Midhat Farooqi, MD, PhD, FCAP
Title | Director, Molecular Oncology, Center for Pediatric Genomic Medicine |
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Institution | Children's Mercy Kansas City |
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Department | Pathology and Laboratory Medicine |
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Address | 2401 Gillham Rd Kansas City MO 64108
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ORCID
| 0000-0002-5238-1349 |
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vCard | Download vCard |
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Title | Professor |
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Institution | University of Missouri-Kansas City |
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Department | Pathology and Laboratory Medicine |
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Title | Adjunct Faculty |
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Institution | University of Kansas Medical Center |
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Department | Pathology and Laboratory Medicine |
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Biography University of Texas Southwestern Medical Center, Dallas, TX | MD, PhD | 2012 | Molecular Genetics | Hospital of the University of Pennsylvania, Philadelphia, PA | Residency | 2013 | Anatomic & Clinical Pathology | University of Texas Southwestern Medical Center, Dallas, TX | Residency | 2015 | Clinical Pathology | Hospital of the University of Pennsylvania, Philadelphia, PA | Fellowship | 2016 | Molecular Genetic Pathology |
Overview Research 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.
(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 |
Bibliography
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Farooqi MS, Hashim IA. A woman with primary biliary cirrhosis and hyponatremia. Clin Chem. 2015 Aug; 61(8):1028-31. PMID: 26220582.
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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.
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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.
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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.
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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.
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2008 | 1 | 2010 | 1 | 2012 | 1 | 2014 | 1 | 2015 | 1 | 2016 | 2 | 2017 | 2 | 2018 | 3 | 2019 | 5 | 2020 | 4 | 2021 | 4 | 2022 | 3 | 2023 | 6 | 2024 | 3 |
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