Alan F. Scott, Ph.D.

Headshot of Alan F. Scott
  • Director of Genetic Resources Core Facility
  • Associate Professor of Genetic Medicine

Research Interests

Evolutionary genomics; Genome annotation; Sequence analysis and interpretation; Genetic/genomic technology more


My current interests are focused on bringing new genomics technologies to Hopkins investigators that enable our faculty to study the structure and function of the human genome more effectively and economically. I have helped establish DNA sequencing, synthesis, and genotyping activities both at the medical school, within the Genetic Resources Core Facility (, and for the NIH through the Center for Inherited Disease Research ( Currently, we are providing high throughput genotyping and next-generation sequencing as services. In addition, we offer DNA isolation, qPCR, Sanger sequencing, and cell culture and cryopreservation, among other services, through the GRCF.

I am also interested in the problem of gene annotation so that functional information can be captured and presented in a way that will help with the discovery of the underlying bases of common disease. As an editor for OMIM ( I attempt to find information about genes reported in the biomedical literature that may help explain disease phenotypes. I am also part of a committee attempting to establish a Clinical Genomics Center at JHM which will translate our research expertise in sequencing and genotyping into clinical practice. Lastly, my research interests include the study of isolated cleft lip and palate with Dr. Beaty in the Bloomberg School of Public Health and in the evolutionary genomics of vertebrates, especially endangered species. more


  • Director of Genetic Resources Core Facility
  • Associate Professor of Genetic Medicine
  • Associate Professor of Medicine
  • Associate Professor of Oncology

Departments / Divisions

Centers & Institutes



  • Ph.D.; University of Connecticut (Connecticut) (1975)

Research & Publications

Research Summary

My current research involves a collaboration with Dr. Terri Beaty in the School of Public Health to understand the genetic bases of cleft lip and palate and, more generally, the interpretation of exon and genome sequence variants that determine phenotype.  Our group is also involved in assessing and improving technologies for next-generation sequencing and the analysis of sequence data so that these can be applied clinically.  Lastly, we are applying these technologies and approaches to the genomics and population genetics of endangered species.  


Lab Website: Alan Scott Lab
Core Facility:

Technology Expertise Keywords

DNA sequencing, next-gen sequencing, genotyping

Selected Publications

View all on PubMed


Barrie, P.A., Jeffreys, A.J. and A.F. Scott, 1981.  Evolution of the beta-globin gene cluster in man and the primates.  J. Mol. Biol. 149:319-336. [PMID: 6273584]


Scott, A.F., Heath, P., Trusko, S., Boyer, S.H., Prass, W., Goodman, M., Czelusniak, J., 

Chang, L.-Y.E. and J.L. Slightom, 1984.  The sequence of the gorilla fetal globin genes: Evidence for multiple gene conversions in human evolution.  Mol. Biol. Evol. 1:371-389. [PMID: 6599972]


George, D.L., Scott, A.F., De Martinville, B. and U. Francke, 1984.  Amplified DNA in Y1 mouse adrenal tumor cells: Isolation of cDNAs complementary to an amplified c-Ki-ras gene and localization of homologous sequences to mouse chromosome 6.  Nuc. Acids Res. 12:2731-2743. [PMID: 6546797]


Scott, A.F., Schmeckpeper, B.J., Abdelrazik, M., Comey, C.T., O'Hara, B., Rossiter, J.P., Cooley, T., Heath, P., Smith, K.D. and L.  Margolet, 1987. Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence.  Genomics 1:113-125. [PMID: 3692483]


Kazazian, H.H., Wong, C., Youssoufian, H., Scott, A.F., Phillips, D.G. and S.E. Antonarakis, 1988.  Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man.  Nature 332:164-166. [PMID: 2831458]


Dombroski, B.A., Mathias, S.L., Nanthakumar, E., Scott, A.F. and H.H. Kazazian, 1991.  Isolation of an active human transposable element.  Science 254:1805-1808.

Mathias, S.L., Scott, A.F., Kazazian, H.H., Boeke, J.D. and A. Gabriel, 1991.  Reverse transcriptase encoded by a human transposable element.  Science 254:1805-1808.


Scott, A.F., Elizaga, A., Morrell, J., Bergen, A., and M.B. Penno, 1994.  Characterization of a gene coamplified in Y1 murine adrenal carcinoma cells that codes for a putative membrane protein.  Genomics 20:227-230. 


Dombroski, B.A., Feng, Q., Mathias, S.L., Sassaman, D.M., Scott, A.F., Kazazian, H.H., Jr. and J.D. Boeke, 1994.  An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae.  Mol. Cell. Biol. 14: 4485-4492.


Jabs, E.W., Li, X., Scott, A.F., Meyers, G., Chen, W., Eccles, M., Mao, J., Charnas, L.R., Jackson, C.E. and M. Jaye, 1994.  Jackson-Weiss and Crouzon syndromes are allelic with mutations in fibroblast growth factor receptor 2.  Nature Genetics 8: 275-279


Hamosh, A., Scott, A.F., Amberger, J., Valle, D. and V. A. McKusick, 2000.  Online Mendelian Inheritance In Man (OMIM), Human Mutation, 15:57-61.


Park J.W., McIntosh, I., Hetmanski, J.B., Jabs, E.W., VanderKolk, C., Wu-Chou, Y.-H., Chen, K.T., Chong, S.S., Jee, S.H., Park, B.Y., Fallin, M.D., Ingersoll, R., Scott, A.F., and T.H. Beaty.  2007. Association between IRF6 and nonsyndromic cleft lip with or without cleft palate in four populations. Genet. Med. 9:219-227.


Beaty TH, Murray JC,Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Liang KY, Wu T, Murray T, Fallin MD, Redett RA, Raymond G, Schwender H, Jin SC, Cooper ME, Dunnwald M, Mansilla MA, Leslie E, Bullard S, Lidral A, Moreno LM, Menezes R, Vieira AR, Petrin A, Wilcox A, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Huang S, Yeow V, Chong SS, Jee SH, Shi B, Christensen K, Doheny K,Pugh EW, Ling H, Castilla EE, Czeizel AE, Ma L, Field LL, Brody L, Pangilinan F, Mills JL, Molloy AM, Kirke PN, Scott JM, Arcos-Burgos M, Scott AF. A genome wide association study of cleft lip with/without cleft palate using case-parent trios of European and Asian ancestry identifies MAFB and ABCA4 as novel candidate genes. Nat Genet. 2010 Jun;42(6):525-9

Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q, Wang L, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu SM, Regnier C, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, and Weir BS.  Accepted.  Detectable clonal mosaicism from birth to old age and its relationship to cancer. (2012) Nat Genet. 44(6):642-50.


Doyle AJ, Doyle JJ, Bessling SL, Maragh S, Lindsay ME, Schepers D, Gillis E, Mortier G, Homfray T, Sauls K, Norris RA, Huso ND, Leahy D, Mohr DW, Caulfield MJ, Scott AF, Destrée A, Hennekam RC, Arn PH, Curry CJ, Van Laer L, McCallion AS, Loeys BL, Dietz HC.  Mutations in the TGF-β repressor SKI cause Shprintzen-Goldberg syndrome with aortic aneurysm. Nat Genet. (2012) Sep 30;44(11):1249-54. [PMID: 23023332}


Scott AF, Mohr DW, Kasch LM, Barton JA, Pattiglio R, Ingersoll R, Craig B, Marosy BA, Doheny KF, Bromley WC, Roderick TH, Chassaing N, Calvas P, Prabhu SS, Jabs EW. Identification of a HMGB3 Frameshift Mutation in a Family with X-linked Colobomatous Microphthalmos using Whole Genome and X-Exome Sequencing  (2014) JAMA ophthalmology. 2014; 132(10):1215-20. [PMID: 24993872]


Scott AF, Mohr DW, Scharpf RB, Ling H, Zhang P, Liptak GS Characterization of the genomic architecture and mutational spectrum of a Small Cell Prostate Carcinoma. (2014). Genes 5:366-84. [PMID:24823478]


Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A.  (2015). Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 43:D789-98 [PMID:25428349]



Scott, A.F. and K.D. Smith, 1982.  DNA methods in systematics and evolutionary biology, In, Macromolecular Sequences in Systematics and Evolutionary Biology, M. Goodman, ed.  Plenum Press, New York

Scott, A.F., Amberger, J.A., Brylawski, B.. and V.A. McKusick. Online Mendelian Inheritance in Man, 1999. In, Bioinformatics: Databases and Systems. S.I. Letovsky, ed. Kluwer Press.

Qin H-D, Scott A, Wang HZ, Shugart YY. (Dec. 30, 2012) From GWAS to Next-Generation Sequencing on Human Complex Diseases: The Implications for Translational Medicine and Therapeutics.  Applied Computational Genomics, YY Shugart, ed.  Springer Press, Bethesda MD.


Mendelian Inheritance in Man: A Catalog of Human Genes and Genetic Disorders (12th Ed), VA McKusick, with the Assistance of SE Antonarakis, CA Francomano, O Hurko, AF Scott, M Smith, D Valle, and Others. Johns Hopkins Press, 1998


Recent Selected Abstracts:

Reconstruction of the Mitochondrial Sequence of an Extinct Species (2016, AGBT). Minhovets AN, Mohr DW, Marosy BA, Zhange P, Gaughran SJ, Amato G and AF Scott

Evaluation of Nanopore Sequencing for Measuring Repeat Expansions in Genetic Disease (2015, AGBT) Mohr DW and AF Scott

The Hawaiian Monk Seal (Neomonachus schauinslandi) Genome (2015, G10K) Scott AF, Mohr DW, Littnan C, Barbieri 

Contact for Research Inquiries

Johns Hopkins University School of Medicine
Institute of Genetic Medicine
600 North Wolfe Street
Baltimore, MD 21287 map
Phone: 410-955-2553
Fax: 410-614-9635

Academic Affiliations & Courses

Graduate Program Affiliation

Human Genetics Graduate Program

Activities & Honors

Professional Activities

  • Director, Genetic Resources Core Facility 
  • Editor, Molecular and Cellular Biology 
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