Faculty > Faculty By Appointment > Shashikant Kulkarni, PhD

Associate Professor, Pathology and Immunology
Associate Professor of Pediatrics
Associate Professor of Genetics
Head of Clinical Genomics, Genomics and Pathology Services
Director, Cytogenomics and Molecular Pathology
4320 Forest Park Blvd., Cortex Building, 2nd Floor, Room 207J
Office: (314) 454-8418
Lab: (314) 362-2258
Pub Med Search


Our lab's principle research interest is delineation of novel GENOMIC STRUCTURAL AND SINGLE NUCLEOTIDE VARIANTS in cancer.

Our focused interest is in studying the GENOMIC VARIANTS in Acute Myeloid Leukemia (AML) and MULTIPLE MYELOMA.

We use genome-wide tools for comprehensive molecular characterization of genomic aberrations associated with cancer including conventional Cytogenetics, FISH, Chromosomal Microarray (CMA), Molecular barcoding and Next-Generation sequencing (NGS). Unveiling key genomic drivers, prognostic and diagnostic indicators in cancer will help bring earlier and better interventions to cancer patients.

Other efforts include molecular pathology and bioinformatic studies to identify genomic signatures that would provide powerful means to understand cancer biology, to develop novel therapeutics and to constantly improve cost-effective, clinically actionable diagnostic markers.

Editorial Responsibilities

2014 - PresentEditorial BoardCancer Genetics
2012 - PresentReviewerElsevier Academic Press
2012 - PresentEditorial BoardClinical Genomics, Clinical and Translational Medicine
2012 - PresentEditorial BoardJournal of Prenatal Medicine
2010 - PresentPeer reviewerExpert Reviews of Molecular Diagnostics
2010 - PresentPeer reviewerJournal of Molecular Diagnostics
2001 - PresentPeer reviewerBlood
1998 - PresentPeer reviewerBone Marrow Transplanatation

Service to the Department

2012 - PresentSiteman Cancer Center Clinical Trials Working Group
2011 - PresentHead of Clinical Genomics, Genomics and Pathology Services at Washington University
2008 - PresentDirector, American Board of Medical Genetics (ABMG) fellowship training program
2006 - PresentMedical Director, Cytogenomics and Molecular Pathology
2006 - PresentDirector, Clinical and Molecular Cytogenetics Core

Service to the University

2012 - PresentSiteman Breast Cancer Research Program Leadership Committee
2011 - PresentCourse Faculty, BIO5285: Fundamentals of Mammalian Genetics
2010 - PresentLecturer, Medical Genetics, Washington University School of Medicine
2009 - PresentMember, Siteman Cancer Center
2009 - PresentExecutive Committee of the Faculty Council (ECFC)- Clinical Department Representative
2006 - PresentCollaborator, Core Resource (CDI) Affymetrix Core Structural Chromosomal Variants in Children with Congenital Anomalies, Children
2006 - PresentLecturer, Human Genetic Course, Washington University
2006 - PresentGenomics Curriculum Working Group- to develop a genomics curriculum plan for medical students

Diagnostic Expertise

Cytogenomics and Molecular Pathology (Prenatal, Pediatrics and Cancer)
Genomic Copy Number and Copy Neutral Aberrations in Cancer and Constitutinal Genomic Disorders
Clinical Genomics, Application of Next Generation sequencing for Cancer and Constitutional Genomic disorders

Clinical Interest

Laboratory and Genomic Medicine - DNA Diagnostics
Laboratory and Genomic Medicine - Molecular Pathology

Selected Publications

Catherine E Cottrell, Hussam Al-Kateb, Andrew J Bredemeyer, Eric J Duncavage, David H Spencer, Haley J Abel, Christina M Lockwood, Ian S Hagemann, Stephanie M O’Guin, Lauren C Burcea, Christopher S Sawyer, Dayna M Oschwald, Jennifer L Stratman, Dorie A Sh. Validation of a next-generation sequencing assay for clinical molecular oncology. The Journal of Molecular Diagnostics, 2014 Abstract

Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, ….Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, Dipersio JF, Ding L, Mardis ER, Wilson RK. The Origin and Evolution of Mutations in Acute Myeloid Leukemia. Cell, Volume 150, Issue 2, 20 July 2012, Pages 264-278,, 2012 Abstract

Vishwanathan Hucthagowder, Rekha Meyer, Chelsea Mullins, Rakesh Nagarajan, John F. DiPersio, Ravi Vij, Michael H. Tomasson and Shashikant Kulkarni. Resequencing Analysis of the Candidate Tyrosine Kinase and RAS Pathway Gene Families in Multiple Myeloma. Cancer Genetics, 2012 Abstract

Amy S Gargis, Lisa Kalman, Meredith W Berry, David P Bick, David P Dimmock, Tina Hambuch, Fei Lu, Elaine Lyon, Karl V Voelkerding, Barbara A Zehnbauer, …, Shashikant Kulkarni, … Ira M Lubin. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature Biotechnology 30, 1033–1036 (2012),, 2012 Abstract

Mills KI, Anderson J, Levy PT, Cole FS, Silva JN, Kulkarni S, Shinawi M. Duplication of 20p12.3 associated with familial Wolff-Parkinson-White syndrome. Am J Med Genet A. 2012 Dec 13., 2012 Abstract

Spencer DH, Abel HJ, Lockwood CM, Payton JE, Szankasi P, Kelley TW, Kulkarni S, Pfeifer JD, Duncavage EJ. Detection of FLT3 Internal Tandem Duplication in Targeted, Short-Read-Length, Next-Generation Sequencing Data. J Mol Diagn. 2012 Nov 13., 2012 Abstract

Hucthagowder V, Liu TC, Paciorkowski AR, Thio LL, Keller MS, Anderson CD, Herman T, Dehner LP, Grange DK, Kulkarni S. Chromosome 2p15p16.1 microdeletion syndrome: 2.5 Mb deletion in a patient with renal anomalies, intractable seizures and a choledochal cyst. Eur J Med Genet. 2012 Apr 22, 2012 Abstract

Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DA, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D……, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis ER, Wilson RK, DiPersio JF. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature (2012)., 2012 Abstract

Uy GL, Rettig MP, Motabi IH, McFarland K, Trinkaus KM, Hladnik LM, Kulkarni S, Abboud CN, Cashen AF, Stockerl-Goldstein K, Vij R, Westervelt P, and DiPersio JF. A phase I/II study of chemosensitization with the CXCR4 antagonist plerixafor in relapsed or refractory acute myeloid leukemia. Blood -2011., 2012 Abstract

Stankiewicz P, Kulkarni S, Dharmadhikari AV, Sampath S, Bhatt SS, Shaikh T, Xia Z, Pursley AN, Cooper LM, Shinawi M, Paciorkowski A, Grange DK, Noetzel M, Saunders S, Simons P, Summar M,Lee B, Scaglia F, Fellmann F, Martinet D, Beckmann JS, Asamoah A, Pl. Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low-copy repeats. Human Mutation. 2012 Jan;33(1):165-79., 2011 Abstract

Klco JM; Kulkarni S; Kreisel FH; Nguyen TDT; Hassan A; Frater JL. Immunohistochemical Analysis of Monocytic Leukemias: Usefulness of CD14 and Kruppel-like Factor 4, a Novel Monocyte Marker. American Journal of Clinical Pathology 2011;135(5):720-30, 2011 Abstract

Kreisel F*, Kulkarni S*, Kerns R, Deshmukh H, Nagarajan R, Frater J, Hassan A, Cashen A. Array Comparative Genomic Hybridization (aCGH) Identifies Genetic Changes Exclusive to Chemotherapy-Refractory or Chemotherapy-Responsive Diffuse Large B-Cell Lymphomas. Cancer Genet. 2011 Mar;204(3):129-37, 2011 Abstract

Link, DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, Bender HF, Fulton LL, Delehaunty KD, Fronick CC, Appelbaum EL, Schmidt H, Maupin R, O’Laughlin M, Chen K,. The identification of a novel TP53 germline mutation through whole genome sequencing of a patient with therapy-related AML. JAMA- The Journal of American Medical Association. 2011;305(15):1568-1576, 2011 Abstract

Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, Wallis J, Chen K, Payton JE, Fulton RS, Veizer J, Schmidt H, Vickery TL, Heath S, Watson MA, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Ley TJ, Wilson RK. Use of whole genome sequencing to diagnose a cryptic fusion oncogene. JAMA-The Journal of American Medical Association. 2011;305(15):1577-158, 2011 Abstract

Copy number variants and infantile spasms: evidence for abnormalities in ventral forebrain development and pathways of synaptic function. Paciorkowski AR, Thio LL, Rosenfeld JA, Gajecka M, Gurnett CA, Kulkarni S, Chung WK, Marsh ED, Gentile M, Reggin JD, Wheless JW, Balasubramanian S, Kumar R, Christian SL, Marini C, Guerrini R, Maltsev N, Shaffer LG, Dobyns WB. Eur J Hum Genet, 2011 Abstract

Martin MG, Welch J, Uy GL, Fehniger TA, Kulkarni S, Duncavage EJ, and Walter MJ. Limited engraftment of low-risk myelodysplastic syndrome cells in NOD/SCID gamma-C chain knockout mice. Leukemia (2010) 24, 1662–1664, 2010 Abstract

Hulick PJ, Noonan KM, Kulkarni S, Donovan DJ, Listewnik M, Ihm C, Stoler JM, Weremowicz S. Cytogenetic and array-CGH characterization of a complex de novo rearrangement involving duplication and deletion of 9p and clinical findings in a 4-month-old female. Cytogenet Genome Res. 2009;126(3):305-12, 2009 Abstract

Zhang B, Chang B, Fu M, Huang J, Kashyap R, Salavaggione E, Jain S, Kulkarni S, Deardorff MA, Uzielli MLG, Dorsett D, Beebe DC, Jay PY, Heuckeroth RO, Krantz I, and Milbrandt J. Dosage Effects of Cohesin Regulatory Factor PDS5 on Mammalian Development: Implications for Cohesinopathies. PLoS ONE, 2009 4(5), 2009 Abstract

McDonald S, Wilson DB, Pumbo E, Kulkarni S, Mason PJ, Else T, Bessler M, Ferkol T and Shenoy S. Acquired Monosomy 7 Myelodysplastic Syndrome in a Child with Clinical Features Suggestive of Dyskeratosis Congenita and IMAGe Association. Pediatr Blood Cancer. 2009 Sep 16;54(1):154-157., 2009 Abstract

Hamvas A. Nogee LM, Wegner DJ, DePass K, Christodoulou J, Bennetts B, McQuade LR, Gray PH, Deterding RR, Carroll TR, Kammesheidt A, Kasch LM, Kulkarni S, Cole FS. Inherited surfactant deficiency due to uniparental disomy of rare mutations in the surfactant protein-B and ATP binding cassette, subfamily A, member 3 genes. J Pediatr. 2009 Jul 31, 2009 Abstract

Mahowald GK, Baron JM, Mahowald MA, Moon C, Bassing CH, Kulkarni S, Bredemeyer A and Sleckman BP. Breakpoint target restrictions for aberrantly resolved DNA double stranded breaks in ATM-deficient lymphocytes. Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18339-44., 2009 Abstract

Kulkarni S, Nagarajan P, Wall J, Donovan D, Donell RL, Ligon AH, Venkatachalam S, Quade BJ. Disruption Of Chromodomain Helicase DNA Binding Protein 2 (CHD2) Causes Scoliosis. Am J Med Genet 2008 May 1;146A(9):1117-27, 2008 Abstract

Klco JM, Kreisel FH, Zehnbauer BA, Kulkarni S, Hassan A, Frater JL. The spectrum of adult B-lymphoid leukemias with BCR-ABL: molecular diagnostic, cytogenetic, and clinical laboratory perspectives. Am J Hematol. 2008 Sep 19. [Epub ahead of print], 2008 Abstract

Higgins AW, Alkuraya FS, Bosco AF, Bruns, GA, Donovan DJ, Eisenman R, Fan Y, Farra CG, Ferguson HL, Gusella JF, Harris DJ, Herrick SR, Kelly C, Kim HG, Kishikawa S, Kocher KM, Korf BR, Kulkarni S, Leach NT, Lemyre E, Lewis J, Ligon AH, Lu W, Mass RL, MacD. Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project.. American Journal of Human Genetics, 82, 712-722, 2008 Abstract

Saharia A, Guittat L, Crocker S, Lim A, Steffen M, Kulkarni S, Stewart SA.. Flap Endonuclease-1 Contributes To Telomere Stability. Current Biology, 2008 Apr 8;18(7):496-500., 2008 Abstract

Kulkarni S and Pfeiffer J. Cytogenetics. Book Chapter in The Washington Manual of Surgical Pathology, 1e edited by Humphrey, Pfeifer, and Dehner. Publisher: Lippincott Williams, June 2008., 2008

Lu W, van Eerde AM, Fan X, Quintero-Rivera, Kulkarni S, Ferguson H, Kim H, Sanlaville D, Andrews W, Sundaresan V, Bi W, Yan J, Giltay JC, Wijmenga C, de Jong TP, Feather S, Woolf AS, Rao Y, Lupski J, Quade BJ, Gusella JF, Morton CCand Maas R. Disruption of ROBO2 is associated with congenital anomalies of the kidney and urinary tract and confers risk of vesicoureteral reflux. Am J Hum Genet: 80(4): 616-32, 2007 Abstract

Goldman F, Bouharich R , Kulkarni S, Freeman S , Du H, Harrington H, Mason PJ, Vallejo A, Bessler M. The effect of TERC haploinsufficiency on the inheritance of telomere length. Proc Natl Acad Sci USA : 102(47): 17119-17124., 2005 Abstract

Knudson M, Kulkarni S, Ballas K, Bessler M, and Goldman F. Association of immune abnormalities with telomere shortening in autosomal-dominant dyskeratosis congenita. Blood: 105: 682-688, 2005 Abstract

Mochizuki Y, He J, Kulkarni S, Bessler M, Mason PJ. Mouse dyskerin mutations affecting mTERC levels, telomerase activity and ribosomal RNA processing. Proc Natl Acad Sci USA : 101(29): 10756-10761, 2004 Abstract

Baxter EJ, Kulkarni S, Vizmanos JL, Jaju R, Martinelli G, Testoni N, Hughes G, Calasanz MJ, Lahortiga I, Pocock CF, Dang R, Fidler C, Wainscoat JS, Boultwood J, Cross NCP. Novel translocations that disrupt the platelet-derived growth factor receptor â (PDGFR â) gene in BCR-ABL negative chronic myeloproliferative disorders. British Journal of Hematology: 120: 251-256, 2003 Abstract

Kulkarni S, Bessler M. Effect of proinflammatory cytokines on PIGA- hematopoiesis. Experimental Hematology:31(9): 770-778, 2003 Abstract

Kulkarni S, Bessler M. The effect of GPI-linked deficiency on apoptosis in mice carrying a Piga gene in hematopoietic cells. Journal of Leukocyte Biology: 72(6): 1228-33, 2002 Abstract

Bessler M, Kulkarni S, Jasinski M, Schaefer A, Keller P and Tremml G. Mice with blood cells deficient in GPI-linked proteins - The generation of murine model to investigate the pathogenesis and pathophysiology of Paroxysmal Nocturnal Hemoglobinuria (PNH). Book Chapter in Paroxysmal Nocturnal Hemoglobinuria (PNH) and Related Disorders-Molecular Aspects of Pathogenesis; 27-41. Springer Veralg Publications, 2001

Kulkarni S, Heath C, Parker S, Chase A, Iqbal S, Pocock CF, Kaeda J, Cwynarski K, Goldman JM, Cross NC. Fusion of H4/D10S170 to the platelet-derived growth factor receptor beta in BCR-ABL-negative myeloproliferative disorders with a t(5;10)(q33;q21). Cancer Res: 60(13): 3592-3598, 2000 Abstract

Kulkarni S, Reiter A, Smedley D, Goldman JM, Cross NCP. The complete genomic structure of ZNF198 and the localisation of breakpoints in t(8;13) myeloproliferative disorders. Genomics: 55: 118-121, 1999 Abstract

Kulkarni S* , Grand F*, Chase A, Goldman JM, Gordon M, Cross NC.. Frequent deletion of hSNF5/INI1, a component of the SWI/SNF complex, in chronic myeloid leukemia.. Cancer Res. 1999 Aug 15;59(16):3870-4., 1999 Abstract

How GF, Lim LC, Kulkarni S, Tan LT, Cross NCP. Two patients with novel BCR/ABL fusion transcripts (e8/a2 and e13a2) resulting from translocation breakpoints within BCR exons. British Journal of Haematology: 105: 434-436, 1999 Abstract

Reiter A, Sohal J, Kulkarni S, Chase A, Macdonald DHC, Aguiar RCT, Goncalves C, Hernandez JM, Jennings BA, Goldman JM , Cross NCP. Consistent fusion of ZNF198 to the fibroblast growth factor receptor-1 in the t(8;13)(p11;q12) myeloproliferative syndrome. Blood: 92(5): 1735-1742, 1998 Abstract

Past Trainees

In Trainings
Kiran Vij, MD