Multispectral image of human FFPE tissue labeled with 7 different fluorescent biomarkers. Image courtesy of Joao Paulo Oliveira-Costa, DDS, PhD.

Overview

The emergence of scalable analytical technologies has generated significant interest in applying these platforms to translational projects focused on human tissue specimens. This has included new multiplexed protein and RNA staining assays applicable to clinical grade FFPE material for a variety of clinical and scientific questions that are of importance to Mass General Cancer Center investigators. These changes in the landscape of clinical oncology and biomarker technologies has created the need to provide a new research infrastructure for clinical and laboratory based investigators to perform translational science. The Biomarker Discovery Lab aims to meet these evolving needs and provide a resource for both clinical and basic science researchers at the Mass General Cancer Center.

A Collaborative Resource

The Biomarker Discovery Lab is formed under the direction of Miguel Rivera, MDDavid Ting, MD, and Vikram Deshpande, MD. The lab has access to human tissue samples, tissue staining by IHC/IF or RNA-ISH, and molecular analysis with next generation sequencing.

The Biomarker Discovery Lab also works collaboratively with the DF/HCC Pathology Core to help investigators execute more routine IHC/IF stains. In addition, the Biomarker Discovery Lab works closely with the Translational Research Lab on potential molecular or tissue based biomarkers that appear to be clinically important to transition into a CLIA setting.

The Biomarker Discovery Lab is designed to provide a collaborative resource that can provide expertise and services on tissue acquisition, preparation, specialized histological stains, and high end digital microscopy quantitative analysis.

Infrastructure Resources

Existing Leica Bond RX automated IHC/RNA-ISH staining platform, Leica automated cover-slipper, one Vectra 2 MSI imaging systems (with Stott lab), 1 Aperio brightfield scanner, 2 Illumina MiSeq, and 1 Illumina NextSeq are existing resources for the lab. Image analysis platforms Viziopharm and Halo have been purchased and provide a range of capabilities for researchers. Data infrastructure include a local server (NetApp FAS8020 NAS) with 576 TB total storage space and data protection using Snapshot technology.

Team

Scientific Directors

  • Miguel Rivera, MD

    Miguel Rivera MD is a molecular pathologist and translational researcher with significant expertise in the development and application of molecular diagnostics. He co-directs the technical operation of tissue based analysis and sequencing with David Ting.

  • David Ting, MD

    David T. Ting MD is a translational cancer researcher with experience in tissue image analysis and next generation sequencing. He provides administrative oversight and directs the technical operation of image analysis with Linda Nieman and next generation sequencing applications with Anna Szabolcs.

  • Vikram Deshpande, MD

    Vikram Deshpande MD is an anatomic pathologist with significant experience in biomarker development. He is director of the MGH Pathology Tissue Bank and the Tissue Microarray (TMA) Core facility. He coordinates all tissue acquisition, construction of TMA, and provides histological review.

Tissue Bank Team

  • Azfar Neyaz, MD

    Azfar Neyaz, MD is an experienced anatomic pathologist who assists with tissue acquisition, tissue staining, and histological analysis for all projects. Under the guidance of Dr. Deshpande, he acquires human tissues and assembles tissue microarrays for a wide variety of projects across the Cancer Center.

Tissue Staining Analysis Team

  • Linda Nieman, PhD

    Linda Nieman, PhD is a staff scientist with a PhD in Physics specializing in optical approaches to understand disease and response to therapy. Over the last 3 years, Dr. Nieman has provided essential expertise in the management of all microscopy platforms at the MGH Cancer Center including multispectral imaging, digital whole slide scanning, and confocal microscopy. In addition, she has developed algorithms for digital microscopy analysis with Halo and Visiopharm to generate quantitative and spatial data from images of tissue slides stained for cancer biomarkers.

  • Anupriya Kulkarni, PhD

    Anupriya Kulkarni, PhD is a post-doctoral researcher has operational oversight of the Leica BondRX for both IHC and RNA-ISH. She has over 3 years experience with automated staining platforms applicable for both laboratory based and clinical translational research projects.

Next Generation Sequencing Team

  • Anna Szabolcs, MD, PhD

    Anna Szabolcs, MD, PhD is a staff scientist with post-doctoral research experience in cancer and molecular biology. She provides oversight of all next generation sequencing projects from the Biomarker Discovery lab.

Contact Us

Please contact the Biomarker Discovery Lab via:

Linda Nieman, PhD
lnieman@mgh.havard.edu
Office: 617-643-9684

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