Englander Institute for Precision Medicine

Precision Pathology

The fusion of histology, pathology, and genomics is a cornerstone of the Englander Institute's ongoing research. We encourage interdepartmental collaborations and welcome trainees and fellows to join us in our research endeavors.

EIPM's Precision Pathology Team Explores: 

  • Fluorescence In Situ Hybridization (FISH): Benefit from our decade-long expertise in FISH, providing in-situ validation of genomic events, including recent discoveries from WGS.
  • Digital Pathology: Whole slide scanning of pathology slides and automated image analysis. With HALO analysis for immunohistochemistry (IHC). 
  • Biobanking: Efforts are targeted and tailored to different research studies and clinician-designed initiatives. We collect various specimen types to support our research. 
  • Manual Specimen Processing: Our expert team performs manual DNA/RNA processing from a range of sources, including tumor tissue, blood, cell lines, and organoids. 
  • Automated Extraction: Our Hamilton easyBlood STARlet can process up to 24 blood tubes simultaneously, streamlining downstream processing and distribution.
  • EIPM Nucleic Acid Extraction Facility: We offer extraction services for various specimen types, ensuring high-quality nucleic acid samples. 
  • Whole-genome and transcriptome characterization of cancer: We lead multidisciplinary studies in cancer that integrate genomics, histopathology and clinical data.

Research Pathology Pipeline 

Our research pipeline involves expert review, annotation, and collaboration for a wide range of disease types. We maintain a digital repository of scanned slides, and our pathologists annotate and quantify tumor content, enabling downstream applications such as NGS profiling. Select details of this process include: 

  • Collect research tissue from a wide subset of disease types are frozen and embedded in OCT at CTP, H&Es are cut, and slides are digitally scanned and maintained in the Aperio/Eslide manager system. 
  • In collaboration with attending pathologists’ expertise in WCM Department of Pathology, tumor areas are annotated, tumor content is quantified, and the best tumor block is determined for various downstream applications, including NGS profiling.  
  • Selected tumor blocks are passed off to the laboratory teams for downstream processing, i.e. nucleic acid extractions. 
  • Histological classifications using PMKB are integrated into EIPM databases and connected to other molecular and clinical metadata, enriching the larger EIPM biobank. 

Rapid Autopsy Program 

The Rapid Autopsy Program at Weill Cornell Medicine (WCM) represents a pioneering initiative co-led by WCM's Department of Pathology & Laboratory Medicine. This program stands as a testament to our unwavering commitment to advancing precision medicine and gaining profound insights into advanced malignant tumors.

Drawing from well-established protocols, our dedicated team has optimized an "autopsy donor" program that is open to all tumor types. This program empowers patients diagnosed with advanced cancer to provide their consent for a post-mortem autopsy immediately after their passing.

The Rapid Autopsy Program at WCM is not just a scientific endeavor; it is a testament to our commitment to unlocking the genetic secrets that hold the key to improved diagnostics and treatment options in the realm of oncology. We invite researchers, clinicians, and investigators to engage with us in this ethical and invaluable initiative, contributing to the advancement of precision medicine through the study of advanced malignant tumors. 

  • An Ethical and IRB-Approved Initiative:  The heart of our Rapid Autopsy Program lies in its ethical foundation. We operate under the umbrella of an Institutional Review Board (IRB)-approved "tumor donor donation program." This ensures that all aspects of the program adhere to rigorous ethical standards and guidelines.
  • Comprehensive Tissue Procurement: Our systematic autopsy protocol is designed to maximize the collection of normal and malignant fresh tissue. This tissue is swiftly processed, including snap freezing and formalin-fixing, to preserve its integrity for research purposes. Fresh tissue is also meticulously transported for xenograft and organoid development, further enhancing the potential for groundbreaking discoveries. Additionally, blood samples are collected for the extraction of germline DNA.

If you are interested in exploring a new translational research collaboration, submit inquires here.

To contribute to research studies and research conference presentations contact ipminfo@med.cornell.edu

Juan Miguel Mosquera, MD, MSc
Director of Research Pathology
Englander Institute for Precision Medicine

Weill Cornell Medicine Englander Institute for Precision Medicine 413 E 69th Street
Belfer Research Building
New York, NY 10021