Mahdi Sarmady, PhD

Mahdi Sarmady, PhD

Mahdi Sarmady, PhD, is the director of bioinformatics of the Division of Genomic Diagnostics at Children's Hospital of Philadelphia.

Locations: Main Campus
Appointments and Referrals: 1-800-TRY-CHOP (1-800-879-2467)

Education and Training

Undergraduate Degree

BSc in Computer Engineering - University of Tehran, Tehran, Iran

Graduate Degree

PhD in Biomedical Engineering - Drexel University, Philadelphia, PA
MSc in Computer Engineering - University of Tehran, Tehran, Iran

Titles and Academic Titles

Director of Bioinformatics, Division of Genomic Diagnostics

Departments and Services

Research Interests

Clinical bioinformatics
Infectious diseases
Clinical genomic diagnostics
Biomedical informatics

Publications

Papers

2015

Kelsen J, Dawany N, Moran CJ, Petersen B, Franke A, Sarmady M, Sasson A, Martinez A, Pauly-Hubbard H, Maurer K, Rappaport E, Mamula P, Piccoli D, Artis D, Sonnenberg GF, Sullivan KE, Winter HS, Daly M, Baldassano RN, Devoto M. Exome Sequencing Analysis of Candidate Primary Immunodeficiency Genes in Very Early Onset Inflammatory Bowel Disease. Gastroenterology. 2015 Nov;149(6):1415-24. doi: 10.1053/j.gastro.2015.07.006. Epub 2015 Jul 17.

Li M, Burnton J, Vijaykumar J, Haley D, Dugan N, Dulik M, Abrudan J, Rajagopalan R, Sasson A, DeChene E, Sarmady M, Conlin L, White P, Spinner NB, Krantz I, Vetter V, Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death. Hum Genomics. 2015 Jul 19;9:15. doi: 10.1186/s40246-015-0038-y.

Nesbitt A, Bhoj E, Gibson K, Denenberg E, Sarmady M, Cao K, Tischler T, Dubbs H, Zackai E, Santani A, “Exome Sequencing Identifies an Intergenic Denovo Mutation in SOX5 associated with intellectual disability syndrome”, American Journal of Medical Genetics, Part A, June 2015.

2013

Zhang Z, Leipzig J, Sasson A, Yu AM, Perin JC, Xie HM, Sarmady M, Warren PV, White PS. “Efficient digest of high- throughput sequencing data in a reproducible report”. BMC Bioinformatics 2013 14(Suppl 11):S3.

Books

Chapters

Lott MT, Leipzig J, Derbeneva O, Xie M, Sarmady M, Procaccio V, Wallace DC, “mtDNA Variation and Analysis Using Mitomap and Mitomaster”, Current Protocols in Bioinformatics 1.23.1-1.23.26 December 2013

Posters and Presentations

2015

Wu C, Jayaraman P, Cao K, Deardorff MA, Krantz ID, Spinner NB, Santani AB, Sarmady M, “Efficient Interpretation of Clinical Exomes Using a Network-based Approach”, Association for Molecular Pathology (AMP) Annual Meeting 2015, Austin TX, Nov. 2015.

Wu C, Deardorff MA, Sarmady M, “Random Walk on Ontology for Rare Disorder Diagnosis”, American Society of Human Genetics (ASHG) Conference 2015, Baltimore MD, Oct 2015.

Cao K, Yu Z, Gibson KM, Funke BH, Santani AB, Sarmady M, “Development and Implementation of a Bioinformatics Framework to Address Pseudogenes in Clinical Whole-Exome Test”, American Society of Human Genetics (ASHG) Conference 2015, Baltimore MD, Oct 2015.

Jayaraman P, Mackiewicz K, Clark PM, Sarmady, M, Monos D, “AnthOligo: Automated design of hybridization oligonucleotides for region-specific extraction of large contiguous DNA fragments”, American Society of Human Genetics (ASHG) Conference 2015, Baltimore MD, Oct 2015.

2014

Basile K, Sasson A, Guy V, Perin C, Sarmady M, Grant S, “Whole Exome Sequencing in Families with Latent Autoimmune Diabetes of Adults (LADA) Reveals Novel Candidate Loci”, American Diabetes Association Scientific Sessions, San Francisco CA, June 2014

Kelsen R, Moran CJ, Sasson A, Sarmady M, Gupta K, Hubbard H, Rappaport E, Stolle C, Mamula P, Grossman A, Piccoli D, Winter H, Baldassano R, DeVoto M, “Exome Sequencing Analysis of Candidate Genes in Very Early Onset IBD”, American Gastroenterological Association Annual Meeting, Chicago IL, May 2014

Italia M, Ruth B, Sarmady M, Perin JC, Naegely D, Santani A, Dulik M, Abrudan J, Spinner NB, Krantz I, Pennington J, White P, “Varify: An open-source solution for genome-scale clinical diagnostics and knowledge capture”, American College of Medical Genetics (ACMG) Annual Clinical Genetics Meeting, Nashville, TN, March 2014

Cao K, Gibson K, Yu Z, Tischler T, Sarmady M, Warren P, Stolle C, Santani A, “Establishing Reliable Performance Characteristics for a Clinical Whole-Exome Sequencing (WES) Test”, American College of Medical Genetics (ACMG) Annual Clinical Genetics Meeting, Nashville, TN, March 2014

Dorschner M, Wagle N, Buhay C, Carneiro M, Muzny D, McGee S, Sasson A, Salisbery J, Leschiner I, Gowrisankar S, Hutter C, Wilhelmsen K, Santani A, Sarmady M, Rehm H, Garraway L, Nickerson D, “Quality of Clinical Sequence Data for Medically Relevant Targets”, American College of Medical Genetics (ACMG) Annual Clinical Genetics Meeting, Nashville, TN, March 2014

Santani A, Manelker D, Rhodenizer D, Cao K, Sasson A, Sarmady M, Yu Z, Tischler T, da Silva C, Shakhbatyan R, Gowrisankar S, Church D, Funke B, Hedge M, “Finishing the Exome: The Medical Exome Project”, American College of Medical Genetics (ACMG) Annual Clinical Genetics Meeting, Nashville, TN, March 2014

Dickinson A, Abrudan J, Brunton J, VijayKumar J, Sasson A, Sarmady M, Dulik M, DeChene E, Noon S, Wilkens A, Kaur M, Conlin L, Tilton R, Spinner NB, White P, Krantz I, “Application of Exome Sequencing as a Diagnostic Tool for Bilateral Sensorineural Hearing Loss”, American College of Medical Genetics (ACMG) Annual Clinical Genetics Meeting, Nashville, TN, March 2014

White P, Italia M, Karavite D, Miller J, Masino A, Naegely D, Perin JC, Ruth B, Sarmady M, Sasson A, Abrudan J, DeChene E, Dulik M, Wilkens A, Michel J, Grundmeier R, Krantz I, Stolle C, Santani A, Spinner NB, Pennington J, “Bedside to Bedside: Seamless Collection, Analysis, and Delivery of Genomic Data in a Diagnostic Setting”, American College of Medical Genetics (ACMG) Annual Clinical Genetics Meeting, Nashville, TN, March 2014

Li M, Burnton J, Vijaykumar J, Haley D, Dugan N, Dulik M, Abrudan J, Rajagopalan R, Sasson A, DeChene E, Sarmady M, Conlin L, White P, Spinner NB, Krantz I, Vetter V, “Utility and limitations of exome sequencing as a genetic
diagnostic tool for pediatric disorders: Sudden cardiac arrest/sudden cardiac death as a model”, American College of Medical Genetics (ACMG) Annual Clinical Genetics Meeting, Nashville, TN, March 2014

2013

Kelsen J, Moran C, Sarmady M, Sasson A, Gupta K, Pauly-Hubbard H, Fish S, Rappaport E, Stolle C, Winter H, Baldassano R, Devoto M, “Exome Sequencing Analysis of Candidate Genes in Very Early Onset Inflammatory Bowel Disease”, Advances in Inflammatory Bowel Diseases: Crohn’s & Colitis Foundations Clinical and Research Conference, Hollywood FL, December 2013

Yu Z, Tanya T, Sarmady M, Sasson A, Perin, Pennington J, White P, Ruth B, Italia M, McLarney B, Brown-Kipphut B, Conlin L, Warren P, Zook J, Stolle C and Santani A. “Development and Validation of a Diagnostic Test For Five Distinct Genetic Disorders with Heterogeneous Genetic Etiology Using Next Generation Sequencing” AMP 2013 Annual Meeting – Phoenix – Az November 2013

Santani A, Gowrisankar S, Mandelker D, Sarmady M, Sasson A, da Silva C, Shakhbatyan R, Hegde M, Funke B. “From genes to genomes – defining and validating the medical exome for clinical diagnostic applications” AMP 2013 Annual Meeting – Phoenix, Az November 2013

Yu Z, Sarmady M, Tischler T, Brown-Kipphut BA, Shafiq M, Fernandes NN, Fan Z, Boltz MS, McKnight JB, McLarney BN, Davidson L, Italia M, Pennington JW, White P, Warren P, Stolle C, Santani A, “Implementation of a Quality Assurance Program for Next Generation Sequencing Based Tests” ASHG 2013 Annual Meeting – Boston, MA October 2013

Italia MJ, Ruth B, Sarmady M, Perin JC, Naegely D, Santani, Dulik M, Spinner NB, Krantz ID, Pennington JW, White PS “From big data to smart data: an open-source solution for genome-scale variant data warehousing and discovery”, ASHG 2013 Annual Meeting – Boston, MA October 2013

Vijayakumar J, Brunton J, Sasson A, Sarmady M, Abrudan JL, Dulik M, DeChene E, Noon S, Wilkens A, Dickinson A, Kaur M, Conlin L, Spinner NB, White P, Krantz I. “Utility and Limitations of Exome Sequencing for the Molecular Diagnosis of Bilateral Sensorineural Hearing Loss” ASHG 2013 Annual Meeting – Boston, MA October 2013

Dulik M, DeChene E, Conlin L, Mulchandani S, Santani A, Abrudan J, Italia M, Sarmady M, Bernhardt B, Stolle C, Pyeritz RE, Wilkens A, Noon S, White P, Krants ID, Spinner NB. “Practical assessment of incidental finding recommendations for use in clinical exome testing” ASHG 2013 Annual Meeting – Boston, MA October 2013

Santani A, Gowrisankar S, da Silva C, Mandelker D, Sasson A, Sarmady M, Shakhbatyan R, Tinker S, Church D, Funke B, Hegde M. “THE MEDICAL EXOME PROJECT: From concept to implementation” ASHG 2013 Annual Meeting – Boston, MA October 2013

2012

Zhang Z, Leipzig J, Sasson A, Perin J, Xie M, Sarmady M, Warren P, White P, “BAMCHOP: A bioinformatics utility to summarize and visualize exome and other types of targeted resequencing data”, BIBM 2012 – Philadelphia, October 2012

Santani A, Tischler T, Sasson A, Perin J, Sarmady M, Frackelton E, Tweddale B, Abdel-Magid N, Panossian S, Warren P, Feret H, Deardorff M, Zackai E, Wilkens A, Italia M, Ruth B, Miller J, Zackai E, Monos D, Rappaport E, Hakonarson H, White P, Stolle C “A Next Generation Sequencing Assay for The Diagnosis of The Noonan Spectrum of Disorders”, ASHG 2012 – San Francisco, November 2012

Nargesian F, Ghanavati S, Sarmady M, “Methods of Finding Common Motifs in Body Proteins and HIV-1 Proteins”, 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2012) – Long Beach – CA, July 2012

Wood A, Levenstien M, Laudenslager M, Krytska K, Sarmady M, Perin J, Rappaport E, Maris J.M, Devoto M, Mossé Y.P, “Identification of a new hereditary neuroblastoma predisposition locus at chromosome 2p25”. Advances in Neuroblastoma Research - Toronto – Canada, June 2012

Awards and Honors

2007-2008, Calhoun Fellowship Drexel University for outstanding PhD students
Dean Awarded Student Member of IEEE, University of Tehran Section

Editorial and Academic Positions

March 2013-present, BMC Bioinformatics Journal, Reviewer