Explore the Center for Integrated Diagnostics


The Center for Integrated Diagnostics (CID) mission is to work across Massachusetts General Hospital to foster development of clinical actionable diagnostics and accelerate the adoption of personalized medicine. While we have made strides in the cancer field it is our goal to expand our testing to other disciplines.

Genotyping Tumors & Targeted Therapies

The primary role of the CID is to genotypically fingerprint patient tumors across the complete spectrum of disease sites in an effort to direct molecularly targeted therapies, thereby enhancing the efficacy of drug treatment offerings as well as supporting prospective clinical trial designs. Patient analyses are performed as CLIA-certified clinical tests and results are generated within a timeframe that allows for direct patient care decision making as well as providing the opportunity for patients whose cancers harbor susceptible genotypes to be offered the most appropriate clinical treatment. In addition, our laboratory pursues retrospective and corollary research studies to support the expansion of our genotyping profiles. To accomplish these goals, the lab utilizes a number of molecular and cellular techniques, including:
  • Fluorescent in situ hybridization (FISH)
  • qPCR
  • DNA sequencing
  • SNPbased approaches
  • DNA sizing analyses
The combination of these approaches allows for the detection of somatic genetic aberrations on multiple levels, including gene copy number, point mutations and small deletions and insertions.

Molecular Diagnostics & Mass General Pathology

In 2005, Mass General's Department of Pathology created the Molecular Diagnostics Laboratory under the direction of A. John Iafrate, MD, PhD. The test offerings started out small; the original two tests were 1P19Q fluorescent in situ hybridization (FISH) and microsatellite instability (MSI). The menu of tests has expanded significantly over time with the key addition of ALK FISH which functions to assist in lung cancer treatment.

In 2008, Dr. Iafrate created the Translational Research Lab (TRL) in collaboration with Mass General Cancer Center. The TRL’s mission was to design a multiplex test that would simultaneously test for the top cancer mutations for all cancer types. The resulting SNaPshot panel tests for 92 commonly mutated loci across 23 cancer genes.

In 2011, clinical molecular diagnostics was unified as the Center for Integrated Diagnostics (CID) at Mass General.

In 2013 the CID rolled out its first next generation sequencing (NGS) assay, AMP translocation, which looks for gene rearrangement of ALK, ROS, and RET. Building on past experience of targeting a specific number of genes in the original SNaPshot Panel and the NGS based technology of the AMP assay, we launched NGS Snapshot in 2014.

The current version of this assay assesses single nucleotide variants and insertions/deletions in 104 known cancer genes, allowing us to provide the most comprehensive clinical assay for actionable cancer genes to date. The laboratory has since continued to expand its NGS assay menu, and now offers comprehensive NGS assays for solid tumors, heme malignancies, and sarcomas.

Licensure & Accreditation

The Center for Integrated Diagnostics has CLIA (Clinical Laboratory Improvement Amendments) certification through CMS (Centers of Medicare and Medicaid Services), and is accredited by the Joint Commission. Please see the Pathology Department Regulatory Compliance website to request a copy of the CLIA certificate. The Center for Integrated Diagnostics is also a New York State CLEP (Clinical Laboratory Evaluation Program) licensed molecular laboratory for performing ROS1 FISH and gene translocation assays, which can generate critical information for treating lung cancer patients. For more information about these assays, please contact the laboratory at the phone numbers listed below.

Leadership & Team

Jochen K Lennerz

Jochen K Lennerz, MD, PhD

Medical Director, Center for Integrated Diagnostics, Massachusetts General Hospital
Associate Chief, Department of Pathology
Associate Professor of Pathology, Harvard Medical School

A. John IafrateA. John Iafrate, MD, PhD

Austin L. Vickery, Jr. Professor of Pathology
Vice Chair of Pathology for Academic Affairs
Pathologist in Pathology, Massachusetts General Hospital 

Long Phi LeLong Phi Le, MD, PhD

Associate Chief of Pathology Informatics, Massachusetts General Hospital
Assistant in Pathology, Massachusetts General Hospital
Assistant Professor of Pathology, Harvard Medical School

Dora Dias Santagata

Dora Dias-Santagata, PhD, FACMG

Assistant Molecular Pathologist, Massachusetts General Hospital
Associate Professor of Pathology, Harvard Medical School

Miguel N. Rivera, MD

Assistant in Pathology, Massachusetts General Hospital
Associate Professor of Pathology, Harvard Medical School

Valentina Nardi, MD

Assistant in Pathology, Massachusetts General Hospital
Assistant Professor of Pathology, Harvard Medical School

Salil GargSalil Garg, MD, PhD

Principal Investigator, The Garg Lab, MIT
Assistant in Pathology, Massachusetts General Hospital

Leadership Team

Julie Miller BattenJulie Miller Batten, MLS (ASCP)

Technical Director, Center for Integrated Diagnostics

Nick JessopNick Jessop

Case Manager, Center for Integrated Diagnostics



Spatial Omics: Ready for Clinical Practice (Download Version 3* here)

CID is performing technology assessments and here is our most recent technology assessment of spatial omics technologies by Max Jorgensen, Emma Gardecki, Joe Lennerz, and Surya Nagaraja; reviewed by Lauren Ritterhouse

Summary: Clinical sequencing technologies have seen a massive growth; however, technologies able to collect morphological and spatial data on these samples is still largely emerging, with limited traction in clinical settings to-date. Examples of technologies able to accomplish this include spatial transcriptomics, spatial profiling, and hyper-plexed proteomics approaches in research settings. Here we present the results of a technology assessment including a questionnaire that focused on the analyte, technology, vendor, number of biomarkers a system can identify on a single tissue sample, resolution in µm, sample type, compatibility with formalin-fixed paraffin embedded tissue samples and/or fresh frozen, and whether a separate instrument is required or can be accomplished with existing laboratory equipment. The results are listed and portrayed against traditional light microscopy, and we included an idealized prototype workflow for spatial omics in clinical practice.

*Version 3 contains the following updates:
Abstract: Clarified the relationship of high-plex spatial technologies and the clinic as limited to-date by stating the field is still emerging and example technologies have largely been used in research settings
Introduction: Corrected that HTS has become a sizable segment of the diagnostic market, not medical device and healthcare markets; Added additional context to what has limited the scope of clinical-scale sequencing (e.g., regulatory, reimbursement); Added a note which clarifies our stance on the most important metrics to measure spatial platforms by, and that plex, cost, and resolution may not be important to some or all potential adopters or clinical use, and other metrics (e.g., throughput) which are not covered may be more important to some or all potential adopters or clinical use
Approach: Added another clarification stating the included metrics may not be the most important to all researchers or clinical use; Removed analysis time from the list of metrics collected as this is not presented in the paper; Clarified when data was collected; Clarified who reviewed the data
Results: Fig. 1 was updated to clarify the originally shown yellow optimal region is for research use and a purple region has been added to highlight the optimal clinical region; Clarified that plex and resolution are not the most important, but two of the most impactful metrics for potential customers and clinical use; Added commentary based on the result of the added optimal clinical region, particularly around Akoya Biosciences' and other proteomics-based platforms; Clarified that additional metrics not considered could impact analysis and change which platforms are in the various "optimal" regions; Added a note clarifying the majority of biomarkers today are protein-based
Conclusion: Clarified discussion that genome-wide IHC may have questionable clinical utility, not questionable utility"


Cancer Testing

  • SNAPSHOT Cancer Genotyping (NGS): Solid tumor and heme versions available. Tumor development and progression rely on the active involvement of a limited set of signaling pathways; defining the genomic signatures of different tumor types has led to the development of a new generation of gene-targeted drugs. In our laboratory, we have developed an assay which identifies these genomic signatures by detecting mutations in over 100 commonly mutated areas in cancer. The results allow for enhanced molecular sub-classification of tumors, which facilitates the selection of appropriate gene-targeted drugs and enables clinicians to identify suitable clinical trials for their patients. The Snapshot Cancer Genotyping assay is clinically relevant for a wide variety of cancers including lung, colon, breast, brain, pancreas, thyroid, skin, leukemia and more
  • Fusion Assays (NGS): Solid tumor, heme and sarcoma versions available. Chromosomal translocations commonly observed in cancer can be identified using high-throughput targeted RNA sequencing (RNA-Seq). Fusion assays developed by the CID use AMP (Anchored Multiplex PCR) technology, which identifies known and novel gene fusions with specific identification of transcript fusion breakpoints and their partners. CID fusion assays provide comprehensive results of actionable translocations, which can be used alongside clinical and pathologic information for diagnostic, prognostic and treatment decisions
  • FISH: Fluorescence in situ Hybridization (FISH) detects a variety of chromosomal aberrations in cancer, including genes that have moved (translocations), duplicated genes (amplifications) and missing genes (deletions). Our laboratory offers a wide selection of FISH assays for various cancers types, including lung, colon, brain and soft tissue. The FISH tests that we offer are ALK, ROS1, RET, EGFR, MET, PDGFRA, FGFR1, HER2, EWSR1, CHOP, SYT, FKHR, 1p19q, MYC, KRAS and PIK3CA, CDKN2A 
  • Microsatellite Instability & MLH1 Promoter Methylation: Microsatellite instability or MSI can occur due to defects in DNA mismatch repair proteins, typically leading to sporadic tumorigenesis in colorectal or endometrial cancers. Subsequent testing for MLH1 promoter methylation status aids in ruling out hereditary nonpolyposis colorectal cancer (HNPCC, or Lynch syndrome). In our laboratory, MSI analysis is performed via molecular and immunohistochemistry techniques
  • MGMT Promoter Methylation: The promoter of MGMT, which is a DNA repair gene, can sometimes be methylated or silenced, effecting tumorigenesis. In patients with glioblastoma who are treated with alkylating agents, MGMT promoter methylation

Non-cancer Testing

  • Microarray/aCGH: aCGH (array-based comparative genomic hybridization), a type of chromosomal microarray, is performed to detect gains or losses at the chromosome level,
    aiding in the diagnosis of many genetic conditions including unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), multiple congenital
    anomalies (MCA), Prader-Willi syndrome and Angelman syndrome. The microarray used at the CID has been validated for the detection of copy number variations (CNVs) and
    uniparental disomy (UPD) to guide patient diagnosis
  • Hemochromatosis: The CID’s hemochromatosis panel tests for the most commonly associated mutations within the genes related to hereditary hemochromatosis. A correlation of
    clinical and genetic laboratory findings is required to determine a diagnosis of hereditary hemochromatosis. Testing is recommended for close family members of individuals
    diagnosed with the condition
  • Chimerism Analysis: Our laboratory uses a microsatellite assay to determine the percentage of donor and/or recipient cells present in the peripheral blood or bone marrow of a
    patient subsequent to allogeneic bone marrow or stem cell transplant. After transplant, the relative amount of DNA that is donor versus recipient is quantified and followed over
    time with subsequent patient samples to provide prognostic information


Fee Schedule

Mass General Patients: Testing completed for Mass General patients will be billed directly to their insurance via their medical record number.

Non-Mass General Patients: Institutional invoice is the only billing option for non-Mass General patients. We cannot bill a patient’s insurance provider unless a patient has been seen by a Mass General clinician within 30 days of sample receipt. Please contact us for specific pricing information, as this is subject to change.

Getting Started

In order for us to process a request for testing, all forms outlined in the Requisition Supplement (PDF) must be completed and submitted along with the specimen. Incomplete paperwork will be returned.

How to Ship

Any materials sent by either standard or express mail must be protected by using proper packaging. Glass slides should be enclosed in a protective slide box. Blood and bone marrow specimens should be in appropriate biohazard packaging and protected from extreme temperatures. All fluid specimens must be expedited to arrive within 5 days from date of draw. We suggest that all materials related to the case be shipped in the same container to ensure that they are received together. The mailing label should include a return address. Original H&E slides and blocks can be returned by our lab upon request. Unstained slides will be used for testing and will not be returned.