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Alan F. Scott, Ph.D.

Photo of Dr. Alan F. Scott, Ph.D.

Director of Genetic Resources Core Facility

Associate Professor of Medicine

Research Interests: Evolutionary genomics; Genome annotation; Sequence analysis and interpretation; Genetic/genomic technology

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


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 Medicine
  • Associate Professor of Oncology

Departments / Divisions

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: Genetic Resources Core Facility (GRCF)

Technology Expertise Keywords

DNA sequencing, next-gen sequencing, genotyping

Selected Publications

View all on Pubmed

Scott AF, Bunn HF, Brush AH. Functional aspects of hemoglobin evolution in the mammals. J Mol Evol. 1976 Dec 30;8(4):311-6. PubMed PMID: 1011262.

Scott AF, Phillips JA 3rd, Migeon BR. DNA restriction endonuclease analysis for localization of human beta- and delta-globin genes on chromosome 11. Proc Natl Acad Sci USA. 1979 Sep;76(9):4563-5. PubMed PMID: 291988; PubMed Central PMCID: PMC411618.

Barrie PA, Jeffreys AJ, Scott AF. Evolution of the beta-globin gene cluster in man and the primates. J Mol Biol. 1981 Jul 5;149(3):319-36. PubMed PMID: 6273584.

Scott AF, Heath P, Trusko S, Boyer SH, Prass W, Goodman M, Czelusniak J, Chang LY, Slightom JL. The sequence of the gorilla fetal globin genes: evidence for multiple gene conversions in human evolution. Mol Biol Evol. 1984 Sep;1(5):371-89. PubMed PMID: 6599972.

Scott AF, Schmeckpeper BJ, Abdelrazik M, Comey CT, O'Hara B, Rossiter JP, Cooley T, Heath P, Smith KD, Margolet L. Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence. Genomics. 1987 Oct;1(2):113-25. PubMed PMID: 3692483.

Dombroski BA, Mathias SL, Nanthakumar E, Scott AF, Kazazian HH Jr. Isolation of an active human transposable element. Science. 1991 Dec 20;254(5039):1805-8. PubMed PMID: 1662412.

Mathias SL, Scott AF. Promoter binding proteins of an active human L1 retrotransposon. Biochem Biophys Res Commun. 1993 Mar 15;191(2):625-32. PubMed PMID: 8384847.

Scott AF, Elizaga A, Morrell J, Bergen A, Penno MB. Characterization of a gene coamplified with Ki-ras in Y1 murine adrenal carcinoma cells that codes for a putative membrane protein. Genomics. 1994 Mar 15;20(2):227-30. PubMed PMID: 8020969.

Jabs EW, Li X, Scott AF, Meyers G, Chen W, Eccles M, Mao JI, Charnas LR, Jackson CE, Jaye M. Jackson-Weiss and Crouzon syndromes are allelic with mutations in fibroblast growth factor receptor 2. Nat Genet. 1994 Nov;8(3):275-9. Erratum in: Nat Genet 1995 Apr;9(4):451. PubMed PMID: 7874170.

Meyers GA, Day D, Goldberg R, Daentl DL, Przylepa KA, Abrams LJ, Graham JM Jr, Feingold M, Moeschler JB, Rawnsley E, Scott AF, Jabs EW. FGFR2 exon IIIa and IIIc mutations in Crouzon, Jackson-Weiss, and Pfeiffer syndromes: evidence for missense changes, insertions, and a deletion due to alternative RNA splicing. Am J Hum Genet. 1996 Mar;58(3):491-8. PubMed PMID: 8644708; PubMed Central PMCID: PMC1914562.

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

Ingersoll RG, Paznekas WA, Tran AK, Scott AF, Jiang G, Jabs EW. Fibroblast growth factor receptor 2 (FGFR2): genomic sequence and variations. Cytogenet Cell Genet. 2001;94(3-4):121-6. PubMed PMID: 11856867.

Fallin MD, Hetmanski JB, Park J, Scott AF, Ingersoll R, Fuernkranz HA, McIntosh I, Beaty TH. Family-based analysis of MSX1 haplotypes for association with oral clefts. Genet Epidemiol. 2003 Sep;25(2):168-75. PubMed PMID: 12916025.

Park JW, Cai J, McIntosh I, Jabs EW, Fallin MD, Ingersoll R, Hetmanski JB, Vekemans M, Attie-Bitach T, Lovett M, Scott AF, Beaty TH.High throughput SNP and expression analyses of candidate genes for non-syndromic oral clefts. J Med Genet. 2006 Jul;43(7):598-608. Epub 2006 Jan 13. PubMed PMID: 16415175; PubMed Central PMCID: PMC2564555.

Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. doi: 10.1093/nar/gkn665. Epub 2008 Oct 8. PubMed PMID: 18842627; PubMed Central PMCID: PMC2686440.

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 AC, Moreno LM, Menezes R, Vieira AR, Petrin A, Wilcox AJ, 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, Melbye M, Doheny KF, 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 and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet. 2010 Jun;42(6):525-9. doi: 10.1038/ng.580. Epub 2010 May 2. Erratum in: Nat Genet. 2010 Aug;42(8):727.

Scott, James M [corrected to Scott, John M]. PubMed PMID: 20436469; PubMed Central PMCID: PMC2941216. Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Murray T, Redett RJ, Fallin MD, Liang KY, Wu T, Patel PJ, Jin SC, Zhang TX, Schwender H, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Lie RT, Jee SH, Christensen K, Doheny KF, Pugh EW, Ling H, Scott AF. Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate. Genet Epidemiol. 2011 Sep;35(6):469-78. doi: 10.1002/gepi.20595. Epub 2011 May 26. PubMed PMID: 21618603; PubMed Central PMCID: PMC3180858.

Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q, Wang LE, 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, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu SM, Regnier C, Lowe WL, Hayes MG, Marazita ML, 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, Weir BS. Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nat Genet. 2012 May 6;44(6):642-50. doi: 10.1038/ng.2271. PubMed PMID: 22561516; PubMed Central PMCID: PMC3366033.

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-? repressor SKI cause Shprintzen-Goldberg syndrome with aortic aneurysm. Nat Genet. 2012 Nov;44(11):1249-54. doi: 10.1038/ng.2421. Epub 2012 Sep 30. PubMed PMID: 23023332; PubMed Central PMCID: PMC3545695.

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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