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Midhat Farooqi, MD, PhD, FCAP

TitleDirector, Molecular Oncology, Center for Pediatric Genomic Medicine
InstitutionChildren's Mercy Kansas City
DepartmentPathology and Laboratory Medicine
Address2401 Gillham Rd
Kansas City MO 64108
ORCID ORCID Icon0000-0002-5238-1349 Additional info
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    Other Positions
    TitleProfessor
    InstitutionUniversity of Missouri-Kansas City
    DepartmentPathology and Laboratory Medicine

    TitleAdjunct Faculty
    InstitutionUniversity of Kansas Medical Center
    DepartmentPathology and Laboratory Medicine


    Collapse Biography 
    Collapse education and training
    University of Texas Southwestern Medical Center, Dallas, TXMD, PhD2012Molecular Genetics
    Hospital of the University of Pennsylvania, Philadelphia, PAResidency2013Anatomic & Clinical Pathology
    University of Texas Southwestern Medical Center, Dallas, TXResidency2015Clinical Pathology
    Hospital of the University of Pennsylvania, Philadelphia, PAFellowship2016Molecular Genetic Pathology

    Collapse Overview 

    Collapse Research 
    Collapse research overview
    As a molecular pathologist, Dr. Farooqi interprets clinical genetic testing results for both pediatric and adult patients in the setting of inherited disease and oncology, including whole exome sequencing and tumor somatic profiling. His clinical interests involve the development of new clinical diagnostic tests, especially for pediatric oncology. His research interests include epigenetic profiling and single cell sequencing of pediatric liquid and solid tumors. Dr. Farooqi works closely with Dr. Erin Guest and other researchers at the Genomic Medicine Center (GMC). The scientists in the GMC have extensive experience in all aspects of sequencing and have supported two clinical trials studying leukemia in children and infants—T2016-003 and AALL0631—by performing and analyzing whole genome, whole exome, bulk RNA, whole genome bisulfite, single cell, and long read sequencing of patient samples in collaboration with Johns Hopkins University and the Children's Hospital of Philadelphia. The research team will be performing similar work for two current trials: AALL15P1 (studying infant leukemia) and NCT02789228 (studying multi-antigen specific lymphocytes for the treatment of pediatric solid tumors); Dr. Farooqi is the Principal Investigator for the sequencing project supporting NCT02789228. He is also the Principal Investigator for a grant from the National Cancer Institute centered around sequence data sharing from pediatric tumors in support of the nationwide Childhood Cancer Data Initiative. Dr. Farooqi looks forward to additional collaborative sequencing projects, especially in the areas of pediatric oncology and cancer immunotherapy.
    Collapse research activities and funding
         (Midhat Farooqi)Dec 1, 2019 - Jun 30, 2024
    Braden’s Hope For Childhood Cancer
    Targeting Solid Tumors with Multi-antigen Specific T cells by Identifying the Genetic and Epigenetic Determinants of Therapeutic Response
    Role: Principal Investigator

    3P30CA168524-09S3     (Midhat Farooqi)Jul 1, 2020 - Jun 30, 2022
    National Cancer Institute
    Free the Data: Open Sharing of Comprehensive Genomic Childhood Cancer Datasets
    Role: Principal Investigator

         (Terrie Flatt)Oct 1, 2020 - Jun 30, 2024
    Masonic Cancer Alliance
    The Genomic and Cellular Landscape in Children and Young Adults with Sarcoma
    Role: Co-Prinicpal Investigator

    Collapse Bibliography 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Guest EM, Kairalla JA, Devidas M, Hibbitts E, Carroll AJ, Heerema NA, Kubaney HR, August MA, Ramesh S, Yoo B, Farooqi MS, Pauly MG, Wechsler DS, Miles RR, Reid JM, Kihei CD, Gore L, Raetz EA, Hunger SP, Loh ML, Brown PA. Azacitidine as epigenetic priming for chemotherapy is safe and well-tolerated in infants with newly diagnosed KMT2A-rearranged acute lymphoblastic leukemia: Children's Oncology Group trial AALL15P1. Haematologica. 2024 Jun 13. PMID: 38867582.
      View in: PubMed
    2. Schmitt AD, Sikkink K, Ahmed AA, Melnyk S, Reid D, Van Meter L, Guest EM, Lansdon LA, Pastinen T, Pushel I, Yoo B, Farooqi MS. Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples. medRxiv. 2024 May 12. PMID: 38765974.
      View in: PubMed
    3. Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. medRxiv. 2024 Mar 26. PMID: 38585974.
      View in: PubMed
    4. Gonzalez E, Flatt TG, Farooqi M, Johnson L, Ahmed AA. Polypyrimidine Tract Binding Protein: A Universal Player in Cancer Development. Curr Mol Med. 2023 Oct 24. PMID: 37877563.
      View in: PubMed
    5. Meredith DM, Cooley LD, Dubuc A, Morrissette J, Sussman RT, Nasrallah MP, Rathbun P, Yap KL, Wadhwani N, Bao L, Wolff DJ, Ida C, Sukhanova M, Horbinski C, Jennings LJ, Farooqi M, Gener M, Ginn K, Kam KL, Sasaki K, Kanagal-Shamanna R, Alexandrescu S, Brat D, Lu X. ROS1 Alterations as a Potential Driver of Gliomas in Infant, Pediatric, and Adult Patients. Mod Pathol. 2023 Nov; 36(11):100294. PMID: 37532182.
      View in: PubMed
    6. Galbraith K, Vasudevaraja V, Serrano J, Shen G, Tran I, Abdallat N, Wen M, Patel S, Movahed-Ezazi M, Faustin A, Spino-Keeton M, Roberts LG, Maloku E, Drexler SA, Liechty BL, Pisapia D, Krasnozhen-Ratush O, Rosenblum M, Shroff S, Bou? DR, Davidson C, Mao Q, Suchi M, North P, Hopp A, Segura A, Jarzembowski JA, Parsons L, Johnson MD, Mobley B, Samore W, McGuone D, Gopal PP, Canoll PD, Horbinski C, Fullmer JM, Farooqui MS, Gokden M, Wadhwani NR, Richardson TE, Umphlett M, Tsankova NM, DeWitt JC, Sen C, Placantonakis DG, Pacione D, Wisoff JH, Teresa Hidalgo E, Harter D, William CM, Cordova C, Kurz SC, Barbaro M, Orringer DA, Karajannis MA, Sulman EP, Gardner SL, Zagzag D, Tsirigos A, Allen JC, Golfinos JG, Snuderl M. Clinical utility of whole-genome DNA methylation profiling as a primary molecular diagnostic assay for central nervous system tumors-A prospective study and guidelines for clinical testing. Neurooncol Adv. 2023 Jan-Dec; 5(1):vdad076. PMID: 37476329.
      View in: PubMed
    7. Gonzalez E, Ahmed AA, McCarthy L, Chastain K, Habeebu S, Zapata-Tarres M, Cardenas-Cardos R, Velasco-Hidalgo L, Corcuera-Delgado C, Rodriguez-Jurado R, Garc?a-Rodr?guez L, Parrales A, Iwakuma T, Farooqi MS, Lee B, Weir SJ, Flatt TG. Perinucleolar Compartment (PNC) Prevalence as an Independent Prognostic Factor in Pediatric Ewing Sarcoma: A Multi-Institutional Study. Cancers (Basel). 2023 Apr 10; 15(8). PMID: 37190159.
      View in: PubMed
    8. Cooley LD, Lansdon LA, Laurence K, Herriges JC, Zhang L, Repnikova EA, Joyce J, Thakor P, Warren L, Smith SC, Yoo B, Gener M, Ginn KF, Farooqi MS. Integrated genetic profiling of archival pediatric high-grade glial tumors and reassessment with 2021 WHO classification of paediatric CNS tumours. Cancer Genet. 2023 06; 274-275:10-20. PMID: 36917897.
      View in: PubMed
    9. Awotoye W, Whitt JC, Yoo B, Farooqi MS, Farrow EG, Allareddy V, Amendt BA, Rengasamy Venugopalan S. Genetic heterogeneity and enrichment of variants in DNA-repair genes in ameloblastoma. J Oral Pathol Med. 2023 Mar; 52(3):263-270. PMID: 36715450.
      View in: PubMed
    10. Elsbernd A, Boulouadnine B, Ahmed A, Farooqi M, Sandritter T, Shakhnovich V, Blanding D, Demoulin JB, Thompson J. Novel Oncogenic PDGFRB Variant in Severe Infantile Myofibromatosis With Response to Imatinib Using Therapeutic Drug Monitoring. JCO Precis Oncol. 2022 Oct; 6:e2200250. PMID: 36201717.
      View in: PubMed
    11. Lansdon LA, Cadieux-Dion M, Herriges JC, Johnston J, Yoo B, Alaimo JT, Thiffault I, Miller N, Cohen ASA, Repnikova EA, Zhang L, Farooqi MS, Farrow EG, Saunders CJ. Clinical Validation of Genome Reference Consortium Human Build 38 in a Laboratory Utilizing Next-Generation Sequencing Technologies. Clin Chem. 2022 09 01; 68(9):1177-1183. PMID: 35869940.
      View in: PubMed
    12. Ahmed AA, Farooqi MS, Habeebu SS, Gonzalez E, Flatt TG, Wilson AL, Barr FG. NanoString Digital Molecular Profiling of Protein and microRNA in Rhabdomyosarcoma. Cancers (Basel). 2022 Jan 21; 14(3). PMID: 35158790.
      View in: PubMed
    13. Shi G, Xu J, Barnes SF, Farooqi MS, Luu HS, Gotway G, Park JY. Chromosomal Microarray Reinterpretation: Applications to Pediatric Practice. J Pediatr. 2022 Apr; 243:219-223. PMID: 34953820.
      View in: PubMed
    14. Ahmed AA, Habeebu S, Farooqi MS, Gamis AS, Gonzalez E, Flatt T, Sherman A, Surrey L, Arnold MA, Conces M, Koo S, Dioufa N, Barr FG, Tsokos MG. MYOD1 as a prognostic indicator in rhabdomyosarcoma. Pediatr Blood Cancer. 2021 09; 68(9):e29085. PMID: 33913590.
      View in: PubMed
    15. Dermott SM, Kucine N, Farooqi MS, Li W, Silvey M. Polycythemia vera in a 2-year-old child with a JAK2 exon 12 deletion. Pediatr Blood Cancer. 2021 07; 68(7):e28994. PMID: 33661568.
      View in: PubMed
    16. Lansdon LA, Cadieux-Dion M, Yoo B, Miller N, Cohen ASA, Zellmer L, Zhang L, Farrow EG, Thiffault I, Repnikova EA, Cooley LD, Alaimo JT, Porath B, Herriges JC, Saunders CJ, Farooqi MS. Factors Affecting Migration to GRCh38 in Laboratories Performing Clinical Next-Generation Sequencing. J Mol Diagn. 2021 05; 23(5):651-657. PMID: 33631350.
      View in: PubMed
    17. Baker TG, Alden J, Dubuc AM, Welsh CT, Znoyko I, Cooley LD, Farooqi MS, Schwartz S, Li YY, Cherniack AD, Lindhorst SM, Gener M, Wolff DJ, Meredith DM. Near haploidization is a genomic hallmark which defines a molecular subgroup of giant cell glioblastoma. Neurooncol Adv. 2020 Jan-Dec; 2(1):vdaa155. PMID: 33392505.
      View in: PubMed
    18. Smith SC, Farooqi MS, Gener MA, Ginn K, Joyce JM, Bendorf TM, Cooley LD. Clinical Validation of Somatic Mutation Detection by the OncoScan CNV Plus Assay. J Mol Diagn. 2021 01; 23(1):29-37. PMID: 33080408.
      View in: PubMed
    19. Farooqi MS, Figueroa S, Gotway G, Wang J, Luu HS, Park JY. Reinterpretation of Chromosomal Microarrays with Detailed Medical History. J Pediatr. 2020 07; 222:180-185.e1. PMID: 32417076.
      View in: PubMed
    20. Burke MJ, Kostadinov R, Sposto R, Gore L, Kelley SM, Rabik C, Trepel JB, Lee MJ, Yuno A, Lee S, Bhojwani D, Jeha S, Chang BH, Sulis ML, Hermiston ML, Gaynon P, Huynh V, Verma A, Gardner R, Heym KM, Dennis RM, Ziegler DS, Laetsch TW, Oesterheld JE, Dubois SG, Pollard JA, Glade-Bender J, Cooper TM, Kaplan JA, Farooqi MS, Yoo B, Guest E, Wayne AS, Brown PA. Decitabine and Vorinostat with Chemotherapy in Relapsed Pediatric Acute Lymphoblastic Leukemia: A TACL Pilot Study. Clin Cancer Res. 2020 05 15; 26(10):2297-2307. PMID: 31969338.
      View in: PubMed
    21. Porath B, Farooki S, Gener M, Amudhavalli SM, Grote L, Cooley LD, Ginn K, Farooqi MS. Occurrence and characterization of medulloblastoma in a patient with Curry-Jones syndrome. Clin Genet. 2020 04; 97(4):670-671. PMID: 31825089.
      View in: PubMed
    22. Ahmed AA, Vundamati D, Farooqi M, Repnikova E, Zinkus T, Hetherington M, Paulson L. Next-Generation Sequencing in the Diagnosis of Rare Pediatric Sinonasal Tumors. Ear Nose Throat J. 2021 Jun; 100(5):NP263-NP268. PMID: 31550935.
      View in: PubMed
    23. Repnikova E, Roberts J, Mc Dermott S, Farooqi MS, Iqbal NT, Silvey M, Nolen J, Taboada E, Li W. Clinical and molecular characterization of novel deletions causing epsilon gamma delta beta thalassemia: Report of two cases. Pathol Res Pract. 2019 Oct; 215(10):152578. PMID: 31451289.
      View in: PubMed
    24. Ahmed IA, Farooqi MS, Vander Lugt MT, Boklan J, Rose M, Friehling ED, Triplett B, Lieuw K, Saldana BD, Smith CM, Schwartz JR, Goyal RK. Outcomes of Hematopoietic Cell Transplantation in Patients with Germline SAMD9/SAMD9L Mutations. Biol Blood Marrow Transplant. 2019 11; 25(11):2186-2196. PMID: 31306780.
      View in: PubMed
    25. Li W, Cooley LD, August KJ, Richardson AI, Shao L, Ahmed AA, Farooqi MS, Zwick DL. Cuplike nuclear morphology is highly associated with IKZF1 deletion in pediatric precursor B-cell ALL. Blood. 2019 07 18; 134(3):324-329. PMID: 31076445.
      View in: PubMed
    26. Ahmed AA, Vundamati DS, Farooqi MS, Guest E. Precision Medicine in Pediatric Cancer: Current Applications and Future Prospects. High Throughput. 2018 Dec 13; 7(4). PMID: 30551569.
      View in: PubMed
    27. Sussman RT, Shaffer S, Azzato EM, DeSloover D, Farooqi MS, Meyer A, Lieberman DB, Bigdeli A, Paolillo C, Ganapathy K, Sukhadia S, Rosenbaum JN, Daber RD, Morrissette JJD. Validation of a next-generation sequencing oncology panel optimized for low input DNA. Cancer Genet. 2018 12; 228-229:55-63. PMID: 30553474.
      View in: PubMed
    28. Rea B, Haun P, Emerson R, Vignali M, Farooqi M, Samimi S, Elenitsas R, Kirsch I, Bagg A. Role of high-throughput sequencing in the diagnosis of cutaneous T-cell lymphoma. J Clin Pathol. 2018 Sep; 71(9):814-820. PMID: 29636372.
      View in: PubMed
    29. Gentile C, Van Deerlin VM, Goldberg DS, Reese PP, Hasz RD, Abt P, Blumberg E, Farooqi MS. Hepatitis C virus genotyping of organ donor samples to aid in transplantation of HCV-positive organs. Clin Transplant. 2018 02; 32(2). PMID: 29220079.
      View in: PubMed
    30. Goldberg DS, Abt PL, Blumberg EA, Van Deerlin VM, Levine M, Reddy KR, Bloom RD, Nazarian SM, Sawinski D, Porrett P, Naji A, Hasz R, Suplee L, Trofe-Clark J, Sicilia A, McCauley M, Farooqi M, Gentile C, Smith J, Reese PP. Trial of Transplantation of HCV-Infected Kidneys into Uninfected Recipients. N Engl J Med. 2017 06 15; 376(24):2394-2395. PMID: 28459186.
      View in: PubMed
    31. Farooqi MS, Mitui M, Londin ER, Park JY. High Concentration Capture Probes Enhance Massively Parallel Sequencing Assays. Clin Chem. 2016 07; 62(7):1032-4. PMID: 27217445.
      View in: PubMed
    32. Davies KD, Farooqi MS, Gruidl M, Hill CE, Woolworth-Hirschhorn J, Jones H, Jones KL, Magliocco A, Mitui M, O'Neill PH, O'Rourke R, Patel NM, Qin D, Ramos E, Rossi MR, Schneider TM, Smith GH, Zhang L, Park JY, Aisner DL. Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation. J Mol Diagn. 2016 07; 18(4):572-9. PMID: 27155050.
      View in: PubMed
    33. Farooqi MS, Hashim IA. A woman with primary biliary cirrhosis and hyponatremia. Clin Chem. 2015 Aug; 61(8):1028-31. PMID: 26220582.
      View in: PubMed
    34. Farooqi MS, Lai Y, Lancaster E, Schmitt SE, Sachais BS. Therapeutic plasma exchange and immunosuppressive therapy in a patient with anti-GAD antibody-related epilepsy: quantification of the antibody response. J Clin Apher. 2015 Feb; 30(1):8-14. PMID: 24961613.
      View in: PubMed
    35. Owen JL, Zhang Y, Bae SH, Farooqi MS, Liang G, Hammer RE, Goldstein JL, Brown MS. Insulin stimulation of SREBP-1c processing in transgenic rat hepatocytes requires p70 S6-kinase. Proc Natl Acad Sci U S A. 2012 Oct 02; 109(40):16184-9. PMID: 22927400.
      View in: PubMed
    36. Evers BM, Farooqi MS, Shelton JM, Richardson JA, Goldstein JL, Brown MS, Liang G. Hair growth defects in Insig-deficient mice caused by cholesterol precursor accumulation and reversed by simvastatin. J Invest Dermatol. 2010 May; 130(5):1237-48. PMID: 20090767.
      View in: PubMed
    37. Schneider JW, Gao Z, Li S, Farooqi M, Tang TS, Bezprozvanny I, Frantz DE, Hsieh J. Small-molecule activation of neuronal cell fate. Nat Chem Biol. 2008 Jul; 4(7):408-10. PMID: 18552832.
      View in: PubMed
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