Email

shashikk@bcm.edu

Positions

Professor

Molecular and Human Genetics
Baylor College of Medicine
Houston, TX US

Vice Chair of Research Affairs

Molecular and Human Genetics
Baylor College of Medicine

Chief Scientific Officer

Baylor Genetics

Senior Vice President of Innovation

Baylor Genetics

Co-Program Director

American Board of Medical Genetics and Genomics (ABMGG) Laboratory Genetics Fellowship, Molecular and Human Genetics
Baylor College of Medicine
Houston, Texas

Member

Dan L Duncan Comprehensive Cancer Center
Baylor College of Medicine
Houston, Texas United States

Education

Clinical Fellowship at Harvard Medical School, Brigham and Women's Hospital

Boston, Massachusetts United States

Research Fellowship at Hammersmith Hospital, Imperial College

London, United Kingdom

PhD from All India Institute of Medical Sciences

New Delhi, India

Medical Genetics

Certifications

Clinical Molecular Genetics and Genomics

#Board Certified

American Board of Medical Genetics and Genomics

Clinical Cytogenetics and Genomics

#Board Certified

American Board of Medical Genetics and Genomics

Professional Statement

Integrated multi-omic approaches to understand constitutional and acquired genomic disorders by elucidating alterations and mechanisms relevant for pathogenesis: We use whole genome, exome and transcriptome sequencing to discover recurring mutations that are potentially relevant for human genomic disorders. Some examples include Acute Myeloid Leukemia (AML) pathogenesis and clonal diversity and relapse (Cell and Nature 2012; NEJM 2013). As a proof of concept, we have successfully performed clinical whole genome sequencing on AML patients with diagnostic uncertainty in clinically relevant timeframe to find clinically actionable findings (JAMA 2012). These efforts are being extended to evaluate the clinical utility of genomic sequencing in several tumor types both in germline and somatic setting (Cell 2018; Hum Mut 2018). Current active translational research collaborations with clinical colleagues and basic researchers focuses on: 1) early detection of pancreatic cancer using proteomics, transcriptomics and genomics; 2) proteo- genomic approaches using kinase coated beads and mass spectrometry to repurpose FDA-approved drugs in breast cancer; 3) transcriptomic profiling in bladder cancer and 4) whole genome and transcriptome- based testing in pediatric cancers.

Developing Standards and Guidelines for the Interpretation of Sequence Variants: One of the major bottlenecks for implementation of individualized genomic medicine is lack of clinical-grade genomic knowledgebase to facilitate consistent clinical interpretation of sequence variants. Our group is one of several participating laboratories of a major NHGRI/NIH funded multi-institutional effort called ClinGen (Clinical Genome Resource Program). The purpose of ClinGen (http://clinicalgenome.org) is to create a centralized repository and interconnected resources of clinically relevant variants, which are critically needed by the clinical and research communities. We are expanding the scope of this effort by creating somatic variant expert curation of clinically actionable knowledge (Gen Med 2017, Hum Mut 2018, Gen Med 2020, NPJ Gen Med 2020). This expert-curated variant interpretation somatic variation database which will be housed at publicly available NCBI’s ClinVar database.

Design and Optimization of Next-Generation Sequencing Technical and Informatics Pipelines for Clinical Laboratory Practice: We are actively involved in defining standards for next generation sequencing in clinical diagnostics in collaboration with the Centers for Disease Control and Prevention through the Clinical Next-Generation Sequencing Quality Standards National Working Group comprised of key opinion leaders in the field (J Mol Diag 2018, Nat Biotech 2012, Nat Biotech 2015). Additionally, we are working with Clinical Laboratory Standards Institute’s (www.CLSI.org) professional guidelines committee. CLSI standards and guidelines are considered gold standard and are followed by clinical labs nationally and internationally for raising levels of quality, safety and efficiency in laboratory testing and reporting.

Websites

Selected Publications

• Marshall CR, Bick D, Belmont JW, Taylor SL, Ashley E, Dimmock D, Jobanputra V, Kearney HM, Kulkarni S, Rehm H "The Medical Genome Initiative: moving whole-genome sequencing for rare disease diagnosis to the clinic.." Genome Med. 2020;12:48.
• Marshall CR, Chowdhury S, Taft RJ, Lebo MS, (..), Kulkarni S, Taylor SL, Belmont JW, Stavropoulos DJ, Lennon NJ "Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease.." NPJ Genom Med. 2020;5:47.
• Hayeems RZ, Dimmock D, Bick D, Belmont JW, Green RC, Lanpher B, Jobanputra V, Mendoza R, Kulkarni S, Grove ME, Taylor SL, Ashley E "Clinical utility of genomic sequencing: a measurement toolkit.." NPJ Genom Med.. 2020;5:56.
• Huselton E, Rettig MP, Fletcher T, (..), Kulkarni S, Ghobadi A, Abboud C, Cashen AF, Stockerl-Goldstein K, Uy GL, Vij R, Westervelt P, DiPersio JF, Schroeder MA "A phase I trial evaluating the effects of plerixafor, G-CSF, and azacitidine for the treatment of myelodysplastic syndromes.." Leuk Lymphoma. 2021;1-14.