The SCOTT LAB relocated in September 2020 from the Department of Genetics and Genomic Sciences at the Icahn School of Medicine at Mount Sinai (and Sema4) to the Department of Pathology at Stanford University. The central aim of the SCOTT LAB is studying genetic determinants of both drug response variability and Mendelian disease, including innovative sequencing and bioinformatic approaches for discovery and diagnostic testing, as well as evaluating clinical provider knowledge and attitudes on implementing progressive forms of genomic testing. Interested students and colleagues can reach out directly to inquire about potential research opportunities.
All studies on pediatric genetic disease are dedicated to the memory of Dr. James WEISFELD-ADAMS from the University of Colorado School of Medicine in Denver and the Icahn School of Medicine at Mount Sinai in New York. Please consider a donation to support the annual James Weisfeld-Adams Memorial Grand Rounds lecture at the Icahn School of Medicine at Mount Sinai in New York.
A major focus of the SCOTT LAB is studying genetic determinants of interindividual drug response variability, with ongoing collaborative research projects on cardiovascular pharmacogenomics, multi-ethnic pharmacogenomic allele discovery, and the development of next-generation sequencing methods for pharmacogenomic research and clinical testing. Our group has made novel discoveries with anticoagulant and antiplatelet pharmacogeomics, characterized several novel CYP450 alleles in various ethnic populations, and participated in the NHLBI-supported COAG warfarin pharmacogenetics trial as a clinical site with the Mount Sinai Genetic Testing Laboratory (now the Sema4 Laboratory) and Mount Sinai Cardiology. In addition, innovative long-read sequencing pharmacogenomic assays and panels are also being developed in collaboration with PacBio for both translational research and clinical implementation.
Translating pharmacogenomic discovery to clinical implementation is an ongoing interest in the laboratory. We are members of the Clinical Pharmacogenetics Implementation Consortium (CPIC), participating in authoring guidelines for pharmacogenetic-based drug therapy and other related initiatives. Dr. SCOTT was a Co-Investigator of the Institute for Personalized Medicine’s (IPM)-PGx and eMERGE-PGx programs by providing expertise in clinical genetics and implementing clinical pharmacogenomic testing at Mount Sinai. Led by Dr. Aniwaa OWUSU OBENG, the implementation projects at IPM are preemptively genotyping a pharmacogenomic panel through the Sema4 Laboratory among patients at selected Mount Sinai clinics as well as patients enrolled in the BioMe biobank. Current implementation effort at Stanford is centered on partnering with PharmGKB and clincial colleagues to define an innovative clinical pharmacogenomic program at Stanford Health Care.
Dr. SCOTT previously was a Director in the Sema4 Laboratory, which is a CLIA and College of American Pathologists (CAP) accredited clinical genetics laboratory led by Dr. Lisa EDELMANN. In 2020, Dr. SCOTT relocated to the Department of Pathology at Stanford University as Director of the Stanford Medicine Clinical Genomics Laboratory. As such, collaborative research projects with clinical colleagues and trainees are always ongoing and frequently centered on clinical molecular or cytogenomic case studies, gene discovery, innovative genomic test development, analytical comparisons of genetic testing platforms, and multi-ethnic population screening. Translational partnerships with innovative companies that support genomic diagnostics are welcome, as an additional aim of the Clinical Genomics Laboratory is supporting Stanford research programs that are centered on Mendelian and/or complex disease genomics.
Another area of focus in the SCOTT LAB is the study of epigenetic DNA modifications and their role in disease pathogenesis. Previous studies investigated promoter hypermethylation of mismatch repair and cell cycle genes implicated in leukemia pathogenesis; however, current efforts are aimed at studying germline epigenetic susceptibility to other common diseases and drug response phenotypes. Additionally, we are interested in DNA methylation detection technologies, including microarray and next-generation sequencing chemistries. Our group developed single-molecule real-time bisulfite sequencing (SMRT-BS), which is a novel quantitative and multiplexed bisulfite sequencing method for targeted CpG methylation analysis that employs the long-read lengths from PacBio single-molecule real-time (SMRT) sequencing. To facilitate the bioinformatic analysis of amplicon bisulfite next-generation sequencing, we are in the process of launching HiTMAP: a High Throughput Methylation Analysis Program for open access targeted bisulfite sequencing analyses.
Stuart A. SCOTT, PhD
Stuart SCOTT got his Ph.D. from the University of Saskatchewan, Canada, under the mentorship of hematopathologist Dr. John F. DECOTEAU. His interest in medical genetics and molecular pathology prompted postdoctoral American Board of Medical Genetics and Genomics (ABMGG) training in Clinical Molecular Genetics and Clinical Cytogenetics and Genomics at the Icahn School of Medicine at Mount Sinai and Board certification in both specialties. In the Sema4 Laboratory he was involved in high-complexity clinical molecular testing, including pharmacogenomics, cytogenomics, and PacBio long-read SMRT sequencing applications. Dr. SCOTT is currently the Director of the Stanford Medicine Clinical Genomics Laboratory and Professor in the Department of Pathology at Stanford University. His research interests are focused on translational molecular biology, particularly in the areas of pharmacogenomics, cytogenomics, epigenomics, and genomic medicine implementation, and he considers himself fortunate to work with the people that he does.
Yao YANG, PhD
Yao YANG got his Ph.D. in Biomedical Engineering from Southeast University, Nanjing, China, before joining the SCOTT LAB as a postdoctoral fellow in 2011. Dr. YANG became an Instructor in 2015 and his primary research interests involve the application and development of next-generation sequencing workflows and bioinformatic pipelines for discovery in epigenomics and pharmacogenomics. He developed both SMRT-BS and CYP2D6 long-read methods using PacBio SMRT sequencing. In addition to other collaborative research projects on epigenomics and pharmacogenomics, Dr. YANG is ABMGG-certified in Clinical Molecular Genetics and Genomics and is developing novel variant calling pipelines for long-read sequencing. Dr. YANG is currently a Co-Director of the Stanford Medicine Clinical Genomics Laboratory and Clinical Assistant Professor in the Department of Pathology at Stanford University.
Kendall SCHMIDT, BS
Kendall SCHMIDT is a first year Masters of Science (M.S.) in Genetic Counseling student in the Department of Genetics at Stanford University. Kendall’s previous experience in drug development and interest in pharmacogenomics prompted her thesis project with the SCOTT LAB, entitled ‘Knowledge and Attitudes on Antidepressant Pharmacogenomics Among Psychiatrists and Primary Care Physicians’.
James WEISFELD-ADAMS, MB, ChB
James WEISFELD-ADAMS was an Assistant Professor at the Children’s Hospital Colorado, University of Colorado School of Medicine in Denver. Board certified in pediatrics and clinical genetics, Dr. WEISFELD-ADAMS dedicated his career to the clinical care of pediatric and adult patients with rare inherited metabolic and neurogenetic diseases. The SCOTT LAB collaborated with Dr. WEISFELD-ADAMS whenever humanly possible, and will always remember the joy and laughter that was shared when both working and not working together.
Hetanshi NAIK, PhD
Hetanshi NAIK is an Assistant Professor in the Departments of Genetics and Genomic Sciences and Population Health Science and Policy, Director of the Genetic Clinical Trials Office, and the Director of Clinical Research for the Master’s Program in Genetic Counseling at the Icahn School of Medicine at Mount Sinai. Her clinical interests include lysosomal storage diseases and the porphyrias, while her research interests include developing clinical trial methodologies that are both scientifically rigorous and feasible in the rare disease setting, understanding the long-term psychosocial issues patients with rare diseases face, Patient Reported Outcomes (PROs) for rare diseases, and pharmacogenomic studies centered on assessing patient and provider knowledge. She has been a frequent collaborator with the SCOTT LAB through student mentoring, and both clinical and educational pharmacogenomic research projects.
Teri E. KLEIN, PhD
Teri KLEIN is a Professor in the Departments of Biomedical Data Science and Medicine (BMIR) at Stanford University and Principal Investigator of PharmGKB, CPIC, PharmCAT and ClinGen. She is internationally recognized for her work in pharmacogenomics, personalized medicine, computational biology and bioinformatics, and her research focus is currently centered on the development of PharmGKB, clinical pharmacogenomic dosing guidelines, clinical genomics and the annotation of the human genome, and the structural basis of disease. She has graciously been a friend and mentor to the SCOTT LAB for ~10 years, with no end in the foreseeable future.
Jorge DUCONGE, PhD, MSc, BSc Pharm
Jorge DUCONGE is a Professor in the Department of Pharmaceutical Sciences at the University of Puerto Rico School of Pharmacy and Principal Investigator of the NIH-funded Adopting a Precision Medicine Paradigm in Puerto Rico: Leveraging Ancestral Diversity to Identify Predictors of Clopidogrel Response in Caribbean Hispanics research program. His independent research is aimed at studying genetic determinants of drug response variability among underrepresented populations, particularly within the Caribbean Hispanic community. The SCOTT LAB has collaborated with Dr. DUCONGE and members of his research team since 2016, with a focus on antiplatelet pharmacogenomic discovery and implementation among ancestrally diverse populations.
Dena MATALON, MD
Dena MATALON is a Clinical Assistant Professor in the Department of Pediatrics and Division of Medical Genetics at Stanford. She is Board certified in pediatrics and clinical genetics, and her research interests include studying genetic causes of pediatric diseases. She is a Co-Investigator of the GREGoR Stanford Site, and the SCOTT LAB collaborates with Dr. MATALON through their MCHRI/Undiagnosed Disease Network (UDN) pilot project entitled Long-Read Genome Sequencing to Increase Diagnostic Yield in Pediatric Genetic Diseases.
Callan RUSSELL, BS
Callan RUSSELL was a second year Masters of Science (M.S.) in Genetic Counseling student in the Department of Genetics at Stanford University. Callan’s interest in pharmacogenomics and genomic medicine implementation prompted her thesis project with the SCOTT LAB and Stanford Cardiology, entitled ‘Knowledge and Attitudes on Implementing Cardiovascular Pharmacogenomic Testing’.
Lanna CERA, MS
Lanna CERA was a second year Masters of Science (M.S.) in Genetic Counseling student at the Icahn School of Medicine at Mount Sinai. Lanna’s interest in genetic test reporting prompted her thesis project with the SCOTT LAB and collaborators at Nemours Children’s Health, entitled ‘Provider Preferences on Clinical Pharmacogenomic Reporting’.
Meghan BARTOS, MS
Meghan BARTOS was a second year Masters of Science (M.S.) in Genetic Counseling student at the Icahn School of Medicine at Mount Sinai. Meghan’s interest in secondary findings prompted her thesis project with the SCOTT LAB, entitled ‘Attitudes Toward Pharmacogenomics as a Secondary Finding’.
Elizabeth LOUDON, MS
Elizabeth LOUDON was a second year Masters of Science (M.S.) in Genetic Counseling student at the Icahn School of Medicine at Mount Sinai. Elizabeth’s interest in genetic counseling education prompted her thesis project with the SCOTT LAB, entitled ‘Pharmacogenetics Education among Genetic Counseling Training Programs’.
Christina LaMAIRE, MS
Christina LaMAIRE was a second year Masters of Science (M.S.) in Genetic Counseling student at the Icahn School of Medicine at Mount Sinai. Christina’s interest in psychiatric genomics prompted her thesis project with the SCOTT LAB, entitled ‘Perceptions of Psychiatric Pharmacogenetic Clinical Trials among Patients with Depression and Psychiatrists’.
Mariana R. BOTTON, PhD
Mariana R. BOTTON is a postdoctoral fellow at the Hospital de Clínicas de Porto Alegre - Universidade Federal do Rio Grande do Sul, in Porto Alegre, Brazil, with undergraduate and graduate degrees in Pharmacy, and Genetics and Molecular Biology, respectively. Dr. BOTTON’s research focus is studying pharmacogenomic variation in diverse populations, and while pursuing a two-year pharmacogenomics fellowship at Mount Sinai and Sema4, she led the development of several PacBio long-read SMRT sequencing assays and studied pharmacogenomic structural variation.
Dagmar F. HERNANDEZ-SUAREZ, MD, MS
Dagmar F. HERNANDEZ-SUAREZ, M.D. was an Internal Medicine Resident at the University of Puerto Rico (UPR) School of Medicine, San Juan, Puerto Rico. His research was mentored by Dr. Jorge DUCONGE at the UPR, and was aimed at determining the clinical and genetic determinants of clopidogrel responsiveness in Caribbean Hispanics. The SCOTT LAB was fortunate to collaborate with Dr. HERNANDEZ-SUAREZ as a visting scholar at Mount Sinai on antiplatelet pharmacogenetics, as he is now pursuing his career in academic clinical cardiology.
Shahad RAHAWI, MS
Shahad RAHAWI was a second year Masters of Science (M.S.) in Genetic Counseling student at the Icahn School of Medicine at Mount Sinai. Shahad’s interest in genomics education prompted her thesis project with the SCOTT LAB, which was aimed at assessing pediatrician knowledge and attitudes on pharmacogenomics in an effort to better inform how to design clinician education tools.
Meredith ROSS, MS
Meredith ROSS received her Bachelor of Arts (B.A.) in Biology/Biological Sciences & Medicine, Health, and Society at Vanderbilt University, and completed her Masters of Science (M.S.) in Genetic Counseling student at the Icahn School of Medicine at Mount Sinai. Meredith’s interest in prenatal genetic counseling prompted her thesis project with the SCOTT LAB, which assessed knowledge and attitudes on non-invasive prenatal pharmacogenetic screening among pregnant and preconception women.
Kevin SANAYCELA was a summer student from the Dalton School in New York City, who completed his high school program in 2017. His interest in getting first hand exposure to science and research lead him to a volunteer position at the SCOTT LAB through the Dalton Science Research Program. He currently worked on validating computational strategies for haplotype phasing from long read third-generation (PacBio) sequencing data, interrogating the CYP2D6 gene in selected ethnic subpopulations.
Benjamin S. PULLMAN, BA
Ben PULLMAN completed his Bachelor of Arts (B.A.) in Computer Science and Music at Amherst College in 2013, including an honors thesis entitled Machine Learning Methods for Detecting Code Obfuscation. He volunteered in the SCOTT LAB from 2014 to 2015 while working as a developer for the social campaign around the film Girl Rising. During that time he spearheaded our High Throughput Methylation Analysis Program (HiTMAP) project, which is a quantitative online tool for amplicon bisulfite sequencing DNA methylation analyses. Ben currently is pursuing a Ph.D. in Computer Science and Engineering at the University of California, San Diego (UCSD) in the Center for Computational Mass Spectrometry.
Zinira MUNSHI was a 2016 summer student from Rutgers University, majoring in Genetics in the School of Arts and Sciences Honors Program, who is expecting to complete her Bachelor of Arts (B.A.) in 2017. Her undergraduate research studied the role of aurora kinases in cancer, and she was the recipient of a Douglass Project stipend from Rutgers University to foster engagement in research. At the SCOTT LAB she developed a database of clinically actionable and informative pharmacogenomic variants and studied their multi-ethnic allele frequencies across world-wide populations.
Irene L. FENG
Irene FENG was an undergraduate student at Dartmouth College doing a Bachelor of Arts (B.A.) in Computer Science/Biology. She volunteered in the laboratory in 2015, and under the direction of Ben PULLMAN, focused her time on programming the user interface of our High Throughput Methylation Analysis Program (HiTMAP) for amplicon bisulfite sequencing data analysis.
Jeff SLOAD initially volunteered in the SCOTT LAB in 2012 in conjunction with the Authentic Science Research (ASR) program at Darien High School, which aimed at getting high school students first-hand scientific research experience. Following completion of the program and graduation from Darien High School in 2013, he continued working in the SCOTT LAB on cardiovascular pharmacogenomics projects as a summer student. Jeff currently is studying Biology at Williams College and enjoys ultimate frisbee, jazz trombone, and the New York Rangers.
Suparna MARTIS, PhD
Suparna MARTIS got her Ph.D. form the University of Delhi in Peptide Chemistry and subsequently pursued postdoctoral research at the Institute of Genomics & Integrative Biology (CSIR) and several Senior Scientist positions at genetics/genomics companies in Asia and North America, eventually landing at Mount Sinai as a postdoctoral fellow in 2010. With a strong background in population pharmacogenetics, Dr. MARTIS lead a number of projects in the SCOTT LAB on multi-ethnic pharmacogenetic allele profiling where she discovered several novel CYP450 variant alleles, including copy-number variants.
Manishkumar PATEL, MS
Manishkumar PATEL was a graduate student at the University of New Haven, CT, who did his M.S. thesis research project with the SCOTT LAB in 2009 entitled: ‘Warfarin Pharmacogenetics: Copy-Number Variation and Novel CYP2C9 Alleles in a Multi-ethnic Population.’ Following successful completion of his M.S. degree, Manish joined Mount Sinai as a Research Associate in a laboratory within the Department of Hematology & Medical Oncology.
Pratt VM, Cavallari LH, Fulmer M, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. TPMT and NUDT15 genotyping recommendations: A joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. [Epub 2022 Aug 2].
Pratt VM, Wang WY, Boone EC, Broeckel U, Cody N, Edelmann L, Lynnes TC, Medeiros EB, Moyer AM, Mitchell MW, Scott SA, Starostik P, Turner A, Gaedigk A, Kalman LV. Characterization of reference materials for TPMT and NUDT15: A GeT-RM collaborative project. J Mol Diagn. [Epub 2022 Aug 2].
Bartos M, Scott SA, Jabs EW, Naik H. Attitudes on pharmacogenomic results as secondary findings among medical genetics providers. Pharmacogenet Genomics. [Epub 2022 Jul 22].
Nadkarni G, Fei K, Ramos MA, Hauser D, Bagiella E, Ellis SB, Sanderson S, Scott SA, Sabin T, Madden E, Cooper R, Pollak M, Calman N, Bottinger EP, Horowitz CR. Effects of testing and disclosing ancestry-specific genetic risk for kidney failure on patients and health care professionals: A randomized clinical trial. JAMA Netw Open. 2022;5:e221048.
Tayeh MK, Gaedigk A, Goetz MP, Klein TE, Lyon E, McMillin GA, Rentas S, Shinawi M, Pratt VM, Scott SA; ACMG Laboratory Quality Assurance Committee. Clinical pharmacogenomic testing and reporting: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med. [Epub 2022 Feb 10].
Lee CR, Luzum JA, Sangkuhl K, Gammal RS, Sabatine MS, Stein CM, Kisor DF, Limdi NA, Lee YM, Scott SA, Hulot J-S, Roden DM, Gaedigk A, Caudle KE, Klein TE, Johnson JA, Shuldiner AR. Clinical Pharmacogenetics Implementation Consortium guideline for CYP2C19 genotype and clopidogrel therapy: 2022 update. Clin Pharmacol Ther. [Epub 2022 Jan 16].
Steiner HE, Giles JB, Patterson HK, Feng J, El Rouby N, Claudio K, Marcatto LR, Tavares LC, Galvez M, Ospina CAC, Sun X, Hutz MH, Scott SA, Cavallari LH, Mendoza DJF, Duconge J, Botton MR, Santos MCJL, Karnes JH. Machine learning for prediction of stable warfarin dose in US Latinos and Latin Americans. Front Pharmacol. 2021;12:749786.
Duconge J, Santiago E, Hernandez-Suarez DF, Moneró M, López-Reyes A, Rosario M, Renta, González P, Fernández-Morales LI, Vélez-Figueroa LA, Arce O, Marín-Maldonado F, Nuñez H, Melin K, Scott SA, Ruaño G. Pharmacogenomic polygenic risk score for clopidogrel responsiveness among Caribbean Hispanics: A candidate gene approach. Clin Transl Sci. 2021;14:2254-2266. [Epub 2021 Aug 20].
Sangkuhl K, Claudio-Campos K, Cavallari LH, Agundez JAG, Whirl-Carrillo M, Duconge J, del Tredici AL, Wadelius M, Botton MR, Lee M, Woodahl EL, Scott SA, Klein TE, Pratt VM, Daly AK, Gaedigk A. PharmVar GeneFocus: CYP2C9. Clin Pharmacol Ther. 2021;110:662-676. [Epub 2021 Jun 11].
Pratt VM, Cavallari LH, Del Tredici AL, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. Recommendations for clinical CYP2D6 genotyping allele selection: A joint consensus recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and European Society for Pharmacogenomics and Personalized Therapy. J Mol Diagn. 2021;S1525-1578(21)00164-1. [Epub 2021 Jun 10].
Schneider TM, Eadon MT, Cooper-DeHoff RM, Cavanaugh KL, Nguyen KA, Arwood MJ, Tillman EM, Pratt VM, Dexter PR, McCoy AB, Orlando LA, Scott SA, Nadkarni GN, Horowitz CR, Kannry JL. Multi-institutional implementation of clinical decision support for APOL1, NAT2, and YEATS4 genotyping in antihypertensive management. J Pers Med. 2021;11:480.
Scott SA, Nicoletti P. Novel pharmacogenomic locus implicated in angiotensin-converting enzyme (ACE) inhibitor-induced angioedema. J Am Coll Cardiol. 2021;78:710-712.
Singh R*, Cohen ASA*, Poulton C, Hjortshøj TD, Akahira-Azuma M, Mendiratta G, Khan WA, Azmanov DN, Woodward KJ, Kirchhoff M, Shi L, Edelmann L, Baynam G, Scott SA, Jabs EW. Deletion of ERF and CIC causes abnormal skull morphology and global developmental delay. Cold Spring Harb Mol Case Stud. 2021;7:a005991. [Epub 2021 Jun 11]. (* equal contribution).
Scott SA, Swen JJ. Pharmacogenomic determinants of interindividual drug response variability: From discovery to implementation. Genes (Basel). 2021;12:393.
Loudon E, Scott SA, Rigobello R, Scott ER, Zinberg R, Naik H. Pharmacogenomic education among genetic counseling training programs in North America. J Genet Couns. 2021;30:1500-1508. [Epub 2021 Apr 21].
Botton MR, Yang Y, Scott ER, Desnick RJ, Scott SA. Phased haplotype resolution of the SLC6A4 promoter using long-read single molecule real-time (SMRT) sequencing. Genes (Basel). 2020;11:E1333.
Naik N, Palaniappan L, Ashley E, Scott SA. Digital health applications for pharmacogenetic clinical trials. Genes (Basel). 2020;11:E1261.
Lima JJ, Thomas CD, Barbarino J, Desta Z, Van Driest SL, El Rouby N, Johnson JA, Cavallari LH, Shakhnovich V, Thacker DL, Scott SA, Schwab M, Uppugunduri CRS, Formea CM, Franciosi JP, Sangkuhl K, Gaedigk A, Klein TE, Gammal RS, Furuta T. Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2C19 and proton pump inhibitor dosing. Clin Pharmacol Ther. 2021;109:1417-1423. [Epub 2020 Aug 8].
Hernandez-Suarez DF, Melin K, Marin-Maldonado F, Nuñez H, González A, Gonzalez-Sepulveda L, Rivas-Tumanyan S, Naik H, Ruaño G, Scott SA, Duconge J. A clinical protocol for implementing a pharmacogenetic-driven algorithm to guide dual antiplatelet therapy (DAPT) in Caribbean Hispanics. BMJ Open. 20206;10(8):e038936.
Scott SA, Scott ER, Seki Y, Chen AJ, Wallsten R, Owusu Obeng A, Botton MR, Cody N, Shi H, Zhao G, Brake P, Nicoletti P, Yang Y, Delio M, Shi L, Kornreich R, Schadt EE, Edelmann L. Development and analytical validation of a 29 gene clinical pharmacogenetic genotyping panel: Multi-ethnic allele and copy number variant detection. Clin Transl Sci. 2021;14:204-213. [Epub 2020 Jul 23].
El Rouby N, Marcatto LR, Claudio K, Tavares LC, Steiner H, Botton MR, Lubitz SA, Fallon EN, Yee K, Kaye J, Scott SA, Karnes J, de Lima PC, Santos PC, Duconge J, Cavallari LH. Multi-site investigation of genetic determinants of warfarin dose variability in Latinos. Clin Transl Sci. 2021;14:268-276. [Epub 2020 Aug 29].
Botton MR, Whirl-Carrillo M, Del Tredici AL, Sangkuhl K, Cavallari LH, Agúndez JAG, Duconge J, Lee MTM, Woodahl EL, Claudio-Campos K, Daly AK, Klein TE, Pratt VM, Scott SA, Gaedigk A. PharmVar GeneFocus: CYP2C19. Clin Pharmacol Ther. 2021;109:352-366. [Epub 2020 Jun 29].
Rigobello R, Rahawi S, Wallsten R, Cody N, Nicoletti P, Owusu Obeng A, Naik H, Dillon MW, Scott SA. Clinical pharmacogenetic testing and the post-test counseling conundrum. Clin Pharmacol Ther. 2020;108:924-928. [Epub 2020 Jun 27].
Dexter P, Ong H, Elsey A, Bell G, Walton N, Chung W, Rasmussen L, Hicks K, Owusu-Obeng A, Scott SA, Ellis S, Peterson J. Development of a Genomic Data Flow Framework: Results of a Survey Administered to NIH-NHGRI IGNITE and eMERGE Consortia Participants. AMIA Annu Symp Proc. 2020;2019:363-370.
Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, Whirl-Carrillo M, Weck KE. Recommendations for clinical warfarin sensitivity genotyping allele selection: A report of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn. 2020;22:847-859. [Epub 2020 Mar 5].
Cohen ASA, Simotas C, Webb BD, Shi H, Khan WA, Edelmann L, Scott SA, Singh R. Haploinsufficiency of the basic helix-loop-helix transcription factor HAND2 causes congenital heart defects. Am J Med Genet A. 2020;182:1263-1267. [Epub 2020 Mar 5].
Rahawi S, Naik H, Blake K, Owusu Obeng A, Wasserman RM, Seki Y, Funanage VL, Oishi K, Scott SA. Knowledge and attitudes on pharmacogenetics among pediatricians. J Hum Genet. 2020;65:437-444. [Epub 2020 Jan 27].
Asiimwe IG, Zhang EJ, Osanlou R, Krause A, Dillon C, Suarez-Kurtz G, Zhang H, Perini JA, Renta JY, Duconge J, Cavallari LH, Marcatto LR, Beasly MT, Perera MA, Limdi NA, Santos PCJL, Kimmel SE, Lubitz SA, Scott SA, Kawai VK, Jorgensen AL, Pirmohamed M. Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis. Clin Pharmacol Ther. 2020;107:1420-1433 [Epub 2020 Jan 28].
Scott ER, Bansal V, Meacham C, Scott SA. VarCover: Genomic allele min-set cover software. J Mol Diagn. 2020;22:123-131. [Epub 2019 Nov 18].
Hicks JK, Bishop JR, Gammal RS, Sangkuhl K, Bousman C, Leeder JS, Llerena A, Mueller DJ, Ramsey LB, Scott SA, Skaar TC, Caudle KE, Klein TE, Gaedigk A. A call for clear and consistent communications regarding the role of pharmacogenetics in antidepressant pharmacotherapy. Clin Pharmacol Ther. 2020;107:50-52. [Epub 2019 Oct 30].
Caudle KE, Sangkuhl K, Whirl-Carrillo M, Swen JJ, Haidar CE, Klein TE, Gammal RS, Relling MV, Scott SA, Hertz DL, Guchelaar HJ, Gaedigk A. Standardizing CYP2D6 genotype to phenotype translation: Consensus recommendations from the Clinical Pharmacogenetics Implementation Consortium (CPIC) and Dutch Pharmacogenetics Working Group (DPWG). Clin Transl Sci. 2020;13:116-124. [Epub 2019 Oct 24].
Botton MR, Lu X, Zhao G, Repnikova E, Seki Y, Gaedigk A, Schadt EE, Edelmann L, Scott SA. Structural variation at the CYP2C locus: Characterization of deletion and duplication alleles. Hum Mutat. 2019;40:e37-e51. [Epub 2019 Jul 1].
Shi L, Bai Y, Kharbutli Y, Oza AM, Amr SS, Edelmann L, Mehta L, Scott SA. Prenatal cytogenomic identification and molecular refinement of compound heterozygous STRC deletion breakpoints. Mol Genet Genomic Med. 2019;7:e806. [Epub 2019 Jun 19].
Hachad H, Ramsey LB, Scott SA. Interpreting and implementing clinical pharmacogenetic tests: perspectives from service providers. Clin Pharmacol Ther. 2019;106:298-301. [Epub 2019 Jun 4].
Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Moyer AM, Scott SA, Whirl-Carrillo M, Weck KE. Recommendations for clinical CYP2C9 genotyping allele selection: A joint recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn. 2019;21:746-755. [Epub 2019 May 7].
Cavallari LH, Van Driest SL, Prows CA, Bishop JR, Limdi NA, Pratt VM, Ramsey LB, Smith DM, Tuteja S, Duong BQ, Hicks JK, Lee JC, Owusu Obeng A, Beitelshees AL, Bell GC, Blake K, Crona DJ, Dressler L, Gregg RA, Hines LJ, Scott SA, Shelton RC, Weitzel KW, Johnson JA, Peterson JF, Empey PE, Skaar TC. Multi-site investigation of strategies for the clinical implementation of CYP2D6 genotyping to guide drug prescribing. Genet Med. 2019;21:2255-2263. [Epub 2019 Mar 21].
Khan WA, Cohen N, Scott SA, Pereira EM. Familial inheritance of the 3q29 microdeletion syndrome: case report and review. BMC Med Genomics. 2019;12:51.
Qiao W, Martis S, Mendiratta G, Shi L, Botton MR, Yang Y, Gaedigk A, Vijzelaar R, Edelmann L, Kornreich R, Desnick RJ, Scott SA. Integrated CYP2D6 interrogation for multi-ethnic copy number and tandem allele detection. Pharmacogenomics. 2019;20:9-20. [Epub 2018 Dec 6].
Danese E, Raimondi S, Montagnana M,…, Scott SA,…, Pirmohamed M, Johnson JA, Fava C. The effect of CYP4F2, VKORC1 and CYP2C9 in influencing coumarin dose. A meta-analysis in more than 15,000 individuals. Clin Pharmacol Ther. 2019;105:1477-1491. [Epub 2018 Dec 2].
Yang JJ, Whirl-Carrillo M, Scott SA, Turner A, Schwab M, Tanaka Y, Suarez-Kurtz G, Schaeffeler E, Miller N, Klein TE, Gaedigk A. Pharmacogene Variation (PharmVar) Consortium gene introduction: NUDT15. Clin Pharmacol Ther. 2019;105:1091-1094. [Epub 2018 Dec 4].
Thorn CF, Whirl-Carrillo M, Hachad H, Johnson JA, McDonagh EM, Ratain MJ, Relling MV, Scott SA, Altman RB, Klein TE. Essential characteristics of pharmacogenomics study publications. Clin Pharmacol Ther. 2019;105:86-91. [Epub 2018 Nov 8].
Vijzelaar R, Botton MR, Stolk L, Martis S, Desnick RJ, Scott SA. Multi-ethnic SULT1A1 copy number profiling with multiplex ligation-dependent probe amplification. Pharmacogenomics. 2018;19:761-770. [Epub 2018 May 23].
Hernandez-Suarez DF, Botton MR, Scott SA, Tomey MI, Garcia MJ, Wiley JM, Villablanca PA, Melin K, Lopez-Candales A, Renta JY, Duconge J. Pharmacogenetic association study on clopidogrel response among Puerto Rican Hispanics with cardiovascular disease. Pharmgenomics Pers Med. 2018;11:95-106. [Epub 2018 Jun 11.]
Roselli C, Chaffin MD, Weng LC, Aeschbacher S,…, Scott SA,…, Zeng L, Lubitz SA, Lunetta KL, Ellinor PT. Multi-ethnic genome-wide association study for atrial fibrillation. Nat Genet. 2018;50:1225-1233 [Epub 2018 Jun 11.]
Pratt VM, Del Tredici A, Hachad H, Ji Y, Kalman L, Scott SA, Weck KE. Recommendations for Clinical CYP2C19 genotyping allele selection: A report of the Association for Molecular Pathology. J Mol Diagn. 2018;20:269-276. [Epub 2018 Feb 20.]
Hernandez-Suarez DF, Núñez-Medina H, Scott SA, Wiley JM, Garcia MJ, Melin K, Nieves-Borrero K, Rodriguez-Ruiz C, Lopez-Candales A, Marshall L, Duconge J. Effect of cilostazol on platelet reactivity among patients with peripheral artery disease on clopidogrel. Drug Metab Pers Ther. 2018;33:49-55. [Epub 2018 Feb 6.]
Reiner J, Pisani L, Qiao W, Singh R, Yang Y, Shi L, Khan WA, Sebra R, Cohen N, Babu A, Edelmann L, Jabs EW, Scott SA. Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet-Biedl Syndrome 9 (BBS9) deletion. npj Genomic Medicine. 2018;3:3.
Scott SA, Owusu Obeng A, Botton MR, Yang Y, Scott ER, Ellis SB, Wallsten R, Kaszemacher T, Zhou X, Chen R, Nicoletti P, Naik H, Kenny EE, Vega A, Waite E, Diaz GA, Dudley J, Halperin JL, Edelmann L, Kasarskis A, Hulot J-S, Peter I, Bottinger EP, Hirschhorn K, Sklar P, Cho JH, Desnick RJ, Schadt EE. Institutional profile: Translational pharmacogenomics at the Icahn School of Medicine at Mount Sinai. Pharmacogenomics. 2017;18:1381-1386. [Epub 2017 Oct 6.]
Hernandez-Suarez DF, Scott SA, Tomey MI, Melin K, Lopez-Candales A, Buckley CE, Duconge J. Clinical determinants of clopidogrel responsiveness in a heterogeneous cohort of Caribbean Hispanics. Ther Adv Cardiovasc Dis. 2017;11:235-241. [Epub 2017 Jul 1.]
Claudio-Campos K, Labastida A, Ramos A, Gaedigk A, Renta-Torres J, Padilla D, Rivera-Miranda G, Scott SA, Ruaño G, Cadilla CL, Duconge-Soler J. Warfarin anticoagulation therapy in Caribbean Hispanics of Puerto Rico: a candidate gene association study. Front Pharmacol. 2017;8:347. [Epub 2017 Jun 7.]
Rasmussen-Torvik LJ, Almoguera B, Doheny KF, Freimuth RR, Gordon AS, Hakonarson H, Hawkins J, Ivacic L, Kullo IJ, Linderman MD, Manolio T, Owusu Obeng A, Pellegrino R, Prows CA, Pugh E, Ritchie MD, Smith M, Stallings SC, Wolf WA, Zhang K, Scott SA. Concordance between research sequencing and clinical pharmacogenetic genotyping in the eMERGE-PGx study. J Mol Diagn. 2017;19:561-566. [Epub 2017 May 11.]
Yang Y*, Botton MR*, Scott ER, Scott SA. Sequencing the CYP2D6 gene: From variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics. 2017;18:673-685. [Epub 2017 May 4.] (* equal contribution)
Christophersen IE, Rienstra M, Roselli C, Yin X, Geelhoed B,…, Scott SA, …, Benjamin EJ, Tanaka T, Lunetta KL, Lubitz SL, Ellinor PT, on behalf of the AFGen Consortium. Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation. Nat Genet. 2017;49:946-952. [Epub 2017 Apr 17.]
Nadkarni GN, Galarneau G, Ellis SB, Nadukuru R, Zhang J, Scott SA, Schurmann C, Li R, Rasmussen-Torvik LJ, Kho AN, Hayes MG, Pacheco JA, Manolio TA, Chisholm RL, Roden DM, Denny JC, Kenny EE, Bottinger EP. Association of Apolipoprotein L1 variants and blood pressure traits in African Americans. J Am Coll Cardiol. 2017;69:1564-1574.
Karger L*, Khan WA*, Calabio R, Singh R, Xiang B, Babu A, Cohen N, Yang A, Scott SA. Maternal uniparental disomy of chromosome 15 and concomitant STRC and CATSPER2 deletion-mediated deafness-infertility syndrome. Am J Med Genet A. 2017;173:1436-1439. [Epub 2017 Mar 20.] (* equal contribution)
Reiner J, Karger L, Cohen N, Mehta L, Edelmann L, Scott SA. Chromosomal microarray detection of constitutional copy number variation using saliva DNA. J Mol Diagn. 2017;19:397-403. [Epub 2017 Mar 15.]
Johnson JA, Caudle K, Gong L, Whirl-Carrillo M, Stein CM, Scott SA, Lee MT, Gage BF, Kimmel SE, Perera MA, Anderson JL, Pirmohamed M, Hines R, Klein TE, Limdi N, Cavallari LH, Wadelius M. Clinical Pharmacogenetics Implementation Consortium (CPIC®) guidelines for warfarin dosing: 2017 update. Clin Pharmacol Ther. 2017;102:397-404. [Epub 2017 Feb 15.]
Stillitano F, Hansen J, Kong CW, Karakikes I, Funck-Brentano C, Scott SA, Reynier S, Ma W, Valogne Y, Desseaux C, Salem JE, Jeziorowska D, Zahr N, Li R, Ivengar R, Hajjar R, Hulot JS. Modeling susceptibility to drug-induced long QT with a panel of subject-specific iPS cells. eLife. 2017;6:e19406.
Moriyama B, Owusu Obeng A, Barbarino JM, Penzak SR, Henning SA, Scott SA, Agúndez JAG, Wingard JR, McLeod HL, Klein TE, Cross S, Caudle KE, Walsh TJ. Clinical Pharmacogenetics Implementation Consortium (CPIC®) guideline for CYP2C19 and voriconazole dosing. Clin Pharmacol Ther. [Epub 2016 Dec 16.]
Owusu Obeng A, Kaszemacher T, Abul-Husn NS, Gottesman O, Vega A, Waite E, Myers K, Cho J, Bottinger EP, Ellis SB, Scott SA. Implementing algorithm-guided warfarin dosing in an ethnically diverse patient population using electronic health records and pre-emptive CYP2C9 and VKORC1 genetic testing. Clin Pharmacol Ther. 2016;100:427-430. [Epub 2016 Jul 9.]
Caudle KE, Dunnenburger HM, Freimuth RR, Peterson JF, Burlison JD, Whirl-Carrillo M, Scott SA, Rehm HL, Williams MS, Klein TE, Relling MV, Hoffman JM. Standardizing terms for clinical pharmacogenetic test results: The Clinical Pharmacogenetics Implementation Consortium (CPIC) term standardization project. Genet Med. 2017;19:215-223. [Epub 2016 Jul 21.]
Scott SA, Collet JP, Baber U, Yang Y, Peter I, Linderman M, Sload J, Qiao W, Kini AS, Sharma SK, Desnick RJ, Fuster V, Hajjar RJ, Montalescot G, Hulot JS. Exome Sequencing of extreme clopidogrel response phenotypes identifies B4GALT2 as a determinant of on-treatment platelet reactivity. Clin Pharmacol Ther. 2016;100:287-294. [Epub 2016 May 23.]
Weisfeld-Adams JD, Tkachuk A, Maclean KN, Meeks N, Scott SA. A de novo 2.78 Mb duplication on chromosome 21q22.11 implicates candidate genes in the partial trisomy 21 phenotype. npj Genomic Medicine. 2016;1:16003.
Ruderfer DM, Charney AW, Readhead B, Kidd BA, Kähler AK, Kenny PJ, Keiser MJ, Moran JL, Hultman CM, Scott SA, Sullivan PF, Purcell SM, Dudley JT, Sklar P. Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. Lancet Psychiatry. 2016;3:350-357. [Epub 2016 Feb 22.]
Bush WS, Crosslin DR, Owusu Obeng A, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D, Doheny KF, Gallego CJ, Gordon AS, Keating B, Kirby J, Kitchner T, Manzi S, Mejia AR, Pan V, Perry CL, Peterson JF, Prows CA, Ralston J, Scott SA, Scrol A, Smith M, Stallings SC, Veldhuizen T, Wolf W, Volpi S, Wiley K, Li R, Manolio T, Bottinger E, Brilliant MH, Carey D, Chisholm RL, Chute CG, Haines JL, Hakonarson H, Harley JB, Holm IA, Kullo IJ, Jarvik GP, Larson EB, McCarty CA, Williams MS, Denny JC, Rasmussen-Torvik LJ, Roden DM, Ritchie MD. Genetic variation among 82 pharmacogenes: The PGRN-Seq data from the eMERGE Network. Clin Pharmacol Ther. 2016;100:160-169. [Epub 2016 Feb 9.]
Qiao W, Wang J, Pullman BS, Chen R, Yang Y, Scott SA. The CYP2D6 VCF translator. Pharmacogenomics J. 2017;17:301-303. [Epub 2016 Mar 15.]
Zhang J*, Fedick A*, Wasserman S, Zhao G, Edelmann L, Bottinger EP, Kornreich R, Scott SA. Analytical validation of a personalized medicine APOL1 genotyping assay for non-diabetic chronic kidney disease risk assessment. J Mol Diagn. 2016;18:260-266. [Epub 2016 Jan 7.] (* equal contribution)
Van Driest SL, Wells QS, Stallings S, Bush WS, Gordon A, Nickerson DA, Kim JH, Crosslin DR, Jarvik GP, Carrell DS, Ralston JD, Larson EB, Bielinski SJ, Olson JE, Ye Z, Kullo IJ, Abul-Husn NS, Scott SA, Bottinger E, Almoguera B, Connolly J, Chiavacci R, Hakonarson H, Rasmussen-Torvik LJ, Pan V, Persell SD, Smith M, Chisholm RL, Kitchner TE, He MM, Brilliant MH, Wallace JR, Doheny KF, Shoemaker MB, Li R, Manolio TA, Callis TE, Macaya D, Williams MS, Carey D, Kapplinger JD, Ackerman MJ, Ritchie MD, Denny JC, Roden DM. Association of arrhythmia-related genetic variants with phenotypes documented in electronic medical records. JAMA. 2016;315:47-57.
Qiao W*, Yang Y*, Sebra R, Mendiratta G, Gaedigk A, Desnick RJ, Scott SA. Long-read single-molecule real-time (SMRT) full gene sequencing of cytochrome P450-2D6 (CYP2D6). Hum Mut. 2016;37:315-323. [Epub 2015 Dec 18.] (* equal contribution)
Kalman LV, Agúndez JAG, Appell MLA, Black JL, Bell G, Boukouvala S, Bruckner C, Bruford E, Bruckner C, Caudle K, Coulthard S, Daly AK, Del Tredici AL, den Dunnen JT, Drozda K, Everts R, Flockhart D, Freimuth R, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Müller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale R, van Schaik RHN, Whirl-Carrillo M, Yeo K-TJ, Zanger UM. Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting. Clin Pharmacol Ther. 2016;99:172-185. [Epub 2015 Nov 20.]
Pratt VM, Everts RE, Aggarwal P, Beyer BN, Broeckel U, Epstein-Baak R, Hujsak P, Kornreich R, Liao J, Lorier R, Scott SA, Smith CH, Toji LH, Turner A, Kalman LV. Characterization of 137 genomic DNA reference materials for 28 pharmacogenetic genes: A GeT-RM collaborative project. J Mol Diagn. 2016;18:109-123. [Epub 2015 Nov 24.]
Yang Y, Lewis JP, Hulot JS, Scott SA. The pharmacogenetic control of antiplatelet response: Candidate genes and CYP2C19. Expert Opin Drug Metab Toxicol. 2015;11:1599-1617. [Epub 2015 Jul 14.] (Invited review)
Hicks JK, Bishop JR, Sangkuhl K, Müller DJ, Ji Y, Leckband SG, Leeder JS, Graham RL, Chiulli DL, LLerena A, Skaar TC, Scott SA, Klein TE, Caudle KE, Gaedigk A. Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 and CYP2C19 genotypes and dosing of selective serotonin reuptake inhibitors. Clin Pharmacol Ther. 2015;98:127-134. [Epub 2015 Jun 29.]
Yang Y, Sebra R, Pullman B, Peter I, Desnick RJ, Geyer CR, DeCoteau JF, Scott SA. Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics. 2015;16:350.
Termsarasab P, Yang AC, Reiner J, Mei H, Scott SA, Frucht SJ. Paroxysmal kinesigenic dyskinesia caused by 16p11.2 microdeletion. Tremor Other Hyperkinet Mov (N Y). 2014;4:274.
Rasmussen-Torvik LJ, Stallings SC, Gordon AS, Almoguera B, Basford MA, Bielinski SJ, Brautbar A, Brilliant M, Carrell DS, Connolly J, Crosslin DR, Doheny KF, Gallego CJ, Gottesman O, Kim DS, Leppig KA, Li R, Lin S, Manzi S, Mejia AR, Pacheco JA, Pan V, Pathak J, Perry CL, Peterson JF, Prows CA, Ralston J, Rasmussen LV, Ritchie MD, Sadhasivam S, Scott SA, Smith M, Vega A, Vinks A, Volpi S, Wolf W, Bottinger E, Chisholm RL, Chute CG, Haines JL, Harley JB, Keating B, Holm IA, Kullo IJ, Jarvik GP, Larson EB, Manolio T, McCarty CA, Nickerson DA, Scherer SE, Williams MS, Roden DM, Denny JC. Design and anticipated outcomes of the eMERGE-PGx project: A multi-center pilot for pre-emptive pharmacogenomics in electronic health record systems. Clin Pharmacol Ther. 2014;96:482-489. [Epub 2014 Jun 24.]
Abul-Husn NS*, Owusu Obeng A*, Sanderson SC, Gottesman O, Scott SA. Implementation and utilization of genetic testing in personalized medicine. Pharmgenomics Pers Med. 2014;7:227-240. (* equal contribution)
Jaja C, Patel N, Scott SA, Gibson R, Kutlar A. CYP2C9 allelic variants and frequencies in pediatric sickle cell disease cohort: Implications for NSAIDs pharmacotherapy. Clin Transl Sci. 2014;7:396-401. [Epub 2014 May 29.]
Yang Y, Peter I, Scott SA. Pharmacogenetics in Jewish populations. Drug Metabol Drug Interact. 2014;29:221-233. [Epub May 27 2014]
Overby CL, Ludtke A, Abul-Husn NS, Ellis S, Scott SA, Owusu Obeng A, Kannry JL, Hripcsak G, Bottinger EP, Gottesman O. Physician attitudes toward adopting genome-guided prescribing through clinical decision support. J Pers Med. 2014;4:35-49.
Scott SA and Lubitz SA. Warfarin pharmacogenetic trials: Is there a future for pharmacogenetic-guided dosing? Pharmacogenomics. 2014;15:719-722. (Invited editorial)
Scott SA, Owusu Obeng A, Hulot JS. Antiplatelet drug interactions with proton pump inhibitors. Expert Opin Drug Metab Toxicol. 2014;10:175-189. [Epub 2013 Nov 9.]
Caudle KE, Klein TE, Hoffman JM, Müller DJ, Whirl-Carrillo M, McDonagh EM, Sangkuhl K, Thorn CF, Schwab M, Agúndez JAG, Freimuth RR, Huser V, Lee MTM, Iwuchukwu OF, Crews KR, Scott SA, Wadelius M, Swen JJ, Tyndale RF, Stein CM, Roden D, Relling MV, Williams MS, Johnson SG. Incorporation of pharmacogenomics into routine clinical practice: The Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline development process. Curr Drug Metab. 2014;15:209-217. [Epub 2014 Jan 30.]
Kadian-Dodov D, van der Zee S, Scott SA, Peter I, Martis S, Doheny DO, Rothlauf EB, Lubitz SA, Desnick RJ, Halperin JH. Warfarin pharmacogenetics: A controlled dose response study in healthy subjects. Vasc Med. 2013;18:290-297. [Epub 2013 Sep 12.]
Scott SA, Tan Q, Baber U, Martis S, Yang Y, Bander J, Kornreich R, Hulot J-S, Desnick RJ. An allele-specific PCR system for rapid detection and discrimination of the CYP2C19*4A, *4B, and *17 alleles: Implications for clopidogrel response testing. J Mol Diagn. 2013;15:783-789. [Epub 2013 Sep 4.]
Scott SA, Sangkuhl K, Stein CM, Hulot J-S, Mega JL, Roden DM, Klein TE, Sabatine MS, Johnson JA, Shuldiner AR. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for cytochrome P450-2C19 (CYP2C19) genotype and clopidogrel therapy: 2013 Update. Clin Pharmacol Ther, 2013;94:317-323. [Epub 2013 May 22.]
Luo M, Liu L, Peter I, Scott SA, Eversley C, Kornreich R, Desnick RJ, Edelmann L. Spinal muscular atrophy: Improved detection of silent (2+0) carriers by identification of SMN1 founder alleles. Genet Med. 2014;16:149-156. [Epub 2013 Jun 20.]
Baber U, Bander J, Karajgikar R, Abraham B, Yadav K, Hadi A, Theodoropolous K, Gukathasan N, Thapi R, Roy S, Sayeneni S, Scott SA, Palkhiwala S, Suleman J, Kovacic J, Yu J, Sartori S, Dangas G, Mehran R, Uribarri J, Badimon J, Muntner P, Moreno P, Kini AS, Sharma SK. Combined and independent impact of diabetes mellitus and chronic kidney disease on residual platelet reactivity. Thromb Haemost, 2013;110:118-123. [Epub 2013 May 16.]
Gottesman O, Scott SA, Ellis SB, Overby CL, Ludtke A, Hulot J-S, Hall J, Chatani K, Myers K, Kannry JL, Bottinger EP. The CLIPMERGE PGx Program: Clinical Implementation of Personalized Medicine through Electronic Health Records and Genomics - Pharmacogenomics. Clin Pharmacol Ther. 2013;94:214-217. [Epub 2013 Apr 3.]
Perera MA, Cavallari LH, Limdi NA, Gamazon ER, Konkashbaev A, Daneshjou R, Pluzhnikov A, Crawford DC, Wang J, Liu N, Tatonetti NJ, Bourgeois S, Takahashi H, Bradford Y, Burkley BM, Desnick RJ, Halperin JL, Khalifa SI, Langaee TY, Lubitz SA, Nutescu EA, Oetjens M, Shahin MH, Shitalben RP, Tector M, Rieder MJ, Scott SA, Wu AHB, Burmester JK, Deloukis P, Wagner MJ, Mushiroda T, Kubo M, Roden DM, Cox NJ, Altman RB, Klein TE, Nakamura Y, Johnson JA. Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study. Lancet. 2013;382:790-796. [Epub 2013 Jun 4.]
Scott SA*, Liu B*, Nazarenko I*, Martis S, Kozlitina J, Yang Y, Ramirez C, Kasai Y, Hyatt T, Peter I, Desnick RJ. Frequency of the Cholesteryl Ester Storage Disease common LIPA E8SJM mutation (c.894G>A) in various racial and ethnic groups. Hepatology. 2013;58:958-965. [Epub 2013 Feb 19.] (* equal contribution)
Scott SA. Clinical pharmacogenomics: Opportunities and challenges at point-of-care. Clin Pharmacol Ther. 2013;93:33-35. [Epub 2012 Dec 5.]
Martis S, Mei H, Vijzelaar R, Edelmann L, Desnick RJ, Scott SA. Multi-ethnic cytochrome-P450 copy number profiling: novel pharmacogenetic alleles and mechanism of copy number variation formation. Pharmacogenomics J. 2013;13:558-566. [Epub 2012 Nov 20.]
Danese E, Montagnana M, Johnson JA, Rettie A, Zambon CF, Lubitz SA, Suarez-Kurtz G, Cavallari LH, Zhao L, Huang M, Nakamura Y, Mushiroda T, Kringen MK, Borgiani P, Ciccacci C, Rieder MJ, Langaee TJ, Siguret V, Loriot MA, Sagreiya H, Altman RB, Shahin MHA, Scott SA, Khalifa SI, Chowbay B, Suriapranata IM, Teichert M, Taljaard M, Botton MR, Zhang JE, Pirmohamed M, Zhang X, Carlquist JF, Horne BD, Lee MTA, Pengo V, Guidi GC, Minuz P, Fava C. Impact of the CYP4F2 p.V433M polymorphism on coumarin dose requirement: a systematic review and meta-analysis. Clin Pharmacol Ther. 2012;92:746-756.
Lyon E, Foster JG, Palomaki GE, Pratt VM, Reynolds K, Sabato F, Scott SA, Vitaska P. A working group of the Molecular Genetics Subcommittee on behalf of the American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee. Laboratory testing of CYP2D6 alleles in relation to tamoxifen therapy. Genet Med. 2012;14:990-1000. [Epub 2012 Sept 6.]
Takahashi N, Miura M, Scott SA, Niioka T, Sawada K. Pharmacokinetics of dasatinib for Philadelphia chromosome-positive acute lymphocytic leukemia with acquired T315I mutation. J Hematol Oncol. 2012;5:23.
Martis S, Peter I, Hulot J-S, Kornreich R, Desnick RJ, Scott SA. Multi-ethnic distribution of clinically relevant CYP2C genotypes and haplotypes. Pharmacogenomics J. 2013;13:369-377. [Epub 2012 Apr 10.]
Scott SA*, Patel M*, Martis S, Lubitz SA, van Der Zee S, Edelmann L, Yoo C, Halperin JL, Desnick RJ. Copy number variation and warfarin dosing: evaluation of CYP2C9, VKORC1, CYP4F2, GGCX, and CALU. Pharmacogenomics. 2012;13:297-307. [Epub 2011 Dec 21.] (* equal contribution)
Scott SA. Personalizing medicine with clinical pharmacogenetics. Genet Med. 2011;13:987-995.
Cayla G, Hulot J-S, O’Connor S, Pathack A, Scott SA, Gruel Y, Silvain J, Vignalou JB, Huerre Y, de la Briolle A, Allanic F, Beygui F, Barthelemy O, Montalescot G, Collet JP. Clinical, angiographic and genetic determinants of early coronary stent thrombosis: the ONASSIST study. JAMA. 2011;306:1765-1774.
Scott SA, Sangkuhl K, Shuldiner AR, Hulot J-S, Thorn CF, Altman RB, Klein TE. PharmGKB summary: very important pharmacogene information for cytochrome P450, family 2, subfamily C, polypeptide 19 (CYP2C19). Pharmacogenet Genomics. 2012;22:159-165. [Epub 2011 Oct 24.]
Hulot JS, Collet JP, Cayla G, Silvain J, Allanic F, Bellemain-Appaix A, Scott SA, Montalescot G. CYP2C19 but not PON1 genetic variants influence clopidogrel pharmacokinetics, pharmacodynamics and clinical efficacy in post-myocardial infarction patients. Circ Cardiovasc Interv. 2011;4:422-428.
Johnson JA, Gong L, Carrillo M, Gage BF, Scott SA, Stein CM, Anderson JL, Kimmel SE, Lee MT, Pirmohamed M, Wadelius M, Klein TE, Altman RB. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing. Clin Pharmacol Ther. 2011;90:625-629.
Varricchio L, Goldbold J, Scott SA, Whitsett C, Da Costa L, Pospisilova D, Garelli E, Quarello P, Ramenghi U, Migliaccio AR. Increased frequency of the glucocorticoid receptor A3669G (rs6198) polymorphism in patients with Diamond-Blackfan Anemia. Blood. 2011;118:473-474.
Scott SA, Sangkuhl K, Gardner EE, Stein CM, Hulot J-S, Johnson JA, Roden DM, Klein TE, Shuldiner AR. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for cytochrome P450-2C19 (CYP2C19) genotype and clopidogrel therapy. Clin Pharmacol Ther. 2011;90:328-332.
Scott SA, Martis S, Peter I, Kasai Y, Kornreich R, Desnick RJ. Identification of CYP2C19*4B: pharmacogenetic implications for drug metabolism including clopidogrel responsiveness. Pharmacogenomics J. 2012;12:297-350. [Epub 2011 Mar 1.]
Takahashi N, Wakita H, Miura M, Scott SA, Nishii K, Masuko M, Sakai M, Maeda Y, Ishige K, Kashimura M, Fujikawa K, Fukazawa M, Katayama T, Monna F, Narita M, Katayama N, Furukawa T, Miyazaki Y, Urase F, Sawada K. Correlation of imatinib pharmacokinetics with clinical response in Japanese patients with chronic phase chronic myeloid leukemia. Clin Pharmacol Ther. 2010;88:809-813.
Takahashi N, Miura M, Scott SA, Kagaya H, Kameoka Y, Tagawa H, Fujishima N, Saito H, Yoshioka T, Hirokawa M, Sawada K. Influence of CYP3A5 and drug transporter polymorphisms on imatinib trough concentration and clinical response among patients with chronic-phase chronic myeloid leukemia. J Hum Genet. 2010;55:731-737.
Scott SA, Edelmann L, Liu L, Luo M, Desnick RJ, Kornreich R. Experience with carrier screening and prenatal diagnosis for sixteen Ashkenazi Jewish genetic diseases. Hum Mut. 2010;31:1240-1250.
Scott SA*, Cohen N*, Brandt T, Warburton PE, Edelmann L. Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome. Hum Mol Genet. 2010;19:3383-3393. (* equal contribution)
Scott SA, Khasawneh R, Peter I, Kornreich R, Desnick RJ. Combined CYP2C9, VKORC1, and CYP4F2 allele frequencies among racial and ethnic groups. Pharmacogenomics. 2010;11:781-791.
Lubitz SA*, Scott SA*, Rothlauf E, Agarwal A, Peter I, Doheny D, van Der Zee S, Jaremko M, Desnick RJ, Halperin JL. Comparative performance of gene-based warfarin dosing algorithms in a multiethnic population. J Thromb Haemost. 2010;8:1018-1026. (* equal contribution)
Scott SA, Cohen N, Brandt T, Desnick RJ, Toruner G, Edelmann L. Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization. Genet Med. 2010;12:85-92.
Lakshmikuttyamma A, Scott SA, DeCoteau JF, Geyer CR. Reexpression of epigenetically silenced AML tumor suppressor genes by SUV39H1 inhibition. Oncogene. 2010;29:576-588.
Scott SA, Jaremko M, Lubitz SA, Kornreich R, Halperin JL, Desnick RJ. CYP2C9*8 is prevalent among African-Americans: implications for pharmacogenetic dosing. Pharmacogenomics. 2009;10:1243-1255.
Takahashi N, Kameoka Y, Yamanaka Y, Ubukawa K, Saito K, Fujishima M, Fujishima N, Saito H, Hirokawa M, Scott SA, Sawada K. Itraconazole oral solution enhanced vincristine neurotoxicity in five patients with malignant lymphoma. Intern Med. 2008;47:651-653.
Yu WP, Scott SA, Dong WF. Induction of ID1 expression and apoptosis by the histone deacetylase inhibitor (trichostatin A) in human acute myeloid leukaemic cells. Cell Prolif. 2008;41:86-97.
Scott SA, Edelmann L, Kornreich R, Desnick RJ. Warfarin pharmacogenetics: CYP2C9 and VKORC1 genotypes predict different sensitivity and resistance frequencies in the Ashkenazi and Sephardi Jewish populations. Am J Hum Genet. 2008;82:495-500.
Scott SA, Edelmann L, Kornreich R, Erazo M, Desnick RJ. CYP2C9, CYP2C19 and CYP2D6 allele frequencies in the Ashkenazi Jewish population. Pharmacogenomics. 2007;8:721-730.
Scott SA, Lakshimikuttysamma A, Sheridan DP, Sanche SE, Geyer CR, DeCoteau JF. Zebularine inhibits human acute myeloid leukemia cell growth in vitro in association with demethylation and reexpression of p15INK4B. Exp Hematol. 2007;35:263-273.
Scott SA*, Dong W*, Ichinohasama R, Hirsch C, Sheridan D, Sanche S, Geyer CR, DeCoteau JF. 5-aza-2’-deoxycytidine (decitabine) can relieve p21WAF1 repression in human acute myeloid leukemia by a mechanism involving release of histone deacetylase 1 (HDAC1) without requiring p21WAF1 promoter demethylation. Leuk Res. 2006;30:69-76. (* equal contribution)
Scott SA*, Kimura T*, Dong WF, Ichinohasama R, Bergen S, Kerviche A, Sheridan D, DeCoteau JF. Methylation status of cyclin-dependent kinase inhibitor genes within the transforming growth factor beta pathway in human T-cell lymphoblastic lymphoma/leukemia. Leuk Res. 2004;28:1293-1301. (* equal contribution)
Scott SA, Kimura T, Ichinohasama R, Bergen S, Magliocco A, Reimer C, Kerviche A, Sheridan D, DeCoteau JF. Microsatellite mutations of Transforming growth factor- receptor type II and Caspase-5 occur in human precursor T-cell lymphoblastic lymphomas/leukemias in vivo but are not associated with hMSH2 or hMLH1 promoter hypermethylation. Leuk Res. 2003;27:23-34.
Lowsky R, Magliocco A, Ichinohasama R, Reitmair A, Scott SA, Henry M, Kadin ME, DeCoteau JF. MSH2-deficient murine lymphomas harbor insertion/deletion mutations in the transforming growth factor beta receptor type 2 gene and display low not high frequency microsatellite instability. Blood. 2000;95:1767-1772.
Eric V, Yi V, Murdock D, Kalla SE, Wu TJ, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei WQ, Chung WK, Weng C, Wiesner GL, Jarvik GP, Muzny D, Gibbs RA; eMERGE Consortium. Neptune: an environment for the delivery of genomic medicine. Genet Med. 2021;23:1838-1846. [Epub 2021 Jul 13]
eMERGE Consortium. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network. Am J Hum Genet. 2019;105:588-605. [Epub 2019 Aug 20]
Gaedigk A, Sangkuhl K, Whirl-Carrillo M, Twist GP, Klein TE, Miller NA; PharmVar Steering Committee. The Evolution of PharmVar. Clin Pharmacol Ther. 2019;105:29-32. [Epub 2018 Dec 7]
Gaedigk A, Ingelman-Sundberg M, Miller NA, Leeder JS, Whirl-Carrillo M, Klein TE; PharmVar Steering Committee. The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database. Clin Pharmacol Ther. 2018;103:399-401. [Epub 2017 Nov 14]
Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS; ClinGen. ClinGen–the Clinical Genome Resource. N Engl J Med. 2015;372:2235-42.
Kimmel SE, French B, Kasner SE, Johnson JA, Anderson JL, Gage BF, Rosenberg YD, Eby CS, Madigan RA, McBane RB, Abdel-Rahman SZ, Stevens SM, Yale S, Mohler ER 3rd, Fang MC, Shah V, Horenstein RB, Limdi NA, Muldowney JA 3rd, Gujral J, Delafontaine P, Desnick RJ, Ortel TL, Billett HH, Pendleton RC, Geller NL, Halperin JL, Goldhaber SZ, Caldwell MD, Califf RM, Ellenberg JH; COAG Investigators. A pharmacogenetic versus a clinical algorithm for warfarin dosing. N Engl J Med. 2013;369:2283-2293. [Epub 2013 Nov 19.]
Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, Sanderson SC, Kannry J, Zinberg R, Basford MA, Brilliant M, Carey DJ, Chisholm RL, Chute CG, Connolly JJ, Crosslin D, Denny JC, Gallego CJ, Haines JL, Hakonarson H, Harley J, Jarvik GP, Kohane I, Kullo IJ, Larson EB, McCarty C, Ritchie MD, Roden DM, Smith ME, Böttinger EP, Williams MS; eMERGE Network. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med. 2013;15:761-771. [Epub 2013 Jun 6.]
Pratt VM, Scott SA. Personalized medicine in cancer treatment. In: Diagnostic Molecular Pathology, 2nd Edition. Coleman WB, and Tsongalis G, eds. Academic Press, New York, NY. In press.
Scott SA. Clopidogrel pharmacogenetics case. In: Genomics in the Clinic. Jabs EW and Kline AD, eds. Elsevier, New York, NY. In press.
Scott SA. Thiopurine for acute lymphoblastic leukemia. In: Genomics in the Clinic. Jabs EW and Kline AD, eds. Elsevier, New York, NY. In press.
Scott SA. Warfarin for atrial fibrillation. In: Genomics in the Clinic. Jabs EW and Kline AD, eds. Elsevier, New York, NY. In press.
Diaz G, McMahon FJ, Scott SA, Hagerman R, Kline AD. Clinical genetics and referrals. In: Genomics in the Clinic. Jabs EW and Kline AD, eds. Elsevier, New York, NY. In press.
Owusu Obeng A, Samwald M, Scott SA. Reactive, point-of-care, pre-emptive and direct-to-consumer pharmacogenomic testing. In: Pharmacogenomics: Challenges and Opportunities in Therapeutic Implementation, 2nd Edition. Lam YWF and Scott SA, eds. Elsevier, New York, NY. pp. 369-384, 2018
Botton MR, Campos KC, Duconge J, Scott SA. Pharmacogenomics in Latin American populations. In: Pharmacogenomics: Challenges and Opportunities in Therapeutic Implementation, 2nd Edition. Lam YWF and Scott SA, eds. Elsevier, New York, NY. pp. 329-368, 2018.
Lam YWF, Scott SA. Pharmacogenomics in cancer therapeutics. In: Pharmacogenomics: Challenges and Opportunities in Therapeutic Implementation, 2nd Edition. Lam YWF and Scott SA, eds. Elsevier, New York, NY. pp. 123-132, 2018.
Yang Y, Scott SA. DNA Methylation profiling using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). In: Functional Genomics, 3rd Edition. Methods Mol Biol; 1654. Kaufmann M, Klinger C, Savelsbergh A, eds. Springer, New York, NY. pp. 125-134, 2017.
Pratt VM, Scott SA. Personalized medicine in cancer treatment. In: Diagnostic Molecular Pathology. Coleman WB, and Tsongalis G, eds. Academic Press, New York, NY. pp. 503-513, 2016.
Obeng AO, Scott SA. Pharmacogenetics of antiplatelet drugs. In: Pharmacogenomics: Applications to Patient Care, 3rd Edition. Johnson JA, Ellingrod V, Kroetz D, and Kuo G, eds. American College of Clinical Pharmacy, Lenexa, KS. pp. 65-78, 2014.
Scott SA, Lyon E. Pharmacogenetics. In: Molecular Pathology in Clinical Practice, 2nd Edition. Leonard DGB, ed. Springer Publishing Company, New York, NY. pp. 301-312, 2016.
Scott SA. Implementing clinical pharmacogenetics: Point-of-care and pre-emptive testing. In: Handbook of Pharmacogenomics and Stratified Medicines. Padmanabdhan S, ed. Elsevier, Oxford, UK. pp. 921-929, 2014.
Scott SA, Desnick RJ. Pharmacogenetics of warfarin. In: Clinical Genomics: Practical Applications in Adult Patient Care. Murray MF, Giovanni MA, and Babyatsky M, eds. McGraw Hill Publishers, Columbus, OH. pp. 24-29, 2013.
Edelmann L, Scott SA, Liu L, Kornreich R. Molecular medical genetics. In: Molecular Genetic Pathology, 1st and 2nd Editions. Cheng L and Zhang D, eds. Humana Press Inc., Totowa, NJ, pp. 415-440, 2008.
1/29/2021: Stanford Launches Clinical Whole-Genome Sequencing for Inherited Cardiovascular Testing. Molika Ashford; GenomeWeb, https://www.genomeweb.com/sequencing/stanford-launches-clinical-whole-genome-sequencing-inherited-cardiovascular-testing#.YX3bfNnMLbc.
3/12/2019: Your Birth Control May Fail if You Have This Genetic Variant, Research Suggests. Susan Scutti; CNN, https://www.cnn.com/2019/03/12/health/birth-control-genetic-variant-study/index.html.
10/15/2017: Copy Number Variation Probes Inform Diverse Applications. Richard A. Stein; GEN News, https://www.genengnews.com/gen-articles/copy-number-variation-probes-inform-diverse-applications/6178.
10/11/2016: Long-Read CYP2D6 Sequencing Enables Full Gene Characterization and Novel Allele Discovery. Stuart A. Scott, Ph.D. and Yao Yang, Ph.D.; Drug Discovery & Development, http://www.dddmag.com/article/2016/10/long-read-cyp2d6-sequencing-enables-full-gene-characterization-and-novel-allele-discovery.
9/26/2016: Researchers Hope PharmCAT Tool Will Help Improve Clinical Implementation of Pharmacogenomics. Julia Karow; GenomeWeb, https://www.genomeweb.com/molecular-diagnostics/researchers-hope-pharmcat-tool-will-help-improve-clinical-implementation.
9/8/2016: Pharmacogenetics: The Right Drug for You. Liam Drew; Nature, 537, S60–S62 (08 September 2016) doi:10.1038/537S60a0.
9/1/2016: Pharmacogenetics Informs Clinical Practice. DeeAnn Visk, Ph.D.; GEN News, http://www.genengnews.com/gen-articles/pharmacogenetics-informs-clinical-practice/5816/.
6/15/2016: Determining a Drug Response. Sonya Collins; Genome Magazine, http://genomemag.com/pharmacogenomics/#.V5NbPY4pOt8.
3/19/2015: The Right Drug the First Time. Aaron Krol; Bio-IT World & Clinical Informatics News, http://www.bio-itworld.com/2015/3/19/right-drug-first-time.html.
3/5/2015: Copy Number Variations’ Effect on Drug Response Still Overlooked. Cassandra Willyard; Nature Medicine, 21, 206 (2015) doi:10.1038/nm0315-206.
3/12/2013: Mount Sinai Group Publishes Allele-Specific PCR Assay for Novel CYP2C19 Variants. Ben Butkus; GenomeWeb, https://www.genomeweb.com/pcrsample-prep/mount-sinai-group-publishes-allele-specific-pcr-assay-novel-cyp2c19-variants.
8/15/2012: Without Tests, Heart Drug May Not Work. Elie Dolgin; The Jewish Daily FORWARD, http://forward.com/articles/160778/without-tests-heart-drug-may-not-work/.
2022-present: Medical Genetics Residency Didactics
Department of Pediatrics, Division of Medical Genetics; Lecturer.
2009, 2017-2020: Molecular Biology and Genetics
New York College of Podiatric Medicine, New York, NY; Lecturer.
2012-present: Spectrum of Methods in Clinical Research 3
Clinical Research Training Program, Icahn School of Medicine at Mount Sinai, New York, NY; Lecturer.
2017-present: Medical Genetics Seminar
Joan H. Marks Graduate Program in Human Genetics, Sarah Lawrence College, Bronxville, NY; Lecturer.
2017-present: Advanced Laboratory Genomics Course
Division of Genomic Diagnostics at CHOP, Philadelphia, PA; Lecturer.
2019-present: Laboratory Management Seminar Series
Sema4/Icahn School of Medicine at Mount Sinai, New York, NY; Lecturer.
2022-present: LGG Core Curriculum Course
Department of Human Genetics, University of Chicago, Chicago, IL; Lecturer.
2010-2020: Medical Genetics
1st year genetic counseling students and ACGME/ABMGG clinical genetics fellows; Lecturer.
2010-2020: Molecular Cellular and Genomic Foundations
1st year medical students; Lecturer.
2011-2017: Translational Genomics, BSR2400
Elective graduate course; Co-Director (with Dr. Andrew SHARP), Lecturer.
2013-2016: Introduction to Human Genome Sequencing, BSR2401
Elective graduate course; Lecturer.
2013-2020: Practical Analysis of Your Human Genome, BSR6402
Elective graduate course; Lecturer.
2016-2020: Laboratory Medicine, Department of Pathology
Seminar Series; Lecturer.
2017-2020: Biomedical Science, BSR1012
Core graduate course; Lecturer.
The CYP2D6 variant call format (VCF) Translator v2.0 converts CYP2D6 sequence variants from a .vcf file with GRCh37/hg19 coordinates to the M33388.1 and AY545216.1 GenBank reference sequence coordinates used for CYP2D6 star (*) allele conversion by the Human Cytochrome P450 (CYP) Allele Nomenclature Committee.
Additional details on the CYP2D6 VCF Translator can be found at Qiao W, et al. Pharmacogenomics J. 2017;17:301-303. [Epub 2016 Mar 15.]
Questions or comments can be sent here.
Amplicon Long-read Error Correction (ALEC) was developed to correct sequencing errors [substitutions and insertion/deletions (indels)] from third-generation PacBio and Oxford Nanopore long-read sequencing. The ALEC script with additional details on its functionality is accessible at Github: https://github.com/scottlab/ALEC.git
For information on the development of ALEC with the CYP2D6 gene and long-read PacBio sequencing, see Qiao W and Yang Y, et al. 2016;37:315-23. [Epub 2015 Dec 18.]
Questions or comments can be sent here.
To address the need for a stand-alone program capable of analyzing data from targeted bisulfite sequencing technologies, we developed HiTMAP: a High Throughput Methylation Analysis Program. HiTMAP is a web tool that takes raw amplicon bisulfite sequence data and demultiplexes against sample barcodes, aligns sequencing reads to in silico converted genomic reference sequences, quantitates CpG methylation levels, and exports resulting methylation data for both individual CpG sites and amplicon regions. The user-facing side of HiTMAP provides an online interface for uploading raw sequence and reference files, setting alignment and methylation quantitation parameters, and for retrieving and saving analysis output data and result figures. HiTMAP eliminates the need for manual data manipulation, local computational resources and expertise, and provides an efficient mechanism to measure CpG methylation from high-throughput next-generation bisulfite sequencing data.
Please note that the HiTMAP manuscript is currently in preparation. Questions or comments can be sent here.
Creative and eager clinical residents and fellows, graduate students, postdoctoral fellows, summer students, international rotation students, and undergraduate students with shared research interests in human genetics and genomics are encouraged to inquire about potential opportunities. If that is you, please email your updated CV directly and include a summary of your research interests, goals, and timeline. Emphasis is currently placed on individuals with experience/interest in bioinformatics, pharmacogenomics, Mendelian disease genomics, and/or clinical provider engagement with genomic medicine implementation.
Stuart A. SCOTT, PhD
Department of Pathology
300 Pasteur Dr
Stanford, CA 94305
Clinical Genomics Laboratory
3375 Hillview Ave
Palo Alto, CA 94304