Center for Integrated Diagnostics

Providing Clinically Actionable Molecular Diagnostics to Accelerate the Adoption of Personalized Medicine

For Technical Questions: 617.643.2716

For Billing, Specimen Submission, and Testing Status Questions : 617.724.1285

Support the Center for Integrated Diagnostics



The CID’s mission is to work across the 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, SNP-based approaches and 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 Massachusetts General Hospital’s department of Pathology created the Molecular Diagnostics Laboratory under the direction of Dr. 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 MGH. 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 and Accreditations

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.


Group Members

John Iafrate

A. John Iafrate, MD, PhD

Medical Director, Center for Integrated Diagnostics
Associate in Pathology, Massachusetts General Hospital
Professor of Pathology, Harvard Medical School
Vice Chair of Academic Affairs

Dr. Iafrate is a board-certified Pathologist who joined the Mass General staff in 2005 and directs Center for Integrated Diagnostics at Mass General and oversees a Translational Research Laboratory that supports both Pathology and the MGH Cancer Center. He is an MD, PhD having received his dual degree from the State University of New York at Stony Brook in 2000 and was trained in Anatomic and Molecular Genetic Pathology at Brigham and Women’s Hospital. His post-doctoral work involved the discovery and description of a novel source of human genetic diversity termed copy number variation (CNV). Since arriving at MGH, he has established a cancer diagnostics lab focusing on genetic fingerprints that help guide novel targeted therapies. His laboratory launched SNAPSHOT several years ago, an assay that tests over 100 of the most common mutations in tumors. His research is focused on lung and brain tumors, and he has been closely involved in the clinical development of crizotinib and companion diagnostics in ALK-positive lung cancers. 


Long Phi Le

Long Phi Le, MD, PhD

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

Dr. Le is a graduate of Massachusetts Institute of Technology (1999) and received his MD, PhD from the University of Alabama at Birmingham School of Medicine in 2006.  He completed his residency training in Clinical Pathology at the Massachusetts General Hospital and his Molecular Genetic Pathology Fellowship at Brigham and Women's Hospital (2010).  He joined the Mass General Department of Pathology as an instructor and assistant pathologist in 2010.  His clinical and research interests in the Diagnostic Molecular Pathology Laboratory include the application of copy number analysis, next generation sequencing, and bioinformatics in molecular diagnostics.



Gad Getz

Gad A. Getz, Ph.D

Director, Bioinformatics Program, Massachusetts General Hospital Cancer Center and Department of Pathology
Paul C. Zamecnik Chair of Oncology, Massachusetts General Hospital Cancer Center
Associate Professor of Pathology, Harvard Medical School
Director, Cancer Genome Computational Analysis, Broad Institute

Dr. Getz is an internationally acclaimed leader in cancer genome analysis and is pioneering widely used cancer genome analysis tools. Dr. Getz joined the Mass General staff in 2013. He directs the Bioinformatics Program at the Mass General Cancer Center and Department of Pathology. Getz is also the inaugural incumbent of the Paul C. Zamecnik Chair of Oncology at the Mass General Cancer Center. In addition to his role at the Massachusetts General Hospital, Getz directs the Cancer Genome Computational Analysis group at the Broad Institute. He has published numerous papers in prominent journals that describe new genes and pathways involved in different tumor types. Getz received his B.S. degree in Physics and Mathematics from Hebrew University and an M.Sc. in Physics from Tel-Aviv University. He later earned a PhD in Physics from the Weizmann Institute of Science in Israel. He completed his postdoctoral training at the Broad Institute of MIT and Harvard with Todd Golub, where he focused on developing computational tools and analyzing expression of miRNAs across cancer.


Dora Dias-Santagata

Dora Dias-Santagata, PhD, FACMG

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

Dr. Dias-Santagata is board-certified in Clinical Molecular Genetics and joined the Mass General staff in 2007 to co-direct the Translational Research Laboratory, a mutual collaboration between the Mass General Department of Pathology and the Cancer Center. She received her PhD from the Mount Sinai School of Medicine in New York (2004), and pursued post-doctoral research work at the Brigham and Women’s Hospital in Boston. She developed and co-directed the clinical implementation of SNaPshot, a pioneering tumor genotyping strategy that has been adopted by the oncology community at Mass General since March 2009, to help guide therapeutic decisions. Her research efforts include the molecular characterization of rare malignancies, lung and thyroid cancers, in an effort to uncover underlying genetic driver amenable for therapeutic intervention and mechanisms of acquired resistance to therapy. 


Darrell Borger

Darrell R. Borger, PhD

Assistant in Biology, Massachusetts General Hospital
Instructor in Medicine, Harvard Medical School

Dr. Borger received his PhD from the University of South Carolina, School of Medicine in Biomedical Science and then received post-doctoral training at the Dana-Farber Cancer Institute, where he identified basic mechanisms that drive cancer development and promote drug resistance. At Mass General, he has helped develop cutting-edge clinical testing platforms that provide genetic “fingerprinting” of patient tumor tissue that is used to support a personalized approach to cancer therapy. As Director of the Translational Research Laboratory, Biomarker Unit, he is developing novel approaches that can help rationally direct patients to experimental cancer therapy trials based on an underlying tumor biomarker. Dr. Borger’s research interests also include identifying new tumor biomarkers that may expand treatment options for cancer patients and identifying mechanisms that promote drug resistance. He has also played a major role in developing a new website that provides disease-specific information on how tumor genotyping can direct cancer care and identify specific trials accruing patients at the Mass General that that are matched to a specific cancer type or genotyping test result. (


Miguel Rivera

Miguel N. Rivera, MD

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

Dr. Rivera is a board certified pathologist who directs a research laboratory at the Mass General Department of Pathology and the Mass General Cancer Center. He also serves as attending physician in the Center for Integrated Diagnostics at Mass General. Dr. Rivera received an AB in Molecular Biology from Princeton University in 1996 and an MD from Harvard Medical School in 2001. He completed his Anatomic Pathology residency at Brigham and Women’s Hospital and a fellowship in Molecular Diagnostics at the Harvard Combined Program. During his postdoctoral fellowship, Dr. Rivera identified the tumor suppressor gene WTX which is implicated in both tumor formation and stem cell biology. His research currently focuses on the connections between cancer and normal developmental processes and on the use of genomic technologies to identify pathways that are active in tumors and that may serve as therapeutic targets.


Valentina Nardi

Valentina Nardi, MD

Assistant in Pathology, Massachusetts General Hospital
Instructor, Harvard Medical School

Dr. Nardi received her MD degree and board certification in Hematology in Genoa, Italy. She pursued post-doctoral research in Boston, under the supervision of Dr. George Daley at Children's Hospital Boston, developing an interest and expertise in chronic myeloid leukemia, resistance to targeted therapies, and development and applications of new technologies to detect and monitor drug resistance over time. Dr. Nardi developed an interest in molecular diagnostics and went on to complete her Anatomic Pathology residency and a Hematopathology fellowship at the Massachusetts General Hospital and the Harvard Medical School Molecular Genetic Pathology Fellowship.



Jochen Lennerz

Jochen K Lennerz, MD, PhD

Assistant in Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital
Assistant Professor of Pathology, Harvard Medical School

Dr. Lennerz is board-certified in Anatomic- and Molecular Genetic Pathology and joined Mass General Department of Pathology and Center for Integrated Diagnostics as a staff pathologist and assistant professor in 2014.  Dr. Lennerz trained as a pathologist assistant in Berlin Germany (1994) and studied both medicine and molecular medicine at the University Erlangen Germany where he also received his MD, PhD.  He did his residency training in Anatomic Pathology (2008) and a fellowship in Molecular Genetic Pathology (2009) at Washington University in St. Louis.  After completion of a two-year gastrointestinal and liver pathology fellowship at Mass General (2011), he led a research group on biomarkers in lymphoma at Ulm University Germany.  Dr. Lennerz joined the CID in 2014 and his interests are biomarkers, digital pathology, and financial sustainability of molecular genetic diagnostics.

Leadership TeamJulie Miller Batten, MLS (ASCP)
Clinical Laboratory Supervisor, Center for Integrated Diagnostics

A. Bernard Collins
Outreach and Clinical Affiliates Manager, Department of Pathology
Technical Director, Research and Development Immunopathology Unit
Associate in Pathology, Harvard Medical School

Hayley Robinson, MLS (ASCP)
Clinical Laboratory Supervisor, Center for Integrated Diagnostics

Nick Jessop
Center for Integrated Diagnostics

Kathy Vernovsky, MB (ASCP)
Compliance and Quality Specialist, Center for Integrated Diagnostics




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, ROS, RET, EGFR, MET, PDGFRA, FGFR1, HER2, EWSR1, CHOP, SYT, FKHR, 1p19q, MYC, KRAS, and PIK3CA.

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 has been associated with longer survival. Therefore, determining MGMT methylation status can provide valuable prognostic information and help guide the course of treatment.

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


MGH Patients:

Testing completed for MGH patients will be billed directly to their insurance via their medical record number.

Non-MGH Patients:Institutional invoice is the only billing option for non-MGH patients. We cannot bill a patient’s insurance provider unless a patient has been seen by an MGH 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 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.


Contact Us

Center for Integrated Diagnostics (CID)

Jackson Building, 10th Floor

55 Fruit Street Boston, MA 02114
  • Phone: 617.643.2716
  • Fax: 617.643.1623


  • Monday through Friday, 8:30 am to 5:00 pm

Mailing Address

Massachusetts General Hospital
Center for Integrated Diagnostics (CID)
Jackson Building, Floor 10
Mailstop: GRJ 1015
55 Fruit Street
Boston, MA 02114

Billing, Specimen Submission, Testing Status Questions: 617.724.1285

For Technical Questions: 617.643.2716

For Billing, Specimen Submission, and Testing Status Questions : 617.724.1285

Support the Center for Integrated Diagnostics

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