Page Banner

United States Department of Agriculture

Agricultural Research Service

Related Topics

Hans H Cheng

Research Geneticist

Hans H. Cheng

USDA, ARS Supervisory Research Geneticist and MSU Adjunct Faculty


Contact information

E-mail:                or

Telephone:                   (517) 337-6758


Education and Employment

1983                            B.S., Michigan State University

1988                            Ph.D., University of California at Berkeley

1988-90                       Postdoctoal Fellow, University of California at Davis

1990-92                       Molecular Geneticist, Petoseed, Woodland, CA

1992-date                    USDA, ARS


Research Interests

My lab is one of five groups in the Avian Disease and Oncology Laboratory, and we all share a common research goal. Thus, with our unique collection of inbred chickens lines and virus strains, we have a well-equipped multidisciplinary effort with expertise in molecular virology, pathology, immunology, and genetics to understand viral-induced cancers of the chicken.


My laboratory uses genomic and functional genomic approaches to identify and functionally characterize genes of agricultural importance in chicken, especially with regard to resistance to Marek’s disease (a herpesvirus-induced T cell cancer). Current projects include:

  • Chicken genetic map - I lead the US effort, which forms the framework for the chicken genome assembly lead by Wes Warren (Genome Institute, Wash. U. in St. Louis)
  • Molecular genetics and genomic selection for Marek’s disease resistance – Using an integrated genomics strategy (e.g., GWAS, RNA seq), we are identifying genes that confer genetic resistance to Marek’s disease. In addition, linked SNP markers, mainly based on allele-specific expression, are being used in genomic selection strategies in both experimental and commercial poultry flocks. Hi-C is also being employed to identify promoter-enhancer interactions with the hope of revealing causative polymorphisms that account for genetic resistance.
  • Driver mutations for Marek’s disease – Hypothesizing that somatic mutations are required for transformation, various genomic strategies (e.g., DNA seq, RNA seq, cytogenetics) are being employed and integrated to identify driver genes.
  • Vaccine synergy – Marek’s disease vaccines form the primary control method, however, very little information in known as to how they actually protect birds.


Current Personnel

Postdoctoral Associates

  • Sudeep Perumbakkam
  • Alexis Black Pyrkosz


Graduate Students

  • Cari Hearn – CMIB
  • Alec Steep – Genetics Program
  • Sudawapee Umthong – Microbiology



  • Laurie Molitor


Additional External Funding Beyond ARS Support

  • USDA AFRI, Enhancing genetic resistance to Marek’s disease in chicken via allele-specific expression screens and genome-wide selection; PI
  • USDA AFRI, Genome biology of Marek’s disease: Viral integration and genome alterations in genetically resistant and susceptible stocks: PI
  • USDA AFRI, The role of host genetic resistance and vaccination on transmission of Marek’s disease virus in poultry; co-PI.
  • USDA National Needs Graduate Fellowship Grants; co-PI


Publications (last 10 years)


  • Kaya, M., Preeyanon, L., Dodgson, J.B., and Cheng, H.H. 2016.       Validation of alternative transcript splicing in chicken lines that differ in genetic resistance to Marek’s disease. Anim. Biotech., 27:238-244.
  • Tuggle, C.K., Giuffra, E., White, S.N., Clarke, L, Zhou, H., Ross, P.J., Acloque, H., Reecy, J.M., Archibald, A., Boichard, M., Chamberlain, A., Cheng, H., Crooijmans, R.P.M.A., Delany, M.E., Groenen, M.A.M., Bayes, B., Lunney, J.K., Plastow, G.S., Schmidt, C.J., Song, J., and Watson, M. 2016.       GO-FAANG meeting: a Gathering On Functional Annotation of ANimal Genomes. Animal Genetics 47:528-533.
  • Tai, S.H.S., Holz, C., Engstrom, M.D., Cheng, H.H., and Maes, R.K. 2016.       In vitro characterization of felid herpesvirus 1 (FHV-1) mutants generated by recombineering in a recombinant BAC vector. Virus Res. 221:15-22.



  • Hildebrandt, E., Dunn, J.R., and Cheng. H.H.       2015. The Mut UL5-I682R Marek’s disease virus with a single nucleotide mutation within the helicase-primase subunit gene not only reduces virulence, but also provides partial vaccinal protection against Marek’s disease. Avian Diseases 59:94-97.
  • Hildebrandt, E., Dunn, J.R., Niikura, M., and Cheng. H.H. 2015.       Mutations within ICP4 acquired during in vitro attenuation do not alter virulence of recombinant Marek’s disease viruses in vivo. Virology Reports 5:10-18.
  • Hildebrandt, E., Dunn, J.R., and Cheng. H.H.       2015. Addition of a UL5 helicase-primase subunit point mutation eliminates bursal-thymic atrophy of Marek’s disease virus ∆Meq recombinant virus but reduces vaccinal protection. Avian Path. 44:254-258.
  • Zhang, X., Misztal, I., Heidaritabar, M., Bastiaansen, J.W.M., Borg, R., Okimoto, R., Saap, R.L., Wing, T., Hawken, R.R., Lourenco, D.A.L., Vitezica, Z.G., Cheng, H.H., and Muir, W.M.       2015. Prior genetic architecture impacting genomic regions under selection: an example using genomic selection in two poultry breeds.       Livestock Science 171:1-11.
  • Hildebrandt, E., Dunn, J.R., and Cheng. H.H.       2015. Characterizing in vivo stability and potential interactions of a UL5 helicase-primase mutation previously shown to reduce virulence and in vivo replication of Marek’s disease virus. Virus Res. 203:1-3.
  • The FAANG Consortium. 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16:57.
  • Preeyanon, L., Brown, C.T., and Cheng, H.H. 2015. Transcriptome variation in response to Marek’s disease virus acute infection.       Cytogenet. Genome Res. 145:154-163.
  • Cheng, H.H., Perumbakkam, S., Black Pyrkosz, A., Dunn, J.R., Legarra, A., and Muir, W.M. 2015. Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek’s disease is predominantly determined by transcriptional regulation. BMC Genomics 16:816.
  • Yan, Y., Yang, N., Cheng, H.H., Song, J., and Qu. L. 2015.       Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease. BMC Genomics 16:843.



  • Kim, D.K., Lillehoj, H.S., Jang, S.I., Lee, S.H., Hong, Y.H., and Cheng, H.H. 2014. Transcriptional Profiles of Host-Pathogen Responses to Necrotic Enteritis and Differential Regulation of Immune Genes in Two Inbreed Chicken Lines Showing Disparate Disease Susceptibility. PLoS One 9(12): e114960.
  • Haunshi, S., and Cheng, H.H. 2014. Differential expression of Toll-like receptor pathway genes in chicken embryo fibroblasts from chickens resistant and susceptible to Marek's disease. Poultry Sci. 93:550-555.
  • Hildebrandt, E., Dunn, J.R., Perumbakkam, S., Niikura, M, and Cheng, H.H. 2014.       Characterizing the molecular basis of attenuation of Marek’s disease virus via in vitro serial passage identifies de novo mutations in the helicase-primase subunit gene UL5 and other candidates associated with reduced virulence. J. Virology 88:6232-6242.
  • Heidaritabar, M., Vereijken, A., Muir, W., Meuwissen, T., Cheng, H., Megens, H.-J., Groenen, M., and Bastiaansen, J.W.M. 2014. Systematic differences in the response of genetic variation to pedigree and genome based selection methods. Heredity 113:503-513.
  • Chang, C.-F., Schock, E.N., O’Hare, E.A., Dodgson, J., Cheng, H.H., Muir, W.M., Edelmann, R.E., Delany, M.E., and Brugmann S.A. 2014.       The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant, talpid2.       Development 141:3003-3012.
  • Robinson, C.M., Cheng, H.H., and Delany, M.E.       2014. Marek’s disease virus and chicken host genome interactions: Viral genome integration occurs early post-infection and over a timeframe associated with latency, yet integration alone is not sufficient for cellular transformation. Cytogen. Genome Res. 144:142-154.
  • Lee, M.O., Yang, E., Morisson, M., Vignal, A., Huang, Y.-Z., Cheng, H.H., Muir, W.M., Lamont. S.J., Lillehoj, H.S., Lee, H.S., and Womack, J.E. 2014.       Mapping and genotypic analysis of the NK-lysin gene in chicken. Gen. Sel. Evol. 46:43.
  • Perumbakkam, S., Hunt, H.D., and Cheng, H.H.       2014. Marek’s disease virus influences the core gut microbiome of the chicken during the early and late phases of viral replication.       FEMS Microbiol. Ecol. 90:300-312.



  • Cheng, H.H., Kaiser, P., and Lamont, S.J.       2013. Integrated genomics approaches to enhance genetic resistance in chickens. Ann. Rev. Anim. Vet. Biosci. 1:239-260.
  • Perumbakkam, S., Muir, W.M., Black-Pyrkosz, A., Okimoto, R., and Cheng, H.H. 2013.       Comparison and contrast of genes and biological pathways responding to Marek’s disease virus infection using allele-specific expression and differential expression in broiler and layer chickens. BMC Genomics 14:64.
  • Cheng, H.H. and Lamont, S.J. 2013. Genetics of disease resistance. In Diseases of Poultry, 13th ed.       D.E. Swayne, J.R. Glisson, L. R. McDonald, L. Nolan, D.L. Suarez, and V. Nair, eds. (Wiley-Blackwell Publishing, Ames, IA), pp. 70-86.
  • Mao, W., Kim, T.J., and Cheng, H.H.       2013. Visualization of Marek’s disease virus in vitro using enhanced green fluorescent protein fused with US10. Virus Genes 47:181-183.
  • Crooijmans, R.P.M.A., Fife, M.S., Fitzgerald, T., Strickland, S., Cheng, H.H., Kaiser, P., Redon, R., and Groenen, M.A.M. 2013. Large scale variation in DNA copy number in chicken breeds. BMC Genomics 14:398.
  • Subramaniam, S., Johnston, J., Preeyanon, L., Brown, C.T., Kung, H.J., and Cheng, H.H. 2013. Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by Marek's disease oncoprotein, Meq. J. Virology 87:9016-9029.
  • Subramaniam, S., Preeyanon, L., and Cheng, H.H.       2013. Transcriptional profiling of Meq-dependent genes in Marek’s disease resistant and susceptible inbred chicken lines.       PLoS One 8:e78171.



  • MacEachern, S., Muir, W.M., Crosby, S., and Cheng, H.H. 2012.       Genome-wide identification and quantification of cis- and trans-regulated genes responding to Marek’s disease virus infection via analysis of allele-specific expression.       Frontier Live. Gen. 2:113.
  • Cheng, H.H., MacEachern, S., Subramaniam, and W.M. Muir. 2012.       Chicks and SNPs – an entrée into identifying genes conferring disease resistance in chicken.       Anim. Prod. Sci. 52:151-156.
  • Kumar, S., Kunec, D., Buza, J., Chiang, H.-I., Zhou, H., Subramaniam, S., Pendarvis, K., Cheng, H.H., and Burgess, S.C. 2012.       Nuclear factor kappa B is central to Marek’s disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo. BMC Systems Biol. 6:123.



  • Dodgson, J.B., Delany, M.E., and Cheng, H.H.       2011. Poultry genome sequences: progress and outstanding challenges. Cytogen. Genome Res. 134:19-26.
  • Niikura, M., Kim, T., Silva, R.F., Dodgson, J., and Cheng, H.H. 2011.       Virulent Marek’s disease virus generated from infectious bacterial artificial chromosome clones with complete DNA sequence and implication of viral genetic homogeneity in pathogenesis.       J. Gen. Virol. 92:598-607.
  • Robb, E.A., Gitter, C.L., Cheng, H.H., and Delany, M.E. 2011.       Single nucleotide polymorphism analysis of chicken genetic resources: variation within and among MHC-congenic lines and mapping of developmental mutations. J. Heredity 102:141-156.
  • Meydan, H., Yildiz, M.A., Dodgson, J.B., and Cheng, H.H. 2011.       Allele-specific expression analysis reveals CD79B has a cis-acting regulatory element that responds to Marek’s disease virus infection in chickens. Poultry Sci. 90:1206-1211.
  • Groenen, M.A.M., Megens, H.-J., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R.P.M.A., Vereijken, A., Okimoto, R., Muir, W.M., and Cheng, H.H. 2011.       The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12:274.
  • MacEachern, S., Muir, W.M., Crosby, S., and Cheng, H.H. 2011.       Genome-wide identification of allele-specific expression (ASE) in response to Marek’s disease virus infection using next generation sequencing. BMC Proc. 5 (Suppl. 4):S14.
  • Luo, J., Zhang, H., Tian, F., Chang, S., Cheng, H.H., and Song, J. 2011. Down-regulation of promoter methylation level of CD4 gene after MDV infection in MD-susceptible chicken line.       BMC Proc. 5 (Suppl. 4):S7.



  • Mao, W., Hunt, H.D., and Cheng, H.H.       2010. Cloning and functional characterization of chicken stem cell antigen 2. Devel. Comp. Immunol. 34:360-368.
  • Kim, T., Hunt, H.D., and Cheng, H.H.       2010. Marek’s disease viruses lacking either R-LORF10 or LORF4 have altered virulence in chickens. Virus Genes 40:410-420.
  • Tai, S.H.S., Niikura, M., Cheng, H.H., Kruger, J.M., Wise, A.G., and Maes, R.K. 2010. Complete genomic sequence and an infectious BAC clone of feline herpesvirus-1 (FHV-1). Virology 401:215-227.
  • Silva, R.F., Dunn, J.R., Cheng, H.H., and Niikura, M. 2010.       A MEQ deleted Marek’s disease virus cloned as a bacterial artificial chromosome is a highly efficacious vaccine. Avian Diseases 54:862-869.
  • Cheng, H.H. 2010. Viral disease in chickens. In Breeding for Disease Resistance in Farm Animals, 3rd ed. S.C. Bishop, R.F.E. Axford, F.W. Nicholas, and J.B. Owen, eds. (CABI, Cambridge, MA), pp. 70-87.
  • Robinson, C.M., Hunt, H.D., Cheng, H., and Delany, M. 2010.       Mapping of Marek’s disease herpesvirus integrations into chicken chromosomes indicates positional preference for telomeres and clonal relationships among tumors.       Herpesviridae 1:5.



  • Groenen, M.A.M., Wahlberg, P., Foglio, M., Cheng, H.H., Megens, H.-J., Crooijmans, R., Besnier, F., Lathrop, M., Muir, W., Wong, G.K., Gut, I., and Andersson, L.   2009. A high density SNP based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 19:510-519.
  • Heifetz, E.M., Fulton, J.E., O’Sullivan, N.P., Arthur, J.A., Cheng, H., Wang, J., Soller, M., and Dekkers, J.C.M.       2009. Mapping QTL affecting resistance to Marek's disease in an F6 advanced intercross population of commercial layer chickens. BMC Genomics 10:20.
  • Megens, H.-J., Crooijmans, R.P.M.A. Bastiaansen, J.W.M., Kerstens, H.H.D., Coster, A., Jalving, R., Vereijken, A., Silva, P., Muir, W.M., Cheng, H.H. Hanotte, O., and Groenen, M.A.M.       2009. Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genetics 10:86.



  • Cheng, H.H. 2008. Integrating genomics to understand the Marek's disease virus-chicken host-pathogen interaction. In Genomics of Disease, 24th Stadler Symposium. P. Gustafson, G. Stacey, and J. Taylor, eds. (Springer, New York), pp. 115-126.
  • Cheng, H.H. and Lamont, S.J. 2008. Genetics of disease resistance. In Diseases of Poultry, 12 ed. Y.M. Saif, A. Fadly, J. Glisson, I. McDonald, L. Nolan, and D. Swayne, eds. (Blackwell Publishing, Ames, IA), pp. 59-72.
  • Muir, W.M., Wong, G.K-S, Zhang, Y., Wang, J. Groenen, M.A.M. Crooijmans, R.P.M.A., Megens, H.-J. Zhang, H.M. McKay, J.C., McLeod, S., Okimoto, R., Fulton, J.E., Settar, P., O'Sullivan, N.P. Vereijken, A., Rattink, A., Albers, G.A.A. Taylor Lawley, C., Delany, M.E., and Cheng, H.H. 2008.       Review of the initial validation and characterization of a 3K chicken SNP array. WPSJ 64:219-225.
  • Mao, W., Niikura, M., Silva, R.F., and Cheng, H.H. 2008.       Quantitative evaluation of viral fitness due to a single nucleotide polymorphism in the Marek’s disease virus UL41 gene via an in vitro competition assay. J. Virol. Methods 148:125-131.
  • Cheng, H., Niikura, M., Kim, T., Mao, W., MacLea, K.S., Hunt, H., Dodgson, J., Burnside, J., Morgan, R., Ouyang, M., Lamont, S., Dekkers, J., Fulton, J., Soller, M., and Muir, W. 2008. Using integrative genomics to elucidate genetic resistance to Marek’s disease in chickens. Developments in Biologicals (Karger, Basel), Vol. 132, pp. 365-372.
  • Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A. M, Crooijmans, R.P.M.A., Megens, H.-J., Zhang, H., Okimoto, R., Vereijken, A., Jungerius, A., Albers, G.A.A., Taylor Lawley, C., Delany, M.E., MacEachern, S., and Cheng, H.H. 2008. Genome-wide assessment of world-wide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. PNAS 105:17312-17317.



  • Cogburn, L.A., Porter, T.E., Duclos, M.J., Simon, S.C., Burgess, S.C., Zhu, J.J., Cheng, H., Dodgson, J.B., and Burnside, J.       2007. Functional genomics of the chicken – a model organism.       Poultry Sci. 86: 2059-2094.
  • Niikura, M., Kim, T., Hunt, H.D., Burnside, J., Morgan, R.W., Dodgson, J.B., and Cheng, H.H. 2007. Marek's disease virus up-regulates major histocompatibility complex class II cell surface expression in infected cells. Virology 359:212-219.
  • Cheng, H.H., Zhang, Y., and Muir, W.M.       2007. Evidence for widespread epistatic interactions influencing Marek’s disease virus viremia levels in chicken. Cytogen. Genome Res. 117:313-318.
  • Hillel, J., Granevitze, Z., Twito, T., Ben-Avraham, D., Blum, S., Lavi, U., David, L., Feldman, M.W., Cheng, H., and Weigend, S. 2007.       Molecular markers for the assessment of chicken biodiversity. World Poul. Sci. J., 63:33-45.
  • Zhang, H.M., Bacon, L.D., Heidari, M., Muir, W.M., Groenen, M.A.M., Zhang, Y., Wong, G.K.S., Albers, G.A.A., Vereijken, A.L.J., Rattink, A.P., Okimoto, R., McKay, J.C., McLeod, S., and Cheng, H.H. 2007.       Genetic variation at the tumor virus B (TVB) locus in commercial and laboratory chicken populations assessed by a medium or a high throughput assay. Avian Path. 36:283-291.
  • MacLea, K.S. and Cheng, H.H. 2007. The threat of Marek’s disease virus is expanding. Microbe 2:238-243.
  • Muir, W.M. and Cheng, H.H. 2007. A world wide and genome wide assessment of biodiversity in commercial poultry populations. Proceedings of the 56th National Breeders Roundtable.
  • Granevitze, Z., Blum, S., Cheng, H., Vignal, A., Morrison, M., Ben-Ari, G., David, L., Feldman, M.W., Weigend, S., and Hillel, J.       2007. Female-specific DNA sequences in the chicken genome. J. Heredity 98:238-242.



  • Niikura, M., Dodgson, J, and Cheng, H.H.       2006. Direct evidence of host genome acquisition by the alphaherpesvirus Marek’s disease virus. Archives of Virology 151:537-549.
  • MacLea, K.S., and Cheng, H.H. 2006. Cloning and expression of deoxyribonuclease II from chicken.       Gene 373:44-51.
  • Niikura, M., Dodgson, J, and Cheng, H.H.       2006. Stability of Marek’s disease virus 132 bp repeats during serial in vitro passages.       Archives of Virology 151:1431-1438.
  • Ben-Avraham, D., Blum, S., Granevitze, Z., Weigend, S., Cheng, H, and Hillel, J. 2006.       W-specific microsatellite loci detected by in silico analysis map to chromosome Z of the chicken genome.       Animal Genetics 37:180-181.
  • Backström, N., Brandström, M., Gustafsson, L., Qvarnström, A., Cheng, H., and Ellegren, H. 2006.       Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): Conserved synteny but gene order rearrangements on the avian Z chromosome. Genetics 174:377-386.
  • Atzmon, G., Ronin, Y.I., Korol, A., Yonash, N., Cheng, H., and Hillel. J. 2006.       QTLs associated with growth traits and abdominal fat weight and their interactions with gender and hatch in commercial meat-type chickens. Animal Genetics 37:352-358.

Last Modified: 9/14/2016
Footer Content Back to Top of Page