Cuccaro ML, Carracedo A, Cecchetti R, Cervera-Carles L, Charbonnier C, Chen HH, Chillotti C, Ciccone S, Claassen JAHR, Clark C, Conti E, Corma-Gomez A, Costantini E, Custodero C, Daian D, Dalmasso MC, Daniele A, Dardiotis E, Dartigues JF, de Deyn PP, de Paiva Lopes K, de Witte LD, Debette S, Deckert J, Del Ser T, Denning N, DeStefano A, Dichgans M, Diehl-Schmid J, Diez-Fairen M, Rossi PD, Djurovic S, Duron E, Duzel E, Dufouil C, Eiriksdottir G, Engelborghs S, Escott-Price V, Espinosa A, Ewers M, Faber KM, Fabrizio T, Nielsen SF, Fardo DW, Farotti L, Fenoglio C, Fernandez-Fuertes M, Ferrari R, Ferreira CB, Ferri E, Fin B, Fischer P, Fladby T, Fliessbach K, Fongang B, Fornage M, Fortea J, Foroud TM, Fostinelli S, Fox NC, Franco-Macias E, Bullido MJ, Frank-Garcia A, Froelich L, Fulton-Howard B, Galimberti D, Garcia-Alberca JM, Garcia-Gonzalez P, Garcia-Madrona S, Garcia-Ribas G, Ghidoni R, Giegling I, Giorgio G, Goate AM, Goldhardt O, Gomez-Fonseca D, Gonzalez-Perez A, Graff C, Grande G, Green E, Grimmer T, Grunblatt E, Grunin M, Gudnason V, Guetta-Baranes T, Haapasalo A, Hadjigeorgiou G, Haines JL, Hamilton-Nelson KL, Hampel H, Hanon O, Hardy J, Hartmann AM, Hausner L, Harwood J, Heilmann-Heimbach S, Helisalmi S, Heneka MT, Hernandez I, Herrmann MJ, Hoffmann P, Holmes C, Holstege H, Vilas RH, Hulsman M, Humphrey J, Biessels GJ, Jian X, Johansson C, Jun GR, Kastumata Y, Kauwe J, Kehoe PG, Kilander L, Stahlbom AK, Kivipelto M, Koivisto A, Kornhuber J, Kosmidis MH, Kukull WA, Kuksa PP, Kunkle BW, Kuzma AB, Lage C, Laukka EJ, Launer L, Lauria A, Lee CY, Lehtisalo J, Lerch O, Lleo A, Longstreth W Jr, Lopez O, de Munain AL, Love S, Lowemark M, Luckcuck L, Lunetta KL, Ma Y, Macias J, MacLeod CA, Maier W, Mangialasche F, Spallazzi M, Marquie M, Marshall R, Martin ER, Montes AM, Rodriguez CM, Masullo C, Mayeux R, Mead S, Mecocci P, Medina M, Meggy A, Mehrabian S, Mendoza S, Menendez-Gonzalez M, Mir P, Moebus S, Mol M, Molina-Porcel L, Montrreal L, Morelli L, Moreno F, Morgan K, Mosley T, Nothen MM, Muchnik C, Mukherjee S, Nacmias B, Ngandu T, Nicolas G, Nordestgaard BG, Olaso R, Orellana A, Orsini M, Ortega G, Padovani A, Paolo C, Papenberg G, Parnetti L, Pasquier F, Pastor P, Peloso G, Perez-Cordon A, Perez-Tur J, Pericard P, Peters O, Pijnenburg YAL, Pineda JA, Pinol-Ripoll G, Pisanu C, Polak T, Popp J, Posthuma D, Priller J, Puerta R, Quenez O, Quintela I, Thomassen JQ, Rabano A, Rainero I, Rajabli F, Ramakers I, Real LM, Reinders MJT, Reitz C, Reyes-Dumeyer D, Ridge P, Riedel-Heller S, Riederer P, Roberto N, Rodriguez-Rodriguez E, Rongve A, Allende IR, Rosende-Roca M, Royo JL, Rubino E, Rujescu D, Saez ME, Sakka P, Saltvedt I, Sanabria A, Sanchez-Arjona MB, Sanchez-Garcia F, Juan PS, Sanchez-Valle R, Sando SB, Sarnowski C, Satizabal CL, Scamosci M, Scarmeas N, Scarpini E, Scheltens P, Scherbaum N, Scherer M, Schmid M, Schneider A, Schott JM, Selbaek G, Seripa D, Serrano M, Sha J, Shadrin AA, Skrobot O, Slifer S, Snijders GJL, Soininen H, Solfrizzi V, Solomon A, Song Y, Sorbi S, Sotolongo-Grau O, Spalletta G, Spottke A, Squassina A, Stordal E, Tartan JP, Tarraga L, Tesi N, Thalamuthu A, Thomas T, Tosto G, Traykov L, Tremolizzo L, Tybjaerg-Hansen A, Uitterlinden A, Ullgren A, Ulstein I, Valero S, Valladares O, Broeckhoven CV, Vance J, Vardarajan BN, van der Lugt A, Dongen JV, van Rooij J, van Swieten J, Vandenberghe R, Verhey F, Vidal JS, Vogelgsang J, Vyhnalek M, Wagner M, Wallon D, Wang LS, Wang R, Weinhold L, Wiltfang J, Windle G, Woods B, Yannakoulia M, Zare H, Zhao Y, Zhang X, Zhu C, Zulaica M, Farrer LA, Psaty BM, Ghanbari M, Raj T, Sachdev P, Mather K, Jessen F, Ikram MA, de Mendonca A, Hort J, Tsolaki M, Pericak-Vance MA, Amouyel P, Williams J, Frikke-Schmidt R, Clarimon J, Deleuze JF, Rossi G, Seshadri S, Andreassen OA, Ingelsson M, Hiltunen M, Sleegers K, Schellenberg GD, van Duijn CM, Sims R, van der Flier WM, Ruiz A, Ramirez A, Lambert JC New insights into the genetic etiology of Alzheimer\'s disease and related dementias. Nature genetics 54(4), 412-436 (2022) [JCR] [WOS]
  6. (Chen HH), Petty LE, North KE, McCormick JB, Fisher-Hoch SP, Gamazon ER, Below JE Novel diabetes gene discovery through comprehensive characterization and integrative analysis of longitudinal gene expression changes. Human molecular genetics 31(18), 3191-3205 (2022) [JCR] [WOS]
  7. Polikowsky HG, Shaw DM, Petty LE, (Chen HH), Pruett DG, Linklater JP, Viljoen KZ, Beilby JM, Highland HM, Levitt B, Avery CL, Mullan Harris K, Jones RM, Below JE, Kraft SJ Population-based genetic effects for developmental stuttering. HGG advances 3(1), 100073 (2022) [JCR] [WOS]
  8. (Chen HH), Petty LE, Sha J, Zhao Y, Kuzma A, Valladares O, Bush W, Naj AC, Gamazon ER, Below JE Genetically regulated expression in late-onset Alzheimer\'s disease implicates risk genes within known and novel loci. Translational psychiatry 11(1), 618 (2021) [JCR] [WOS]
  9. (Chen HH), Shaw DM, Petty LE, Graff M, Bohlender RJ, Polikowsky HG, Zhong X, Kim D, Buchanan VL, Preuss MH, Shuey MM, Loos RJF, Huff CD, Cox NJ, Bastarache JA, Bastarache L, North KE, Below JE Host genetic effects in pneumonia. American journal of human genetics 108(1), 194-201 (2021) [JCR] [WOS]
  10. Pruett DG, Shaw DM, (Chen HH), Petty LE, Polikowsky HG, Kraft SJ, Jones RM, Below JE Identifying developmental stuttering and associated comorbidities in electronic health records and creating a phenome risk classifier. Journal of fluency disorders 68, 105847 (2021) [JCR] [WOS]
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