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Learn how FoundationOne can open up more treatment possibilities for your patients

Tumor Mutational Burden, a quantitative genomic biomarker known to predict response to immunotherapy, now available on FoundationOne® reports.

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How is the Genomic
Profiling Approach Different?

Today, we know more about the complexity of cancer than ever before. Cancers have long been categorized and treated by where they are found in the body: lung, breast, colon, skin, blood, lymph nodes etc. However, we have known for some time that cancers are more accurately categorized by underlying alterations in DNA that drive cancer growth, which can occur in any cancer. As we understand more about these underlying alterations, traditional cytotoxic treatments are rapidly being replaced by less toxic, potentially more effective therapies that specifically target these changes in DNA that are important for cancer cell survival.

FoundationOne, FoundationOne Heme and FoundationACT help physicians reveal the alterations that are driving the growth of a patient's cancer and identify targeted treatment options that may not have been otherwise considered. Our assays are more comprehensive and identify more potential treatment options than other available tests because they analyze all genes known to be relevant in human cancers.

 
About FoundationOne

FoundationOne, the first clinical product from Foundation Medicine, is a fully informative genomic profile that complements traditional cancer treatment decision tools and often expands treatment options by matching each patient with targeted therapies and clinical trials that are relevant to the molecular changes in their tumor based on the most recent scientific and medical research. The test utilizes next-generation sequencing to identify alterations in all genes known to be somatically altered in human solid tumor cancers.

Test results are provided in a user-friendly interpretive report that highlights the genomic alterations that are relevant to the individual patient and provides information about targeted therapies and clinical trials to inform treatment decisions.

FoundationOne interrogates the entire coding sequence of 315 cancer-related genes plus select introns from 28 genes often rearranged or altered in solid tumor cancers. These genes are known to be somatically altered in solid cancers based on recent scientific and clinical literature and are sequenced at great depth to identify the relevant, actionable somatic alterations, including single base pair change, insertions, deletions, copy number alterations, and selected fusions.

[View the FoundationOne Technical Spec]

 
FoundationOne / FoundationOne Heme: Latest Updates

An update has been made to the list of disease ontologies used to determine which of our clinical tests, FoundationOne(R) or FoundationOne(R) Heme, is most appropriately applied to each patient sample. The most notable change is that samples will no longer be qualified based on age, and solid tumor samples from pediatric patients will now be profiled by FoundationOne. Going forward, regardless of the age of the patient:

  • FoundationOne will be utilized for the vast majority of all patients with solid tumors
  • FoundationOne Heme will be utilized for patients with hematologic malignancies or sarcomas

Our expert pathologists will continue to review each and every case, and in the rare cases where your patient will be best served using a test other than the one ordered, we will contact you and provide you with the opportunity to appropriately modify the test order.


About FoundationOne Heme

FoundationOne Heme is a fully informative genomic profile for hematologic cancers (leukemia, lymphoma and myeloma) and sarcomas, designed to provide physicians with clinically actionable information to guide treatment options for patients based on the genomic profile of their cancer. It is Foundation Medicine's second commercially available targeted sequencing assay.

FoundationOne Heme uses comprehensive, clinical grade next-generation sequencing (NGS) to assess routine cancer specimens for all genes that are currently known to be somatically altered and unambiguous drivers of oncogenesis in hematologic malignancies and sarcomas. FoundationOne Heme simultaneously detects all classes of genomic alterations, including base pair substitutions, insertions and deletions, copy number alterations and select gene rearrangements in 405 cancer-related genes. In addition to DNA sequencing, FoundationOne Heme employs RNA sequencing across 265 genes to capture a broad range of gene fusions, a type of alteration that is a common driver of hematologic cancers and sarcomas.

View the FoundationOne Heme Technical Specifications

 
About FoundationACT

FoundationACT™ is Foundation Medicine’s best-in-class, blood-based circulating tumor DNA assay, that provides new options for patients when tissue biopsy is not feasible. FoundationACT is designed to interrogate 62 cancer-related genes and identifies all four classes of alterations. Detecting accurate results from liquid biopsy poses a significant challenge due to the relative proportion of tumor content in blood. FoundationACT was created to address these challenges and, as a result, achieves the superior performance you can expect from Foundation Medicine with:

  • Unparalleled accuracy with 99% sensitivity and 99% specificity (PPV)
  • Analytically and clinically validated for all four types of alterations - Base substitutions, Insertions and deletions, Copy number variations and Rearrangements / gene fusions
  • Connectivity with FoundationOne - Compare FoundationACT results with previous FoundationOne or FoundationACT testing results. FoundationACT is the only platform that allows you to get an integrated view of your patient’s tumor genomics by connecting blood with tissue results

To order a FoundationACT specimen kit, please contact a Client Services Representative at client.services@foundationmedicine.com

[View FoundationACT Brochure]
[View FoundationACT Technical Specifications]
[View FoundationACT Specimen Guidelines]
[View FoundationACT Validation White Paper]
[View FoundationACT Sample Report]

[View Physician FAQs]
[View Patient FAQs]

 
Immunotherapy

Tumor Mutational Burden (TMB) Available On FoundationOne Reports

FoundationOne and FoundationOne Heme comprehensive genomic profiling reports include tumor mutational burden, which is a validated, quantitative genomic biomarker associated with response to cancer immunotherapies in a number of tumor types. Patients with a high TMB are more likely to benefit from certain cancer immunotherapies.

TMB status is provided on every FoundationOne and FoundationOne Heme report and does not require additional tissue, or result in increased turnaround time, or cost.

  • For all types of solid and hematologic malignancies that are TMB-High, the information will be on the front page of the report
  • For colorectal cancer, non-small cell lung cancer, melanoma, and urothelial and endometrial carcinomas, the full TMB status (including TMB-High, TMB-Intermediate and TMB-Low) will be provided on the front page of the report
  • In all other scenarios, the TMB status can be found in the variants of unknown significance (VUS) section of the report

For customers who previously had standing orders for TMB, these orders are no longer needed and will not continue as TMB will be automatically provided.

Please contact our client services department with questions.

 
Interactive Cancer Explorer
 

The latest version of Interactive Cancer Explorer - FoundationICE offers:

Improved efficiency

  • Sample Tracking - Know where your patient samples are in the testing process
  • Enhanced Search - Find your patients by gene, alteration or tumor type
  • Notifications- See when you have new or shared reports

Enhanced actionability

  • PatientMatch - Learn from the experience of other physicians treating patients with similar genomic profiles

Download the guide to learn about how FoundationICE can help effectively leverage comprehensive genomic profiling in your practice.

If you are a FoundationOne or FoundationOne Heme user and do not yet have access to our FoundationICE platform, please contact your sales representative or email ice-support@foundationmedicine.com to haven an account created.

All of your patient reports available online with links to current research and clinical trials.

View, Download, And Share

  • Access your FoundationOne and FoundationOne Heme reports securely through one easily accessible site
  • Save and print reports--anytime, anywhere
  • Share reports through FoundationICE

Inform Your Treatment Plan

  • Current information about genomic alterations, associated therapies and clinical trials, curated by genomic experts in oncology and pathology
  • Direct links to patient-specific journal articles & clinical trials information
  • Connect directly to clinicaltrials.gov, PubMed and other online references

Explore And Discover

  • Confidence to make treatment recommendations tailored to each patient
  • Incorporate the latest medical and scientific literature into your practice

You may access report and interactive information through the Interactive Cancer Explorer.

You may also receive your report as a PDF or fax. Download a guide to the FoundationOne report.

 
 
FoundationACCESS

We deliver an end-to-end solution from testing to getting access to targeted therapies enabling you to deliver the best possible care for your patients.

  • FoundationACCESS program addresses any financial, access and claim issues for FoundationOne and FoundtaionOne Heme Testing
  • FoundationACCESS Careline program offers comprehensive case management services to help uninsured, underinsured and insured patients who are facing obstacles obtaining prescribed targeted therapies and increase physicians' ability to act on FoundationOne results
  • FoundationACCESS Trial Navigator program helps match patients to clinical trials and assist with the enrollment process

Download FoundationACCESS Careline brochure for physicians
Download FoundationACCESS Careline brochure for patients
Download FoundationACCESS Trial Navigator brochure for physicians
Download FoundationACCESS Trial Navigator brochure for patients

Click Here to apply online for our financial assistance program.

 
FAQs: Patients
 
 
What are genomic alterations and what role do they play in cancer?

A genomic alteration is a change in the DNA sequence that makes up a gene and can affect the way a cell functions. These genomic changes are a normal part of life, and most won't have a negative effect on our health. But some alterations lead to diseases, including cancer. Cancers are caused by alterations within a few hundred specific genes that are found normally in the cells of our bodies. When changes occur in these genes, cells can grow in an abnormal fashion, causing cancerous tumors to form. Over time, these tumors can spread throughout the body. Alterations in DNA can occur in two ways: they can be inherited from our parents or acquired during a person's lifetime. Hereditary changes are called genetic mutations and are a contributing factor in about 5-10 percent of cancers. Acquired alterations are responsible for the majority of cancers. While some acquired alterations may be caused by environmental factors such as smoking, sun exposure and viruses like HPV, many have no known cause. There may be multiple alterations contributing to your cancer.

Watch this video for more information on what cancer is and available treatment options.

 
 
 
How can knowing my cancer's genomic information help my treatment?

Studies have shown that tumors with some genomic alterations respond better to certain treatments. In addition, promising new drugs, called targeted therapies, can be more successful in treating cancer by targeting specific underlying genomic alterations that are contributing to tumor growth. By attacking the cancer and sparing the healthy surrounding tissue, targeted therapies can be more effective and have fewer and less pronounced side effects than some chemotherapies. Since there are hundreds of cancer genes, and many possible alterations in each gene, the number and combination of genomic alterations make each person's cancer unique. FoundationOne can be used as a tool to identify the genomic changes causing and contributing to your cancer's growth to inform your doctor of therapies that may not otherwise have been considered.

 
 
 
What's the likelihood that FoundationOne will find a treatable genomic alteration?

In 85 percent* of cases, FoundationOne test results in an "actionable" outcome, meaning that the results help:

  1. Identify a therapy approved to treat your specific tumor type and shown to be effective in targeting one or more of the alterations found by the test,
  2. Identify a therapy approved in another tumor type but possibly effective in targeting one or more of the genomic alterations found by the test, or
  3. Identify an open clinical trial of an experimental treatment which may work by targeting an alteration found by the test or a relevant pathway.

*Data on file
Similar studies with FoundationOne Heme are ongoing.

 
 
 
Will I need to have another biopsy taken for the test?

The test can be run on a tissue sample from an earlier biopsy of either the primary tumor or cancer cells that have spread to other parts of the body. If there is not enough tissue remaining from an earlier biopsy to run the test an additional biopsy may need to be collected. Your doctor may recommend a new biopsy to get a more recent sample.

 
 
 
What can I expect if my doctor orders FoundationOne or FoundationOne Heme and how long will it take to get the results?

If you and your doctor decide that one of these tests is right for you, your doctor will place an order for the test. Foundation Medicine, the company that developed the tests, will work with your doctor and treatment facilities to obtain a biopsy sample of your tumor to analyze. After the test is completed, results are provided to your doctor. It typically takes 11-14 days from the time your tissue sample is received to get the results for FoundationOne. FoundationOne Heme results may take longer.

 
 
 
Does it matter what kind of cancer I have or how advanced the cancer is?

FoundationOne and FoundationOne Heme are designed to analyze any type of tumor regardless of where it is found in the body or how advanced the cancer. However, the tests are generally used for more advanced disease or disease that has spread. Talk with your doctor to see if FoundationOne or FoundationOne Heme is right for you.

 
 
 
Are the test results intended to provide information on both hereditary and acquired genomic alterations found in my tumor?

The results will provide information on any acquired genomic alterations found in your tumor but are not intended to provide information on inherited genetic alterations. It is important to remember that only 5-10 percent of cancers are caused by hereditary alterations. However, since these alterations can be inherited by multiple family members and passed down from generation to generation, information about inherited alterations affects entire families, raising personal and ethical considerations that factor into the decision to receive that information. FoundationOne and FoundationOne Heme are not tests for these inherited alterations. If you are interested in testing for inherited alterations, we recommend discussing it with your doctor.

 
 
 
What are the limitations of the tests?

In about 15-20 percent of cases, FoundationOne test results don't identify an actionable genomic alteration, meaning there are no approved treatments or therapies in clinical trials that have been shown to be effective against the alterations found in your tumor. Studies are ongoing to determine similar information for FoundationOne Heme. Additionally, there may be obstacles to obtaining therapy in cases where the test finds actionable alterations. For example, if the therapy has been approved in a different tumor type, your insurance may not cover the cost of that treatment for an unapproved tumor type. It is also possible that you may not be eligible for, or able to enroll in an ongoing clinical trial of a therapy targeted against an alteration found by the test.

It is important to understand that while the test often provides valuable information to help you and your doctor make the best possible decisions about treatment, there is no guarantee that the treatment will work for you. While significant progress has been made in treatments targeting the underlying genomic alterations that cause cancer, cancer is a complex disease driven by multiple factors, no therapy is 100 percent effective and responses to therapies vary.

 
 
 
How much do FoundationOne and FoundationOne Heme cost?

The list price of FoundationOne is $5,800. The list price of FoundationOne Heme is $7,200, and is priced higher due to the costs associated with the technical complexities of performing RNA sequencing (in addition to DNA sequencing). These are the amounts that are billed to your insurance. If you don't have insurance coverage we offer a prompt pay discount. Payment plans may be available to you through our Patient Assistance Program based on your financial situation. If you are uninsured, or if you have insurance and cannot afford the applicable out-of-pocket cost please contact our Client Services Team with regards to eligibility.

If you would like more information about these services, please contact us at (888) 988-3639. We are available to answer your questions from 8 a.m. to 8 p.m. ET Monday through Friday. You can also email us at client.services@foundationmedicine.com.

 
 
FAQs: Physicians and Healthcare Providers
 
 
Who is eligible for the FoundationOne test?

FoundationOne is available for any patient with a malignant solid tumor. It may reveal additional relevant treatment options to consider for patients based on the molecular profile of their tumor or may help provide additional information for patients who are searching for clinical trial options.

 
 
 
Who is eligible for the FoundationOne Heme test?

FoundationOne Heme is available for patients with hematologic malignancies and sarcomas. It may reveal additional treatment options to consider based on the genomic factors driving a patient's cancer.

 
 
 
How do I order FoundationOne?

FoundationOne utilizes routine formalin-fixed, paraffin-embedded clinical samples, which may be available from a previous biopsy or surgery. We have made the ordering process as simple as possible, so all your office needs to do is complete a requisition form and we will contact pathology to obtain the sample. We will take care of insurance and reporting. Click here for more ordering information.

 
 
 
What are the specimen requirements for FoundationOne?

FoundationOne requires 40 \0x03BCm of FFPE tissue, of which ~20% or more is of malignant origin, on 8 to 10 unstained slides or from a block reviewed and approved by a pathologist as the most representative block for the patient diagnosis. All solid tumor types are acceptable. Click here to download detailed specimen requirements.

Foundation Medicine is able to process any clinical sample that meets these guidelines. Should your sample be insufficient, we will notify you within approximately two days of receipt..

 
 
 
How do I order FoundationOne Heme?

FoundationOne Heme utilizes both routine FFPE samples, which may be available from a previous biopsy or surgery, and peripheral whole blood or bone marrow aspirate specimens. We have made the ordering process as simple as possible. If you are submitting an FFPE sample all your office needs to do is complete a requisition form and we will contact pathology to obtain the sample. For peripheral whole blood or bone marrow aspirate samples, complete a requisition form and send it along with the liquid specimen. We will take care of insurance and reporting. Click here for more ordering information.

 
 
 
What are the specimen requirements for FoundationOne Heme?

For FFPE specimens, FoundationOne Heme requires 80 \0x03BCm of tissue from a block reviewed and approved by a pathologist as the most representative block for the patient diagnosis. Click here to download detailed specimen requirements for FFPE.

For peripheral blood specimens, FoundationOne Heme requires 2mL whole blood collected in an EDTA, sodium citrate or sodium heparin tube and an additional 2.5mL whole blood collected in a PAXgene Blood RNA tube. Click here to view PAXgene Blood RNA collection instructions, Click here to watch a PAXgene Blood RNA tube collection video.

For bone marrow aspirate specimens, FoundationOne Heme requires 0.5-2.0 mL bone marrow collected in an EDTA tube.

Click here to download detailed specimen requirements for liquid specimens.

Foundation Medicine is able to process any clinical sample that meets these guidelines. Should your sample be insufficient, we will notify you within approximately two days of receipt.

 
 
 
Are FoundationOne and FoundationOne Heme covered by insurance?

Foundation Medicine bills the patient's insurance company for each test as the provider of service. Typically, it takes 60 to 90 days for the insurance company to respond to Foundation Medicine's claims. During this time the patient may receive an Explanation of Benefits; this is not a bill and will explain the coverage initially offered by the insurance company.

If the insurance company denies coverage, Foundation Medicine works on behalf of the patient to attempt to obtain coverage and will assist in pursuing appeals on your behalf to minimize the financial burden when appropriate. We may also contact your office for assistance in the appeals process.

Click here for a more detailed explanation of billing financial services.

 
 
 
How long does it take to get results?

Your office will receive a report 11-14 days after Foundation Medicine receives your patient's sample for FoundationOne. Turnaround time may be slightly longer for FoundationOne Heme. Click here for more information about understanding the results.

 
 
 
How do I obtain the results?

We will send the results via fax, and you may also access reports and links to additional information through the Interactive Cancer Explorer. This secure, online resource provides current information about genomic alterations, associated therapies and clinical trials; all curated by genomic experts in oncology and pathology. It connects directly to resources like ClinicalTrials.gov, PubMed and other online references to give you the supporting information you need to make treatment recommendations tailored to each patient.

The Interactive Cancer Explorer is available for ordering physicians. Please contact your sales representative or call Client Services at (888) 988-3639 to set up your Interactive Cancer Explorer account.

 
 
 
How might FoundationOne or FoundationOne Heme be useful in my practice?

FoundationOne and FoundationOne Heme identify and report genomic alterations that can guide informed treatment recommendations for targeted therapies, either approved or in clinical trials, with extremely high sensitivity and specificity for alterations within hundreds of relevant cancer genes.

 
 
 
Do these tests predict response to chemotherapy or the likelihood of recurrence?

No, these tests were not designed to predict response to chemotherapy or recurrence. They help match the genomic alterations present in a cancer with specific targeted therapies or clinical trials.

 
 
 
Who can I contact if I have additional questions?

Foundation Medicine Customer Services Team: (888) 988-3639

Hours of operation: Monday through Friday, 8:00 am EST - 8:00 pm EST

 
 
Medicare Compliance

FMI is committed to doing things the right way in all facets of its business – by providing quality testing for patients, by offering timely and reliable customer service, and by billing for its services responsibly and correctly. Compliance with Medicare rules and regulations is critical to achieving this goal.

One of the more complex Medicare billing rules with which FMI , and its customers, must comply, is the so-called 14-day-rule. The 14-day rule helps to establish who will be billed for a test provided to a Medicare patient. In some cases, Medicare is billed directly for FMI testing. In other cases, the 14-day rule requires that FMI bill its hospital customers for testing that is performed on Medicare patients.

To see how the 14 day rule is applied in specific circumstances, click here. Additional information can also be found by going to Frequently Asked Questions.

 
Publications

FoundationOne Heme

Case Studies (5)

Clinical response to everolimus in a patient with Hodgkin's Lymphoma Harboring a TSC2 Mutation.Perini GF, Campregher PV, Ross JS, Ali S, Hamerschlak N, Santos FPS. Blood Cancer Journal.May 2016.

Evaluation of a Congenital Infantile Fibrosarcoma by Comprehensive Genomic Profiling Reveals an LMNA-NTRK1 Gene Fusion Responsive to Crizotinib Wong V, Paylick D, Brennan T, Yelensky R, Crawford J, Ross JS, Miller VA, Malicki D, Stephens PJ, Ali SM, Ahn H. J Natl Cancer Inst. Nov 2015.

Novel FNDC3B and MECOM fusion and WT1 L378fs* 7 frameshift mutation in an acute myeloid leukaemia patient with cytomorphological and immunophenotypic features reminiscent of acute promyelocytic leukaemia. Wang H, McMahon C, Ali SM, Young LE, Yekezare S, Ross JS, Ball ED. British J Heme. 6 July 2015.

Optimal Molecular Methods in Detecting p190 (BCR-ABL) Fusion Variants in Hematologic Malignancies: A Case Report and Review of the Literature. Sonu RJ, Jonas BA, Dwyre DM, Gregg JP, Rashidi HH. Case Rep Hematol. 8 April 2015 [Epub ahead of print]

Comprehensive genomic profiling identifies a novel TNKS2-PDGFRA fusion that defines a myeloid neoplasm with eosinophilia that responded dramatically to imatinib therapy. Chalmers ZR, Ali SM, Ohgami RS, Campregher PV, Frampton GM, Yelensky R, Elvin JA, Palma NA, Erlich R, Vergilio JA, Chmielecki J, Ross JS, Stephens PJ, Hermann R, Miller VA, Miles CR. Blood Cancer J. 2015 Feb 6

 

Publications (2)

Antitumor Response of VEGFR2- and VEGFR3-Amplified Angiosarcoma to Pazopanib Ravi V, Sanford EM, Wang W, Ross JS, Ramesh N, Futreal A, Patel S, Stephens PJ, Miller VA, Ali SM.JNCCN April 2016.

Patient-derived xenotransplants can recapitulate the genetic driver landscape of acute leukemias.Wang K, Sanchez-Martin M, Wang X, Knapp KM, Koche R, Vu L, Nahas MK, He J, Hadler M, Stein EM, Tallman MS, Donahue AL, Frampton GM, Lipson D, Roels S, Stephens PJ, Sanford EM, Brennan T, Otto GA, Yelensky R, Miller VA, Kharas MG, Levine RL, Ferrando A, Armstrong SA, Krivtsov AV. Leukemia July 2016.

Posters and Presentations (33)

Posters and presentations from the 2015 American Society of Hematology Annual Meeting (7)

Posters and presentations from the 2014 American Society of Hematology Annual Meeting (12)

Posters and presentations from the 2013 American Society of Hematology Annual Meeting (10)

Identification of ANLN as ETV6 partner gene in recurrent t(7;12)(p15;p13): a possible role of deregulated ANLN expression in leukemogenesisCampregher PV, Pereira Wde O, Lisboa B, Puga R, Helman R, Miyagi M, da Mata EH, Datoguia TS, Velloso ED, Bacal NS, Ross JS, Ali S, Miller V, Costa FF, Hamerschlak N, Santos FP. Mol Cancer. 19 Nov 2015.

Development and Analytical Validation of a Clinical Next Generation Sequencing-based Assay for Hematolymphoid Malignancies He J, Lipson D, Nahas M, Otto G, Wang K, Knapp KM, Brennan KW, Donahue AL, Young LE, Young G, Fichtenholtz A, Ross JR, Yelensky R, Stephens, PJ, Miller VA, Levine RL Presented at American Association for Cancer Research Annual Meeting 2014; 2014 April 5-9; San Diego, CA.

Comprehensive genomic profiling of hematologic malignancies by a clinical next generation sequencing-based assay Ross JS, Nahas M, Lipson D, Otto GA, Yelensky R, Abdel-Wahab O, Wang K, He J, Intlekofer AM, Rampal RK, Brennan K, Young G, Donahue A, Frampton G, Young L, Klimstra D, Dogan A, Armstrong SA, van den Brink MRM, Miller VA, Stephens PJ, Levine RL. Presented at United States and Canada Association of Pathologists Annual Meeting 2014; 2014 Mar 1-7; San Diego, CA.

 

FoundationOne

Validation (1)

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, Sun J, Juhn F, Brennan K, Iwanik K, Maillet A,Buell J, White E, Zhao M, Balasubramanian S, Terzic S, Richards T, Banning V, Garcia L, Mahoney K, Zwirko Z, Donahue A, Beltran H, Mosquera JM, Rubin MA,Dogan S, Hedvat CV, Berger MF, Pusztai L, Lechner M, Boshoff C, Jarosz M, Vietz C, Parker A, Miller VA, Ross JS, Curran J, Cronin MT, Stephens PJ, Lipson D,Yelensky R. Nat Biotechnol. 2013 Oct 20. [Epub ahead of print]

 

Case Studies and Case Series (46)

High MET amplification level as a resistance mechanism to osimertinib (AZD9291) in a patient that symptomatically responded to crizotinib treatment post-osimertinib progression. Ou SH, Agarwal N, Ali SM. Lung Cancer. August 2016.

Genomic profiling and treatment of HER2+, ER+, PgR+ “triple positive” breast cancer: A case report and literature review Schwab RB, Koehler M, Ali SM, Murray BW Cancer Treatment and Research Communications June 2016.

Acquired ALK L1152R Mutation Confers Resistance to Ceritinib and Predicts Response to Alectinib. Journal of Thoracic Oncology. April 2016. 

A Combination of Targeted Therapy with Chemotherapy Backbone Induces Response in a Treatment-Resistant Triple-Negative MCL1-Amplified Metastatic Breast Cancer Patient. Ali SM, Watson J, Wang K, Chung JH, McMahon C, Ross JS, Dicke KA. Case Rep Oncol. Feb 2016.

A metastatic colon adenocarcinoma harboring BRAF V600E has a durable major response to dabrafenib/trametinib and chemotherapyWilliams CB, McMahon C, Ali SM, Abramovitz M, Williams KA, Klein J, McKean H, Yelensky R, George TJ, Elvin JA, Soman S, Lipson D, Chmielecki J, Morosini D, Miller VA, Stephens PJ, Ross JS, Leyland-Jones B. OncoTargets and Therapy. Dec 2015.

 Identification of BRAF Kinase Domain Duplications Across Multiple Tumor Types and Response to RAF Inhibitor Therapy. Klempner SJ, Bordoni R, Gowen K, Kaplan H, Stephens PJ, Ou SI, Ali SM.  JAMA Onc. 12 Nov 2015.

Renal carcinoma associated with a novel succinate dehydrogenase A mutation: a case report and review of literature of a rare subtype of renal carcinoma. Ozluk Y, Taheri D, Matoso A, Sanli O, Berker NK, Yakirevich E, Balasubramanian S, Ross JS, Ali SM, Netto GJ. Human Pathology. 5 Sept 2015.

FGFR3-TACC3: A novel gene fusion in cervical cancer. Carneiro BA, Elvin JA, Kamath SD, Ali SM, Paintal AS, Restrepo A, Berry E, Giles FJ, Johnson ML. Gyn Onc Rep. August 2015 [Epub ahead of print]

Selective Response to Mammalian Target of Rapamycin Inhibition in a Patient with Metastatic Renal Cell Carcinoma Bearing TSC1 MutationAli SM, Stephens PJ, Miller VA, Ross JS, Pal SK. Eur Urol. August 2015.

FGFR3-TACC4 fusion defines subset of cervical ca responsive to FGFRiCarneiro BA, Elvin JA, Kamath SD, Ali SM, Paintal AS, Restrepo A, Berry E, Giles FJ, Johnson ML. Gynecologic Oncology Reports. August 2015.

STUMP un"stumped": anti-tumor response to anaplastic lymphoma kinase (ALK) inhibitor based targeted therapy in uterine inflammatory myofibroblastic tumor with myxoid features harboring DCTN1-ALK fusion. Vivek S, McMahon C, Patel S, Zinner R, Silva EG, Elvin JA, Subbiah IM, Ohaji C, Moorthy Ganeshan D, Anand D, Levenback CF, Berry J, Brennan T, Chmielecki J, Chalmers ZR, Mayfield J, Miller VA, Stephens PJ, Ross JS, Ali SM. J Hematol Oncol. 11 June 2015

Identification of a novel TMEM106B-ROS1 fusion variant in lung adenocarcinoma by comprehensive genomic profiling. Ou SI, Chalmers ZR, Azada MC, Ross JS, c, Stephens PJ, Ali SM, Miller VA. Lung Discovery. June 2015.

Prolonged Response to Trastuzumab in Patient With HER2-Nonamplified Breast Cancer With Elevated HER2 Dimerization. Chumsri S, Weidler J, Ali S, Balasubramanian S, Wallweber G, DeFazio-Eli L, Chenna A, Huang W, DeRidder A, Goicocheal L and Perez EA. Journal of the National Comprehensive Cancer Network.  11 May 2015.

Systemic and CNS activity of the RET inhibitor vandetanib combined with the mTOR inhibitor everolimus in KIF5B-RET re-arranged non-small cell lung cancer with brain metastases. Subbiah V, Berry J, Roxas M, Guha-Thakurta N, Subbiah IM, Ali SM, McMahon C, Miller V, Cascone T, Pai S, Tang Z, Heymach JV. Lung Cancer. 22 April 2015 [Epub ahead of print]

Optimal Molecular Methods in Detecting p190 (BCR-ABL) Fusion Variants in Hematologic Malignancies: A Case Report and Review of the Literature. Sonu RJ, Jonas BA, Dwyre DM, Gregg JP, Rashidi HH. Case Rep Hematol. 8 Apr 2015. [Epub ahead of print]

Detection of Crizotinib-Sensitive Lung Adenocarcinomas With MET, ALK, and ROS1 Genomic Alterations via Comprehensive Genomic Profiling. Le X, Freed JA, VanderLaan PA, Huberman MS, Rangachari D, Jorge SE, Lucena-Araujo AR, Kobayashi SS, Balasubramanian S, He J, Chudnovsky Y, Miller VA, Ali SM, Costa DB. Clin Lung Cancer. 25 Mar 2015. [Epub ahead of print]

Identification of a novel TMEM106B-ROS1 fusion variant in lung adenocarcinoma by comprehensive genomic profiling Ou SH, Chalmers ZR, Azada MC, Ross JS, Stephens PJ, Ali SM, Miller VA. Lung Cancer. 21 Mar 2015. [Epub ahead of print]

Selective response to mammalian target of rapamycin inhibition in patient with metastatic renal cell carcinoma bearing TSC1 mutation Ali SM, Stephens PJ, Miller VA, Ross JS, Pal SK. Eur Urology. 18 Mar 2015. [Epub ahead of print]

N of 1 case reports of exceptional responders accrued from pancreatic cancer patients enrolled in first-in-man studies from 2002 through 2012. Garrido-Laguna I, Tometich D, Hu N, Ying J, Geiersbach K, Whisenant J, Wang K, Ross JS, Sharma S. Oncoscience. 14 March 2015

Exceptional response to pazopanib in a patient with urothelial carcinoma harboring FGFR3 activating mutation and amplification. Palma N, Morris JC, Ali SM, Ross JS, Pal SK. Eur Urology. 9 Mar 2015. [Epub ahead of print]

A novel SDHA-deficient renal cell carcinoma revealed by comprehensive genomic profiling. Yakirevich E, Ali SM, Mega A, McMahon C, Bridsky AS, Ross JS, Allen J, Elvin JA, Safran H, Rsnick MB. Am J Surg Pathol. 2015 Feb 25. [Epub ahead of print]

I1171 missense mutation (particularly I1171N) is a common resistance mutation in ALK-positive NSCLC patients who have progressive disease while on alectinib and is sensitive to ceritinib. Ou SH, Greenbowe J, Khan ZU, Azada MC, Ross JS, Stephens PJ, Ali SM, Miller VA, Gitlitz B. Lung Cancer. 2015 Feb 12. [Epub ahead of print]

Exceptional Response on Addition of Everolimus to Taxane in Urothelial Carcinoma Bearing an NF2 Mutation. Ali SM, Miller VA, Ross JS, Pal SK. Eur Urol. 2015 Jan 24. [Epub ahead of print]

RET fusion as a novel driver of medullary thyroid carcinoma. Grubbs EG, Ng PK, Bui J, Busaidy NL, Chen K, Lee JE, Lu X, Lu H, Meric-Bernstam F, Mills GB, Palmer G, Perrier ND, Scott KL, Shaw KR, Waguespack SG, Williams MD, Yelensky R, Cote GJ. J Clin Endocrinol Metab. 2014 Dec 29 [Epub ahead of print]

Melanoma BRAF Fusions-Response. Hutchinson KE, Ross JS, Stephens PJ, Miller VA, Sosman JA, Pao W. Clin Cancer Res. 2014 Dec 15.

Identification of a Novel HIP1-ALK Fusion Variant in Non-Small-Cell Lung Cancer (NSCLC) and Discovery of ALK I1171 (I1171N/S) Mutations in Two ALK-Rearranged NSCLC Patients with Resistance to Alectinib Ou SH, Klempner SJ, Greenbowe JR, Azada M, Schrock AB, Ali SM, Ross JS, Stephens PJ, Miller VA. J Thorac Oncol. 2014 Dec.

Effect of the RET Inhibitor Vandetanib in a Patient With RET Fusion-Positive Metastatic Non-Small-Cell Lung Cancer. Falchook GS, Ordonez NG, Bastida CC, Stephens PJ, Miller VA, Gaido L, Jackson T, Karp DD. J Clin Oncol. 2014 Nov 3. [Epub ahead of print]

RET-Rearranged Lung Adenocarcinomas with Lymphangitic Spread, Psammoma Bodies, and Clinical Responses to Cabozantinib Mukhopadhyay, S, Pennell, N, Ali, SM, Ross, JS, Ma, P, and Velcheti, V. J Thor Onc. 2014 Nov.

Response to Crizotinib in a Patient with MET-mutant Papillary Renal Cell Cancer After Progression on Tivantinib. Stein MN, Hirshfield KM, Zhong H, Singer EA, Ali SM, Ganesan S. Eur Urol. 2014 Oct 27. [Epub ahead of print]

Treatment of metastatic extramammary Paget's disease associated with adnexal adenocarcinoma, with anti-HER2 drugs based on genomic alteration ERBB2 S310F. Vornicova O, Hershkovitz D, Yablonski-Peretz T, Ben-Itzhak O, Keidar Z, Bar-Sela G. Oncologist. 2014 Sep

A Poorly Differentiated Malignant Neoplasm Lacking Lung Markers Harbors an EML4-ALK Rearrangement and Responds to Crizotinib Chung JH, Ali SM, Davis J, Robstad K,
McNally R, Gay LM, Erlich RL, Palma NA, Stephens PJ, Miller VA, Cutugno A, Ross JS. Case Rep Oncol. 2014 Sep

Unique metastases of ALK mutated lung cancer activated to the adnexa of the uterus West AH, Yamada SD, MacMahon H, Acharya SS, Ali SM, He J, Lukas RV, Miller VA, Salgia R. Case Reports in Clinical Pathology. 2014 Sep.

Sclerosing epithelioid fibrosarcoma presenting as intraabdominal sarcomatosis with a novel EWSR1-CREB3L1 gene fusion Stockman DL, Ali SM, He J, Ross JS, Meis JM. Hum Pathol. 2014 Jun 2. [Epub ahead of print]

Durable Response to Crizotinib in a MET-Amplified, KRAS-Mutated Carcinoma of Unknown
Primary
Palma NA, Ali SM, O'Connor J, Dutta D, Wang K, Soman S, Palmer GA, Morosini D,
Ross JS, Lipson D, Stephens PJ, Patel M, Miller VA, Koutrelakos N. Case Rep Oncol. 2014 Jul 23. [Epub ahead of print]

Epidermal Growth Factor Receptor P753S Mutation in Cutaneous Squamous Cell Carcinoma Responsive to Cetuximab-Based Therapy Ganesan P, Ali SM, Wang K, Blumenschein GR, Esmaeli B, Wolff RA, Miller VA, Stephens PJ, Ross JS, Palmer GA, Janku F. J Clin Oncol. 2014 Jun 16. [Epub ahead of print]

Vemurafenib Response in 2 Patients With Posttransplant Refractory BRAF V600E-Mutated Multiple Myeloma Sharman JP, Chmielecki J, Morosini D, Palmer GA, Ross JS, Stephens PJ, Stafl J, Miller VA, Ali SM. Clin Lymphoma Myeloma Leuk. 2014 Jun 11. [Epub ahead of print]

Successful treatment of a patient with Li-Fraumeni syndrome and metastatic lung adenocarcinoma harboring synchronous EGFR L858R and ERBB extracellular domain S310F mutations with the pan HER-inhibitor afatinib Jia Y, Ali SM, Saad S, Chan CA, Miller VA, Halmos B. Cancer Biol Ther. 2014 May 16

Extended Antitumor Response of a BRAF V600E Papillary Thyroid Carcinoma to Vemurafenib Ali SM, He J, Carson W, Stephens PJ, Fiorillo J, Lipson D, Palmer GA, Ross JS, Miller VA, Sharman J. Case Rep Oncol. 2014 May 24.

Acquired Resistance of EGFR-Mutant Lung Adenocarcinomas to Afatinib plus Cetuximab Is Associated with Activation of mTORC1 Pirazzoli V, Nebhan C, Song X, Wurtz A, Walther Z, Cai G, Zhao Z, Jia P, de Stanchina E, Shapiro EM, Gale M, Yin R, Horn L, Carbone DP, Stephens PJ, Miller V, Gettinger S, Pao W, Politi K. Cell Rep. 2014 May 22

Inflammatory Myofibroblastic Tumors harbor multiple potentially actionable kinase fusions Lovly CM, Gupta A, Lipson D, Otto G, Brennan T, Chung CT, Borinstein SC, Ross J, Stephens PJ, Miller VA, Coffin CM. Cancer Discov. 2014 May 29

Next-Generation Sequencing Reveals a Novel NSCLC ALK F1174V Mutation and Confirms ALK G1202R Mutation Confers High-Level Resistance to Alectinib (CH5424802/RO5424802) in ALK-Rearranged NSCLC Patients Who Progressed on Crizotinib Ignatius Ou SH, Azada M, Hsiang DJ, Herman JM, Kain TS, Siwak-Tapp C, Casey C, He J, Ali SM, Klempner SJ, Miller VA. J Thorac Oncol. 2014 Apr.

Antitumor Response of an ERBB2 Amplified Inflammatory Breast Carcinoma With EGFR Mutation to the EGFR-TKI Erlotinib Ali SM, Alpaugh RK, Buell JK, Stephens PJ, Yu JQ, Wu H, Hiemstra CN, Miller VA, Lipson D, Palmer GA, Ross JS, Cristofanilli M. Clin Breast Cancer. 2014 Feb

Response of an ERBB2-Mutated Inflammatory Breast Carcinoma to Human Epidermal Growth Factor Receptor 2-Targeted Therapy Ali SM, Alpaugh RK, Downing SR, Stephens PJ, Yu JQ, Wu H, Buell JK, Miller VA, Lipson D, Palmer GA, Ross JS, Cristofanilli M. J Clin Oncol. 2014 Feb 10. [Epub ahead of print]

Targeted therapy by combined inhibition of the RAF and mTOR kinases in malignant spindle cell neoplasm harboring the KIAA1549-BRAF fusion protein Subbiah V, Westin SN, Wang K, Araujo D, Wang WL, Miller VA, Ross JS, Stephens PJ, Palmer GA, Ali SM. J Hematol Oncol. 2014 Jan 14.

Next-generation sequencing identifies and immunohistochemistry confirms a novel crizotinib-sensitive ALK rearrangement in a patient with metastatic non-small-cell lung cancer Peled N, Palmer G, Hirsch FR, Wynes MW, Ilouze M, Varella-Garcia M, Soussan-Gutman L, Otto GA, Stephens PJ, Ross JS, Cronin MT, Lipson D, Miller VA. J Thorac Oncol. 2012 Sept.

 

Publications (110)

Clinical utility and treatment outcome of comprehensive genomic profiling in high grade glioma patients. Blumenthal DT, Dvir A, Lossos A, Tzuk-Shina T, Lior T, Limon D, Yust-Katz S, Lokiec A, Ram Z, Ross JS, Ali SM, Yair R, Soussan-Gutman L, Bokstein F. J Neurooncol. August 2016.

Individualized Molecular Analyses Guide Efforts (IMAGE): A Prospective Study of Molecular Profiling of Tissue and Blood in Metastatic Triple Negative Breast Cancer.Parsons HA, Beaver JA, Cimino-Mathews A, Ali SM, Axilbund J, Chu D, Connolly R, Cochran R, Croessmann S, Clark T, Gocke CD, Jeter SC, Kennedy M, Lauring J, Lee J, Lipson D, Miller V, Otto G, Rosner GL, Ross JS, Slater SA, Stephens PJ, VanDenBerg DA, Wolff AC, Young L, Zabansky DJ, Zhang Z, Zorzi J, Stearns V, Park BH. Clin Cancer Research. August 2016.

The BATTLE-2 Study: A Biomarker-Integrated Targeted Therapy Study in Previously Treated Patients With Advanced Non-Small-Cell Lung Cancer.Papadimitrakopoulou V, Lee JJ, Wistuba II, Tsao AS, Fossella FV, Kalhor N, Gupta S, Byers LA, Izzo JG, Gettinger SN, Goldberg SB, Tang X, Miller VA, Skoulidis F, Gibbons DL, Shen L, Wei C, Diao L, Peng SA, Wang J, Tam AL, Coombes KR, Koo JS, Mauro DJ, Rubin EH, Heymach JV, Hong WK, Herbst RS. J Clin Oncol. August 2016.

Presence of both alterations in FGFR/FGF and PI3K/AKT/mTOR confer improved outcomes for patients with metastatic breast cancer treated with PI3K/AKT/mTOR inhibitors. Wheler JJ, Atkins JT, Janku F, Moulder SL, Stephens PJ, Yelensky R, Valero V, Miller V, Kurzrock R, Meric-Bernstam F. Oncoscience June 2016.

Predicting Significance of Unknown Variants in Glial Tumors Through Sub-Class Enrichment Fichtenholtz AM, Camarda ND, Neumann EK. Pac Symp BiocomputAugust 2016.

Implementing and Improving Automated Electronic Tumor Molecular Profiling Rioth MJ, Staggs DB, Hackett L, Haberman E, Tod M, Levy M, Warner J. Journal of Oncology Practice March 2016.

TP53 Alterations Correlate with Response to VEGF/VEGFR Inhibitors:Implications for Targeted Therapeutics Wheler JJ, Janku F, Naing A, Li Y, Stephen B, Zinner R, Subbiah V, Fu S, Karp D, Falchook GS, Tsimberidou AM, Piha-Paul S, Anderson R, Ke D, Miller V, Yelensky R, Lee JJ, Hong D, Kurzrock R. Molecular Cancer Therapeutics August 2016.

Primary Undifferentiated Sarcoma of the Kidney Harboring a Novel Variant of CIC-DUX4 Gene Fusion.Mangray S, Somers GR, He J, Zhong S, Shago M, Treaba DO, Lombardo KA, Ali SM, Yakirevich E. Am J Surg Pathol. June 2016.

Characterization of 298 Patients with Lung Cancer Harboring MET Exon 14 Skipping Alterations.Schrock AB, Frampton GM, Suh J, Chalmers ZR, Rosenzweig M, Erlich RL, Halmos B, Goldman J, Forde P, Leuenberger K, Peled N, Kalemkerian GP, Ross JS, Stephens PJ, Miller VA, Ali SM, Ou SH. J Thorac Oncol.June 2016.

Profiling of 149 salivary duct carcinomas, carcinoma ex pleomorphic adenomas, and adenocarcinomas, not otherwise specified reveals actionable genomic alterations. Wang K, Russell JS, McDermott JD, Elvin JA, Khaira D, Johnson A, Jennings TA, Ali SM, Murray M, Marshall C, Oldham D, Washburn D, Wong S, Chmiekecki J, Yelensky R, Lipson D, Miller V, Serracino HS, Stephens PJ, Ross JS, Bowles DW. Clin Cancer Res. June 2016.

Nonamplification ERBB2 genomic alterations in 5605 cases of recurrent and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies.Ross JS, Gay LM, Wang K, Ali SM, Chumsri S, Elvin JA, Bose R, Vergilio JA, Suh J, Yelensky R, Lipson D, Chmielecki J, Waintraub S, Leyland-Jones B, Miller VA, Stephens PJ. CancerJune 2016

Comprehensive Genomic Profiling Identifies a Subset of Crizotinib-Responsive ALK-Rearranged Non-Small Cell Lung Cancer Not Detected by Fluorescence In Situ Hybridization. Ali SM, Hensing T, Schrock AB, Allen J, Sanford E, Gowen K, Kulkarni A, He J, Suh JH, Lipson D, Elvin JA, Yelensky R, Chalmers Z, Chmielecki J, Peled N, Klempner SJ, Firozvi K, Frampton GM, Molina JR, Menon S, Brahmer JR, MacMahon H, Nowak J, Ou SH, Zauderer M, Ladanyi M, Zakowski M, Fischbach N, Ross JS, Stephens PJ, Miller VA, Wakelee H, Ganesan S, Salgia R. Oncologist June 2016.

Yield and Clinical Utility of Next-Generation Sequencing in Selected Patients With Lung Adenocarcinoma.DiBardino DM, Saqi A, Elvin JA, Greenbowe J, Suh JH, Miller VA, Ali SM, Stoopler M, Bulman WA. Clin Lung Cancer June 2016.

Comprehensive Genomic Profiling of Clinically Advanced Medullary Thyroid Carcinoma.Heilmann AM, Subbiah V, Wang K, Sun JX, Elvin JA, Chmielecki J, Sherman SI, Murthy R, Busaidy NL, Subbiah I, Yelensky R, Nangia C, Vergilio JA, Khan SA, Erlich RL, Lipson D, Ross JS, Miller VA, Shah MH, Ali SM, Stephens PJ.Oncology May 2016.

Cancer Therapy Directed by Comprehensive Genomic Profiling: A Single Center Study.Wheler JJ, Janku F, Naing A, Li Y, Stephen B, Zinner R, Subbiah V, Fu S, Karp D, Falchook GS, Tsimberidou AM, Piha-Paul S, Anderson R, Ke D, Miller V, Yelensky R, Lee JJ, Hong DS, Kurzrock R.Cancer Res. May 2016.

Immune activation and response to pembrolizumab in POLE-mutant endometrial cancer Mehnert JM, Panda A, Zhong H, Hirshfield K, Damare S, Lane K, Sokol L, Stein MN, Rodriguez-Rodriquez L, Kaufman HL, Ali S, Ross JS, Pavlick DC, Bhanot G, White EP, DiPaola RS, Lovell A, Cheng J, Ganesan S.J Clin Invest.June 2016.

Relationship of smoking status to genomic profile, chemotherapy response and clinical outcome in patients with advanced urothelial carcinomaJoshi M, Vasekar M, Grivas P, Emamekhoo H, Hsu J, Miller VA, Stephens PJ, Ali SM, Ross JS, Zhu J, Warrick J, Drabick JJ, Holder SL, Kaag M, Li M, Pal SK.Oncotarget.May 2016.

Comprehensive Genomic Profiling Facilitates Implementation of the National Comprehensive Cancer Network Guidelines for Lung Cancer Biomarker Testing and Identifies Patients Who May Benefit From Enrollment in Mechanism-Driven Clinical Trials. Suh JH, Johnson A, Albacker L, Wang K, Chmielecki J, Frampton G, Gay L, Elvin JA, Vergilio J, Ali S, Miller VA, Stephens PJ, Ross JS. The Oncologist. May 2016. 

TPD52L1-ROS1, a new ROS1 fusion variant in lung adenosquamous cell carcinoma identified by comprehensive genomic profiling.  Zhu VW, Upadhyay D, Schrock AB, Gowen K, Ali SM, Ou SI. Lung Cancer. April 2016. 

EGFR fusions as novel therapeutic targets in lung cancer. Konduri K, Gallant J, Chae YK, Giles FJ, Gitlitz BJ, Gowen K, Ichihara E, Owonikoko TK, Peddareddigari V, Whiteley A, Chen H, Yan Y, Sheehan JH, Meiler J, Morosini D, Ross JS, Stephens PJ, Miller VA, Ali SM, Lovly CM. Cancer Discovery. April 2016.

Triple-negative breast cancers with amplification of JAK2 at the 9p24 locus demonstrate JAK2-specific dependence. Balko JM, Schwarz LJ, Luo N, Estrada MV, Giltnane JM, Davila-Gonzalez D, Wang K, Sanchez V, Dean PT, Combs SE, Hicks D, JA Pinto, Landis MD, Doimi FD, Yelensky R, Miller VA, Stephens PJ, Rimm DL, Gomez H, Chang JC, Sanders ME, Cook RS, Arteaga CL. Science Translational Medicine. April 2016. 

Genomic Alterations Observed in Colitis-Associated Cancers Are Distinct From Those Found in Sporadic Colorectal Cancers and Vary by Type of Inflammatory Bowel Disease. Yaeger R, Shah MA, Miller VA, Kelsen JR, Wang K, Heins ZJ, Ross JS, He Y, Sanford E, Yantiss RK, Balasubramanian S, Stephens PJ, Schultz N, Oren M, Tang L, Kelsen D. Gastroenterology. April 2016. 

Comprehensive Genomic Profiling of Anal Squamous Cell Carcinoma Reveals Distinct Genomically Defined Classes. Chung JH, Sanford E, Kelmpner SJ, Schrock AB, Palma NA, Erlich RL, Frampton GM, Chalmers ZR, Vergilio J, Rubinson DA, Sun JX, Chmielecki J, Yelensky R, Suh JH, Lipson D, George TJ, Elvin JA, Stephens PJ, Miller VA, Ross JS, Ali SM. Annals of Oncology. April 2016. 

BRAFV600E Mutations in High Grade Colorectal Neuroendocrine Tumors May Predict Responsiveness to BRAF-MEK Combination Therapy. Klempner SJ, Gershenhorn B, Tran P, Lee TK, Erlander MG, Gowen K, Schrock AB, Morosini D, Ross JS, Miller VA, Stephens PJ, Ou SI, Ali SM. Cancer Discovery. April 2016. 

Use of comprehensive genomic profiling to direct point-of-care management of patients with gynecologic cancers. Rodriguez-Rodriguez L, Hirshfield KM, Rojas V, DiPaola RS, Gibbon D, Hellmann M, Isani S, Leiser A, Riedlinger GM, Wagreich A, Ali SM, Elvin JA, Miller VA, Ganesan S. Gynecol Oncol. April 2016. 

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Rosenberg JE, Hoffman-Censits J, Powles T, van der Heijden MS, Balar AV, Necchi A, Dawson N, O'Donnell PH, Balmanoukian A, Loriot Y, Srinivas S, Retz MM, Grivas P, Joseph RW, Galsky MD, Fleming MT, Petrylak DP, Perez-Gracia JL, Burris HA, Castellano D, Canil C, Bellmunt J, Bajorin D, Nickles D, Bourgon R, Frampton GM, Cui N, Mariathasan S, Abidoye O, Fine GD, Dreicer R. Lancet. March 2016.

Genomic Profiling of Lung Adenocarcinoma patients reveals therapeutic targets and confers clinical benefit when standard molecular testing is negative. Lim SM, Kim EY, Kim HR, Ali SM, Greenbowe JR, Shim HS, Chang H, Lim S, Paik S, Cho BC. Oncotarget. March 2016. 

Oncogenic ALK Fusion in Rare and Aggressive Subtype of Colorectal Adenocarcinoma as a Potential Therapeutic Target. Yakirevich E, Resnick MB, Mangray S, Wheeler M, Jackson CL, Lombardo KA, Lee J, Kim KM, Gill AJ, Wang K, Gowen K, Sun J, Miller VA, Stephens PJ, Ali SM, Ross JS, Safran H. Clin Cancer Res. March 2016. 

Comprehensive Genomic Profiling Identifies Frequent Drug Sensitive EGFR Exon 19 Deletions in NSCLC Not Identified by Prior Molecular Testing. Schrock AB, Frampton GM, Herndon D, Greenbowe J, Wang K, Lipson D, Yelensky R, Chalmers Z, Chmielecki J, Elvin JA, Wollner M, Dvir A, Soussan-Guttman L, Bordonii R, Peled N, Braiteh F, Raez LE, Erlich R, Ou SI, Mohamed M, Ross JS, Stephens PJ, Ali SM, Miller VA. Clinical Cancer Research. March 2016. 

Next-generation sequencing reveals somatic mutations that confer exceptional response to everolimus. Lim SM, Park HS, Kim S, Kim S, Ali SM, Greenbowe JR, Yang IS, Kwon N, Lee JL, Ryu M, Ahn J, Lee J, Lee MG, Kim HS, Kim H, Kim HR, Moon YW, Chung HC, Kim J, Kang Y, Cho BC. Oncotarget. Feb 2016. 

Genomic Characterization of Renal Cell Carcinoma with Sarcomatoid Dedifferentiation Pinpoints Recurrent Genomic Alterations. Malouf GG, Ali SM, Wang K, Balasubramanian S, Ross JS, Miller VA, Stephens PJ, Khayat D, Pal SK, Xiaoping S, Sircar K, Tamboli P, Jonasch E, Tannir NM, Wood CG, Karam JA. European Urology. Feb 2016. 

Comprehensive Genomic Profiling of Renal Cell Carcinoma at Initial Diagnosis and Putative Local Recurrence. Chalmers ZR, Johnson A, Ali SM, Frampton GM, Miller VA, Ross JS, Pal SK. European Urology. Feb 2016. 

Next-generation sequencing reveals somatic mutations that confer exceptional response to everolimus. Lim SM, Park HS, Kim S, K S, Ali SM, Greenbowe JR, Yang IS, Kwon N, Lee JL, Ryu M, Ahn J, Lee J, Lee MG, Kim HS, Moon YW, Chung HC, Kim J, Kang Y, Cho BC. Feb 2016. 

Clinically Advanced and Metastatic Pure Mucinous Carcinoma of the Breast: A Comprehensive Genomic Profiling Study. Ross JS, Gay LM, Nozad S, Wang K, Ali SM, Boguniewicz A, Khaira D, Johnson A, Elvin JA, Vergilio J, Suh J, Miller VA, Stephens PJ. Breast Cancer Research and Treatment. Jan 2016. 

A novel acquired ALK F1245C mutation confers resistance to crizotinib in ALK -positive NSCLC but is sensitive to ceritinibKodityal S, Elvin JA, Squillace R, Agarwal N, Miller VA, Ali SM, Klempner SJ, Ou SI. Lung Cancer. Dec 2015.

Correlation Between Molecular Subclassifications of Clear Cell Renal Cell Carcinoma and Targeted Therapy Response. Ho TH, Choueiri TK, Wang K, Karam JS, Chalmers Z, Frampton G, Elvin JA, Johnson A, Liu X, Lin Y, Joseph RW, Stanton ML, Miller VA, Stephens PJ, Ross JS, Ali SM, Pal SK. European Urology.Dec 2015. 

Comprehensive Genomic Profiling of Advanced Penile Carcinoma Suggests a High Frequency of Clinically Relevant Genomic Alterations.  Ali SM, Pal SK, Wang K, Palma NA, Sanford E, Bailey M, He J, Elvin JA, Chmieleckia J, Squillace R, Dow E, Morosini D, Buell J, Yelensky R, Lipson D, Frampton GM, Howley P, Ross JS, Stephens PJ, Miller VA. The Oncologist. Dec 2015.  

Comprehensive genomic profiling of 295 cases of clinically advanced urothelial carcinoma of the urinary bladder reveals a high frequency of clinically relevant genomic alterationsRoss JS, Wang K, Khaira D, Ali SM, Fisher H, Mian B, Nazeer Tipu, Elvin JA, Palma N, Yelensky R, Lipson D, Miller VA, Stephens PJ, Subbiah V, Pal SK. Cancer. Dec 2015.

MET 14 Deletion in Sarcomatoid Non–Small-Cell Lung Cancer Detected by Next-Generation Sequencing and Successfully Treated with a MET InhibitorLee C, Usenko D, Frampton GM, McMahon C, Ali SM, Weiss J. Journal of Thoracic Oncology. Dec 2015.

Defects in DNA Repair Genes Predict Response to Neoadjuvant Cisplatin-based chemotherapy in Muscle-invasive Bladder Cancer Plimack ER , Dunbrack RL, Brennan TA , Andrake MD, Zhou Y, Serebriiskii IG, Slifker M, Alpaugh K, Dulaimi E, Palma N, Hoffman-Censits J, Bilusic M, Wong Y, Kutikov A, Viterbo R, Greenberg RE, Chen DYT, Lallas CD, Trabulsi EJ, Yelensky R, McConkey DJ, Miller VA , Golemis EA and Ross EA. Euro Urol. 1 Dec 2015.

Diverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms

EGFR kinase domain duplication (EGFR-KDD) is a novel oncogenic driver in lung cancer that is clinically responsive to afatinibGallant JN, Sheehan JH, Shaver TM, Bailey M, Lipson D, Chandramohan R, Red Brewer M, York SJ, Kris MG, Pietenpol JA, Ladanyi M, Miller VA, Ali SM, Meiler J, Lovly CM. Cancer Discovery. 5 Nov 2015.

Comprehensive Genomic Profiling of Inflammatory Breast Cancer Cases Reveals a High Frequency of Clinically Relevant Genomic Alterations Ross JS, Ali SM, Wang K, Khaira D, Palma NA, Chmielecki J, Palmer GA, Morosini D, Elvin JA, Fernandez SV, Miller VA, Stephens PJ, Cristofanilli M. Breast Cancer Research and Treatment. Nov 2015.

Comprehensive genomic profiling of extrahepatic cholangiocarcinoma reveals a long tail of therapeutic targets. Lee H, Wang K, Johnson A, Jones DM, Ali SM, Elvin JA, Yelensky R, Lipson D, Miller VA, Stephens PJ, Javle M, Ross JS. J. Clin Pathol. 23 Oct 2015.

Comprehensive Genomic Profiling of Advanced Esophageal Squamous Cell Carcinomas and Esophageal Adenocarcinomas Reveals Similarities and DifferencesWang K, Johnson A, Ali SM, Klempner SJ, Bekaii-Saab T, Vacirca JL, Khaira D, Yelensky R, Chmielecki J, Elvin JA, Lipson D, Miller VA, Stephens PJ, Ross JS. Oncologist. 20 Oct 2015

Evaluation of 122 Advanced Stages Cutaneous Squamous Cell Carcinomas by Comprehensive Genomic Profiling Opens the Door for New Routes to Targeted TherapiesAl-Rohil RN, Tarasen AJ, Carlson JA, Wang K, Johnson A, Yelensky R, Lipson D, Elvin JA, Vergilio J, Ali SM, Suh J, Miller VA, Stephens PJ, Ganesan P, Janku F, Karp DD, Subbiah V, Mihm MC, and Ross JS. Cancer. 19 Oct 2015.

RICTOR amplification defines a novel subset of lung cancer patients who may benefit from treatment with mTOR1/2 inhibitorsCheng H, Zou Y, Ross JS, Wang K, Liu X, Halmos B, Ali SM, Liu H, Verma A, Montagna C, Chachoua A, Goel S, Schwartz EL, Zhu C, Shan J, Yu Y, Gritsman K, Yelensky R, Lipson D, Otto G, Hawryluk M, Stephens PJ, Miller VA, Piperdi B and Perez-Soler R. Cancer Discovery. 14 Sept 2015.

ALK F1174V mutation confers sensitivity while ALK I1171 mutation confers resistance Q1 to
alectinib. The importance of serial biopsy post progression. Ou SI, Milliken JC, Azada MC, Miller VA, Ali SM, Klempner SJ. Lung Cancer Journal. 12 Sept 2015.

The distribution of BRAF gene fusions in solid tumors and response to targeted therapyRoss JS, Wang K, Chmielecki J, Gay L, Johnson A, Chudnovsky J, Yelensky R, Lipson D, Ali SM, Elvin JA, Vergilio J, Roels S, Miller VA, Nakamura BN, Gray A, Wong MK, Stephens PJ. International Journal of Cancer. 8 Sept 2015.

Inhibiting MEK in MAPK pathway activated MyelomaC J Heuck, Y Jethava, R Khan, F van Rhee, M Zangari, S Chavan, K Robbins, S E Miller, A Matin, M Mohan, S M Ali, P J Stephens, J S Ross, V A Miller, F Davies, B Barlogie and G Morgan. Leukemia. 1 Sept 2015.

Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer. Young CD, Zimmerman LJ, Hoshino D, Formisano L, Hanker AB, Gatza ML, Morrison MM, Moore PD, Whitwell CA, Dave B, Stricker T, Bhola NE, Silva GO, Patel P, Brantley-Sieders DM, Levin M, Horiates M, Palma NA, Wang K, Stephens PJ, Perou CM, Weaver AM, O'Shaughnessy JA, Chang JC, Park BH, Liebler DC, Cook RS, Arteaga CL. Mol Cell Proteomics. 14 July 2015.

Characterization of Clinical Cases of Collecting Duct Carcinoma of the Kidney Assessed by Comprehensive Genomic Profiling. Pal KS, Choueiri TK, Wang K, Khaira D, Karam JA, Van Allen E, Palma NA, Stein MN, Johnson A, Squillace R, Elvin JA, Chmielecki J, Yelensky R, Yakirevich E, Lipson D, Lin DI, Miller VA, Stephens PJ, Ali SM, Ross JS. European Urology. 3 July 2015.

Durable clinical benefit to trastuzumab and chemotherapy in a patient with metastatic colon adenocarcinoma harboring ERBB2 amplification. Umut Disel, Alexis Germain, Bahar Yilmazel, Huseyin Abali, Filiz Aka Bolat, Roman Yelensky, Julia A. Elvin, Doron Lipson, Juliann Chmielecki, Kai Wang, Philip J. Stephens, Jeffrey S. Ross, Vincent A. Miller, Siraj M. Ali, Thomas J. George Jr. Oncoscience. 1 July 2015.

Detection of novel and potentially actionable anaplastic lymphoma kinase (ALK) rearrangement in colorectal adenocarcinoma by immunohistochemistry screeningLee J, Kim HC, Hong JY, Wang K, Kim SY, Jang J, Kim ST, Park JO, Lim HY, Kang WK, Park YS, Lee J, Lee WY, Park YA, Huh JW, Yun SH, Do I, Kim SH, Balasubramanian S, Stephens PJ, Ross JS, Li GG, Hornby Z, Ali SM, Miller VA, Kim K, and Ou SI. Oncotarget. 1 July 2015. 

Emergence of RET rearrangement co-existing with activated EGFR mutation in EGFR-mutated NSCLC patients who had progressed on first- or second-generation EGFR TKI. Klempner SJ, Bazhenova LA, Braiteh FS, Nikolinakos PG, Gowen K, Cervantes CM, Chmielecki J, Greenbowe JR, Ross JS, Stephens PJ, Miller VA, Ali SM, Ou SH. Lung Cancer. 29 June 2015.

Identification and Characterization of RET Fusions in Advanced Colon Cancer. Le Rolle A, Klempner SJ, Garrett CR, Seery T, Sanford EM, Balasubramanian S, Ross JS, Stephens PJ, Miller VA, Ali SM, Chiu VK. Oncotarget. 30 May 2015. 

Genomic profiling of advanced-stage, metaplastic breast carcinoma by next-generation sequencing reveals frequent, targetable genomic abnormalities and potential new treatment options. Ross JS, Badve S, Wang K, Sheehan CE, Boguniewicz AB, Otto GA, Yelensky R, Lipson D, Ali S, Morosini D, Chliemlecki J, Elvin JA, Miller VA, Stephens PJ. Arch Pathol Lab Med. May 2015

Multiple Gene Aberrations and Breast Cancer: Lessons from Super-Responders. Wheler JJ, Atkins JT, Janku F, Moulder SL, Yelensky R, Stephens PJ, Kurzrock R. BMC Cancer. 29 May 2015.

Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. Frampton GM, Ali SM, Rosenzweig M, Chmielecki J, Lu X, Bauer TM, Akimov M, Bufill J, Lee C, Jentz D, Hoover R, Ou I, Salgia R, Brennan T, Chalmers Z, Elvin JA, Erlich R, Fichtenholtz A, Gowen KA, Greenbowe J, Johnson A, Khaira D, McMahon C, Sanford EM, Roels S, White J, Lipson D, Yelensky R, Morosini D, Ross JS, Collisson E, Peters M, Stephens PJ, Miller VA. Cancer Discov. 13 May 2015 [Epub ahead of print]

Prospective comprehensive genomic profiling of advanced gastric carcinoma cases reveals frequent clinically relevant genomic alterations and new routes for targeted therapies. Ali SM, Sanford EM, Klempner SJ, Rubinson DA, Wang K, Palma NA, Chmielecki J, Yelensky R, Palmer GA, Morosini D, Lipson D, Catenacci DV, Braiteh F, Erlich R, Stephens PJ, Ross JS, Ou SH, Miller VA. Oncologist. 16 April 2015 [Epub ahead of print]

Genomic alterations in DNA repair and chromatin remodeling genes in estrogen receptor-positive metastatic breast cancer patients with exceptional responses to capecitabine. Levin MK, Wang K, Yelensky R, Cao Y, Ramos C, Hoke N, Pippen J Jr, Blum JL, Brooks B, Palmer G, Palma N, Balasubramanian S, Ross JS, O'Shaughnessy J. Cancer Medicine. 13 April 2015 [Epub ahead of print]

The Clinical Use of Genomic Profiling to Distinguish Intrapulmonary Metastases From Synchronous Primaries in Non-Small-Cell Lung Cancer: A Mini-Review. Klempner SJ, Ignatius Ou SH, Costa DB, VanderLaan PA, Sanford EM, Schrock A, Gay L, Ali SM, Miller VA. Clin Lung Cancer. 26 Mar 2015. [Epub ahead of print]

Comparative analysis of primary tumour and matched metastases in colorectal cancer patients: Evaluation of concordance between genomic and transcriptional profiles. Vignot S, Lefebvre C, Frampton GM, Meurice G, Yelensky R, Palmer G, Capron F, Lazar V, Hannoun L, Miller VA, Andre F, Stephens PJ, Soria JC, Spano JP. Eur J Cancer. 2015 Mar 18. [Epub ahead of print]

Fluorescence in situ hybridization, immunohistochemistry, and next-generation sequencing for detection of EML4-ALK rearrangement in lung cancer. Pekar-Zlotin M, Hirsch FR, Soussan-Gutman L, Ilouze M, Dvir A, Boyle T, Wynes M, Miller VA, Lipson D, Palmer GA, Ali SM, Dekel S, Brenner R, Bunn PA Jr, Peled N. Oncologist. 26 Feb 2015 [Epub ahead of print]

Genetic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Chung CH, Guthrie VB, Masica DL, Tokheim C, Kang H, Richmon J, Agrawal N, Fakhry C, Quon H, Subramaniam RM, Zuo Z, Seiwert T, Chalmers ZR, Frampton GM, Ali SM, Yelensky R, Stephens PJ, Miller VA, Karchin R, Bishop JA. Ann Oncol. 2015 Feb 23. [Epub ahead of print]

Next generation sequencing of exceptional responders with BRAF-mutant melanoma: implications for sensitivity and resistance. Wheler J, Yelensky R, Falkchook G, Kim KB, Hwu P, Tsimberidou AM, Stephens PJ, Hong D, Cronin MT, Kruzrock R. BMC Cancer. 2015 Feb 18.

Lung Master Protocol (Lung-MAP)- A biomarker-driven protocol for accelerating development of therapies for squamous cell lung cancer: SWOG S1400. Herbst RS, Gandara DR, Hirsch FR, Redman MW, LeBlanc M, Mack PC, Schwartz LH, Vokes E, Ramalingam SS, Bradley JD, Sparks D, Zhou Y, Miwa C, Miller VA, Yelensky R, Li Y, Allen JD, Sigal EV, Wholley D, Sigman CC, Blumenthal GM, Malik S, Kelloff GJ, Abrams JS, Blanke CD, Papadimitrakopoulou VA. Clin Cancer Res. 2015 Feb 13 [Epub ahead of print]

Comprehensive Genomic Profiling of Carcinoma of Unknown Primary Site: New Routes to Targeted Therapies. Ross JS, Wang K, Gay L, Otto GA, White E, Iwanik K, Palmer G, Yelensky R, Lipson DM, Chmielecki J, Erlich RL, Rankin AN, Ali SM, Elvin JA, Morosini D, Miller VA, Stephens PJ. JAMA Oncol. 2015 Feb 12. [Epub ahead of print]

Broad, hybrid capture-based next-generation sequencing identifies actionable genomic alterations in "driver-negative" lung adenocarcinomas. Drilon A, Wang L, Arcila ME, Balasubramanian S, Greenbowe JR, Ross JS, Stephens PJ, Lipson D, Miller VA, Kris MG, Ladanyi M, Rizvi NA. Clin Cancer Res. 2015 Jan 7. [Epub ahead of print]

Genomic and functional analysis of leukemic transformation of myeloproliferative neoplasms. Rampal R, Ahn J, Abdel-Wahab O, Nahas M, Wang K, Lipson D, Otto GA, Yelensky R, Hricik T, McKenney AS, Chiosis G, Chung YR, Pandey S, van den Brink MR,
Armstrong SA, Dogan A, Intlekofer A, Manshouri T, Park CY, Verstovsek S, Rapaport F, Stephens PJ, Miller VA, Levine RL. Proc Natl Acad Sci USA. 2014 Dec 16

Oncogenic Alterations in ERBB2/HER2 Represent Potential Therapeutic Targets Across Tumors From Diverse Anatomic Sites of Origin. Chmielecki J, Ross JS, Wang K, Frampton GM, Palmer GA, Ali SM, Palma N, Morosini D, Miller VA, Yelensky R, Lipson D, Stephens PJ. Oncologist. 2014 Dec 5. [Epub ahead of print]

Loss of Heterozygosity at the CYP2D6 Locus in Breast Cancer: Implications for Germline Pharmacogenetic Studies. Goetz MP, Sun JX, Suman VJ, Silva GO, Perou CM, Nakamura Y, Cox NJ, Stephens PJ, Miller VA, Ross JS, Chen D, Safgren SL, Kuffel MJ, Ames MM, Kalari KR, Gomez HL, Gonzalez-Angulo AM, Burgues O, Brauch HB, Ingle JN, Ratain MJ, Yelensky R. J Natl Cancer Inst. 2014 Dec 8.

TP53 mutations detected in circulating tumor cells (CTCs) present in the blood of metastatic triple negative breast cancer patients Fernandez SV, Bingham C, Fittipaldi P, Austin L, Palazzo J, Palmer G, Alpaugh RK, Cristofanilli M. Breast Cancer Research. 2014 Oct 9.

Identification of recurrent FGFR3-TACC3 fusion oncogenes from lung adenocarcinoma Capelletti M, Dodge ME, Ercan D, Hammerman PS, Park SI, Kim J, Sasaki H, Jablons DM, Lipson D, Young L, Stephens PJ, Miller VA, Lindeman N, Munir KJ, Richards WG, Janne PA. Clin Cancer Res. 2014 Oct 7. [Epub ahead of print]

Comprehensive genomic profiling of pancreatic acinar cell carcinomas identifies recurrent RAF fusions and frequent inactivation of DNA repair genes Chmielecki J, Hutchinson KE, Frampton GM, Chalmers ZR, Johnson A, Shi C, Elvin J, Ali SM, Ross JS, Basturk O, Balasubramanian S, Lipson D, Yelensky R, Pao W, Miller VA, Klimstra DS, Stephens PJ. Cancer Discov. 2014 Sep 29. [Epub ahead of print]

Triple Negative Breast Cancer Patients Treated at MD Anderson Cancer Center in Phase I Trials: Improved Outcomes with Combination Chemotherapy and Targeted Agents Ganesan P, Moulder S, Lee JJ, Janku F, Valero V, Zinner RG, Naing A, Fu S, Tsimberidou AM, Hong D, Stephen B, Stephens P, Yelensky R, Meric-Bernstam F, Kurzrock R, Wheler JJ. Mol Cancer Ther. 2014 Sep 24. [Epub ahead of print]

Cell-Cycle Reprogramming for PI3K Inhibition Overrides a Relapse-Specific C481S BTK Mutation Revealed by Longitudinal Functional Genomics in Mantle Cell Lymphoma. Chiron D, Di Liberto M, Martin P, Huang X, Sharman J, Blecua P, Mathew S, Vijay P, Eng K, Ali S, Johnson A, Chang B, Ely S, Elemento O, Mason CE, Leonard JP, Chen-Kiang S. Cancer Discov. 2014 Jul 31. [Epub ahead of print]

Next-generation sequencing of adrenocortical carcinoma reveals new routes to targeted therapies Ross JS, Wang K, Rand JV, Gay L, Presta MJ, Sheehan CE, Ali SM, Elvin JA, Labrecque E, Hiemstra C, Buell J, Otto GA, Yelensky R, Lipson D, Morosini D, Chmielecki J, Miller VA, Stephens PJ. J Clin Pathol. 2014 Jul 30. [Epub ahead of print]

Dual Inhibition of EGFR with Afatinib and Cetuximab in Kinase Inhibitor-Resistant EGFR-Mutant Lung Cancer with and without T790M Mutations Janjigian YY, Smit EF, Groen HJ, Horn L, Gettinger S, Camidge DR, Riely GJ, Wang B, Fu Y, Chand VK, Miller VA, Pao W. Cancer Discov. 2014 Jul 29. [Epub ahead of print]

Next-generation sequencing reveals frequent consistent genomic alterations in small cell undifferentiated lung cancer Ross JS, Wang K, Elkadi OR, Tarasen A, Foulke L, Sheehan CE, Otto GA, Palmer G, Yelensky R, Lipson D, Chmielecki J, Ali SM, Elvin J, Morosini D, Miller VA, Stephens PJ. J Clin Pathol. 2014 Jun 24. [Epub ahead of print]

Anastrozole and everolimus in advanced gynecologic and breast malignancies: activity and molecular alterations in the PI3K/AKT/mTOR pathway Wheler JJ, Moulder S, Naing A, Janku F, Piha-Paul SA, Falchook GS, Zinner RG, Tsimberidou AM, Fu S, Hong D, Atkins JT, Yelensky R, Stephens PJ, Kurzrock R. Oncotarget. 2014 May 30.

Unique Molecular Signatures as a Hallmark of Patients with Metastatic Breast Cancer: implications for current treatment paradigms Wheler JJ, Parker BA, Lee JJ, Atkins JT, Janku F, Tsimberidou AM, Zinner R, Subbiah V, Fu S, Schwab R, Moulder S, Valero V, Schwaederle M, Yelensky R, Miller VA, Stephens MP, Meric-Bernstam F, Kurzrock R. Oncotarget. 2014 May 15.

Accelerated methotrexate, vinblastine, doxorubicin and cisplatin (AMVAC) is safe, effective and efficient neoadjuvant treatment for muscle invasive bladder cancer: Results of a multicenter Phase II study with molecular correlates of response and toxicity Plimack E, Hoffman JH, Viterbo R, Trabulisi EJ, Ross EA, Greenberg RE, Chen D, Lallas CD, Wong Y, Kutikov A, Dotan E, Brennan TA, Palma N, Dulaimi E, Boorjian SA, Kelly, WK, Uzzo RG, Hudes GR. J Clin Oncol. 2014 Jun 20. [Epub ahead of print]

A targeted next-generation sequencing assay detects a high frequency of therapeutically targetable alterations in primary and metastatic breast cancers: implications for clinical practiceVasan N, Yelensky R, Wang K, Moulder S, Dzimitrowicz , Avritscher R, Wang B, Wu Y, Cronin MT, Palmer G, Symmans WF, Miller VA, Stephens P, Pusztai L. Oncologist. 2014 April 7. [Epub ahead of print]

Concordance of genomic alterations between primary and recurrent breast cancer Meric-Bernstam F, Frampton GM, Ferrer-Lozano J, Yelensky R, Perez-Fidalgo JA, Wang Y, Palmer GM, Ross JS, Miller VA, Su X, Eroles P, Barrera JA, Burques O, Lluch AM, Zheng X, Sahin A, Stephens PJ, Mills GB, Cronin MT, Gonzalez-Anqulo AM. Mol Cancer Ther. 2014 Mar 7. [Epub ahead of print]

New Routes to Targeted Therapy of Intrahepatic Cholangiocarcinomas Revealed by Next-Generation Sequencing Ross JS, Wang K, Gay L, Al-Rohil R, Rand JV, Jones DM, Lee HJ, Sheehan CE, Otto GA, Palmer G, Yelensky R, Lipson D, Morosini D, Hawryluk M, Catenacci DV, Miller VA, Churi C, Ali S, Stephens PJ. Oncologist. 2014 Feb 21. [Epub ahead of print]

Comprehensive genomic profiling of relapsed and metastatic adenoid cystic carcinomas by next-generation sequencing reveals potential new routes to targeted therapies Ross JS, Wang K, Rand JV, Sheehan CE, Jennings TA, Al-Rohil RN, Otto GA, Curran JC, Palmer G, Downing SR, Yelensky R, Lipson D, Balasubramanian S,Garcia L, Mahoney K, Ali SM, Miller VA, Stephens PJ. Am J Surg Pathol. 2014 Feb.

Kinase fusions are frequent in Spitz tumours and spitzoid melanomasWiesner T, He J, Yelensky R, Esteve-Puig R, Botton T, Yeh I, Lipson D, Otto G, Brennan K, Murali R, Garrido M, Miller VA, Ross JS, Berger MF,Sparatta A, Palmedo G, Cerroni L, Busam KJ, Kutzner H, Cronin MT, Stephens PJ, Bastian BC. Nat Commun. 2014 Jan 20.

Targeted therapy by combined inhibition of the RAF and mTOR kinases in malignant spindle cell neoplasm harboring the KIAA1549-BRAF fusion protein Subbiah V, Westin SN, Wang K, Araujo D, Wang WL, Miller VA, Ross JS, Stephens PJ, Palmer GA, Ali SM. J. Hematol Oncol. 2014 Jan 14.

Emergence of constitutively active estrogen receptor-\0x03B1 mutations in pretreated advanced estrogen receptor positive breast cancerJeselsohn R, Yelensky R, Buchwalter G, Frampton GM, Meric-Bernstam F, Gonzalez-Angulo AM, Ferrer-Lozano J, Perez-Fidalgo A, Cristofanilli M, Gomez H,Arteaga CL, Giltnane J, Balko JM, Cronin MT, Jarosz M, Sun J, Hawryluk M, Lipson D, Otto G, Ross J, Dvir A, Soussan-Gutman L, Wolf I, Rubinek T, Gilmore L,Schnitt SJ, Come SE, Pusztai L, Stephens PJ, Brown M, Miller VA. Clin Cancer Res. 2014 Jan 7. [Epub ahead of print]

Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets Balko JM, Giltnane JM, Wang K, Schwarz LJ, Young CD, Cook RS, Owens P, Sanders ME, Kuba MG, Sanchez V, Kurupi R, Moore PD, Pinto JA, Doimi FD, Gomez H, Horiuchi D, Goga A, Lehmann BD, Bauer JA, Pietenpol JA, Ross JS, Palmer GA, Yelensky R, Cronin M, Miller VA, Stephens PJ, Arteaga CL. Cancer Discov. 2013 Dec 19. [Epub ahead of print]

BRAF fusions define a distinct molecular subset of melanomas with potential sensitivity to MEK inhibition Hutchinson KE, Lipson D, Stephens PJ, Otto G, Lehmann BD, Lyle PL, Vnencak-Jones CL, Ross JS, Pietenpol JA, Sosman JA, Puzanov I, Miller VA, Pao W. Clin Cancer Res. 2013 Dec 15.

D538G mutation in estrogen receptor-\0x03B1: A novel mechanism for acquired endocrine resistance in breast cancer Merenbakh-Lamin K, Ben-Baruch N, Yeheskel A, Dvir A, Soussan-Gutman L, Jeselsohn R, Yelensky R, Brown M, Miller VA, Sarid D, Rizel S, Klein B, Rubinek T, Wolf I. Cancer Res. 2013 Nov 11. [Epub ahead of print]

A high frequency of activating extracellular domain ERBB2 (HER2) mutation in micropapillary urothelial carcinoma Ross JS, Wang K, Gay LM, Al-Rohil RN, Nazeer T, Sheehan CE, Jennings TA, Otto GA, Donahue A, He J, Palmer G, Ali S, Nahas M, Young G, Labrecque E, Frampton G, Erlich R, Curran JA, Brennan K, Downing SR, Yelensky R, Lipson D, Hawryluk M, Miller VA, Stephens PJ. Clin Cancer Res.2013 Nov 5. [Epub ahead of print]

Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer Vaishnavi A, Capelletti M, Le AT, Kako S, Butaney M, Ercan D, Mahale S, Davies KD, Aisner DL, Pilling AB, Berge EM, Kim J, Sasaki H, Park SI, Kryukov G,Garraway LA, Hammerman PS, Haas J, Andrews SW, Lipson D, Stephens PJ, Miller VA, Varella-Garcia M, Jaenne PA, Doebele RC. Nat Med. 2013 Oct 27. [Epub ahead of print]

Antitumor response of an ERBB2 amplified inflammatory breast carcinoma with EGFR mutation to the EGFR-TKI erlotinib Ali SM, Alpaugh RK, Buell JK, Stephens PJ, Yu JQ, Wu H, Hiemstra CN, Miller VA, Lipson D, Palmer GA, Ross JS, Cristofanilli M. Clin Breast Cancer. 2013 Sep 27. [Epub ahead of print]

Advanced urothelial carcinoma: next-generation sequencing reveals diverse genomic alterations and targets of therapy Ross JS, Wang K, Al-Rohil RN, Nazeer T, Sheehan CE, Otto GA, He J, Palmer G, Yelensky R, Lipson D, Ali S, Balasubramanian S, Curran JA, Garcia L, Mahoney K, Downing SR, Hawryluk M, Miller VA, Stephens PJ. Mod Pathol. 2013 Jul 26.

Clinical next-generation sequencing successfully applied to fine-needle aspirations of pulmonary and pancreatic neoplasms Young G, Wang K, He J, Otto G, Hawryluk M, Zwirco Z, Brennan T, Nahas M, Donahue A, Yelensky R, Lipson D, Sheehan CE, Boguniewicz AB, Stephens PJ, Miller VA, Ross JS. Cancer Cytopathol. 2013 Jun 24. [Epub ahead of print]

Comprehensive Genomic Profiling Of Epithelial Ovarian Cancer By Next Generation Sequencing-Based Diagnostic Assay Reveals New Routes To Targeted Therapies Ross JS, Ali SM, Wang K, Palmer G, Yelensky R, Lipson D, Miller VA, Zajchowski D, Shawver LK, Stephens PJ. Gynecologic Oncology. 2013 Jun 19.

Thymoma Patients Treated in a Phase I Clinic at MD Anderson Cancer Center: Responses to mTOR Inhibitors and Molecular Analyses Wheler J, Hong D, Swisher SG, Falchook G, Tsimberidou AM, Helgason T, Naing A, Stephen B, Janku F, Stephens PJ, Yelensky R, Kurzrock R. Oncotarget. 2013 Jun 10.

Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors Lechner M, Frampton GM, Fenton T, Feber A, Palmer G, Jay A, Pillay N, Forster M, Cronin MT, Lipson D, Miller VA, Brennan TA, Henderson S, Vaz F, O'Flynn P, Kalavrezos N, Yelensky R, Beck S, Stephens PJ, Boshoff C. Genome Med. 2013 May 29.

Next-Generation Sequencing Reveals High Concordance of Recurrent Somatic Alterations Between Primary Tumor and Metastases From Patients With Non-Small-Cell Lung Cancer Vignot S, Frampton GM, Soria JC, Yelensky R, Commo F, Brambilla C, Palmer G, Moro-Sibilot D, Ross JS, Cronin MT, Andre F, Stephens PJ, Lazar V, Miller VA, Brambilla E. Journal of Clinical Oncology. 2013 April 29.

Relapsed classic E-cadherin (CDH1) mutated invasive lobular breast cancer demonstrates a high frequency of HER2 (ERBB2) gene mutations Ross JS, Wang K, Sheehan CE, Boguniewicz AB, Otto G, Downing SR, Sun J, He J, Curran JA, Ali S, Yelensky R, Lipson D, Palmer G, Miller VA, Stephens PJ. Clinical Cancer Research. 2013 April 10.

Response to Cabozantinib in Patients with RET Fusion-Positive Lung Adenocarcinomas Drilon A, Wang L, Hasanovic A, Suehara Y, Lipson D, Stephens PJ, Ross J, Miller VA, Ginsberg MS, Zakowski MF, Kris MG, Ladanyi M, Rizvi NA. Cancer Discovery. 2013 Mar 26. [Epub ahead of print]

Targeted genomic sequencing of pediatric Burkitt lymphoma identifies recurrent alterations in antiapoptotic and chromatin-remodeling genes Giulino-Roth L, Wang K, MacDonald TY, Mathew S, Tam Y, Cronin MT, Palmer G, Lucena-Silva N, Pedrosa F, Pedrosa M, Teruya-Feldstein J, Bhagat G,Alobeid B, Leoncini L, Bellan C, Rogena E, Pinkney KA, Rubin MA, Ribeiro RC, Yelensky R, Tam W, Stephens PJ, Cesarman E. Blood. 2012 Oct 22. [Epub ahead of print]

Targeted Next-generation Sequencing of Advanced Prostate Cancer Identifies Potential Therapeutic Targets and Disease Heterogeneity Beltran H, Yelensky R, Frampton GM, Park K, Downing SR, MacDonald TY, Jarosz M, Lipson D, Tagawa ST, Nanus DM, Stephens PJ, Mosquera JM, Cronin MT, Rubin MA. Eur Urol. 2012 Sep 5. [Epub ahead of print]

Next Generation Sequencing Identifies and Immunohistochemistry Confirms a Novel Crizotinib Sensitive ALK Rearrangement in a Patient with Metastatic Non-small Cell Lung Cancer Peled N, Palmer G, Hirsch FR, Wynes MW, Ilouze M, Varella-Garcia M, Soussan-Gutman L, Otto GA, Stephens PJ, Ross JS, Cronin MT, Lipson D, Miller VA. J Thoracic Oncology. 2012 Sep.

Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies Lipson D, Capelletti M, Yelensky R, Otto G, Parker A, Jarosz M, Curran JA, Balasubramanian S, Bloom T, Brennan KW, Donahue A, Downing SR, Frampton GM, Garcia L, Juhn F, Mitchell KC, White E, White J, Zwirko Z, Peretz T, Nechushtan H, Soussan-Gutman L, Kim J, Sasaki H, Kim HR, Park SI, Ercan D,Sheehan CE, Ross JS, Cronin MT, Jaenne PA, Stephens PJ. Nature Medicine. 2012 Feb 12.

Next-generation pathology. Ross JS. Am J Clin Pathol. 2011 May

Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology Cronin M, Ross JS. Biomark Med. 2011 Jun.

 

Oral Presentations (5)

The Genomics of Young Lung Cancer Study. Gitlitz BJ, Morosini D, Sable-Hunt A, Addario BJ, Jennings MB, Novello S, Vavala T, Mach S, Jones C, Oxnard GR. WCLC 2015. Sept 2015.

Comprehensive genomic profiling of advanced cancers identifies MET exon 14 alterations that are sensitive to MET inhibitors. Frampton GM, Ali SM, Goldman JW, Lee C, Weiss J, Bufill JA, Salgia R, Jahanzeb M, Konduri K, Forde P, Morosini D, Ross JS, Stephens PJ, Miller V and Ou I. WCLC 2015. Sept 2015.

Comprehensive Genomic Profiling identifies EGFR exon 19 deletions in NSCLC not identified by standard of care testing. Schrock AB, Ali SM, Herndon D, Frampton GM, Greenbowe J, Wang K, Lipson D, Yelensky R, Chalmers Z, Chmielecki J, Elvin JA, Wolner M, Bordoni R, Braiteh F, Dvir A, Erlich R, Mohamed M, Ross JS, Stephens PJ, Miller V. WCLC 2015. Sept. 2015

Clinical applications of comprehensive genotyping in solid tumors: Obstacles and opportunities Miller V. AACR 2012 Presentation.

Massively Parallel Sequencing in NSCLC: Comparison to Traditional Hot Spot Analysis for Selection of Approved and Novel Targeted Therapies Ross JS, Parker A, Jarosz M, Downing S, Yelensky R, Lipson D, Stephens P, Palmer G, Cronin M, Sheehan CE. Modern Pathol 2012; 25(suppl2): 488A. Oral presentation.

 

Posters (100)

Posters and presentations from the 2016 American Society of Clinical Oncologists Annual Meeting (ASCO) (27)

Posters and presentations from the 2015 San Antonio Breast Cancer Symposium (7)

Posters and presentations from the 2015 American Society of Hematology Annual Meeting (7)

Posters and presentations from the 2015 European Cancer Congress (10)

Posters and presentations from the 2015 American Society of Clinical Oncologists Annual Meeting (22)

Posters and presentations from the 2015 US and Canadian Academy of Pathologists Annual Meeting (20)

Posters and presentations from the 2014 American Society of Clinical Oncologists Annual Meeting (17)

A computational method for somatic vs. germ\0x2010line variant status determination from targeted
next\0x2010generation sequencing of clinical cancer specimens without a matched normal control Sun J, Frampton G, Wang K, Ross JS, Miller VA, Stephens PJ, Lipson D, Yelensky R. Presented at American Association for Cancer Research Annual Meeting 2014; 2014 April 5-9; San Diego, CA.

Analytical validation of solid tumor fusion gene detection in a comprehensive NGS\0x2010based clinical cancer genomic test Yelensky R, Donahue A, Otto G, Nahas M, Chalmers ZR, He J, Juhn F, Downing S, Frampton GM, Chmielecki J, Ross JS, Wang L, Zakowski M, Ladanyi M, Miller VA, Stephens PJ, Lipson D. Presented at American Association for Cancer Research Annual Meeting 2014; 2014 April 5-9, San Diego, CA.

An unbiased survey of cancer-related rearrangements in 5,917 solid tumors identifies actionable fusions across multiple disease subtypes Chmielecki J, Frampton GM, Lipson D, He J, Otto GA, Ali SM, Ross JS, Miller VA, Stephens PJ. Presented at American Association for Cancer Research Annual Meeting 2014; 2014 April 5-9, San Diego, CA.

Prospective next generation sequencing (NGS) of rare or poor prognosis cancers Hirshfield KM, Tolkunov D, Ali SM, Miller VA, Stephens PJ, Karantza V, DiPaola RS, Rodriguez-Rodriguez L, Ganesan S. Presented at American Association for Cancer Research Annual Meeting 2014; 2014 April 5-9, San Diego, CA.

Comprehensive Genomic Profiling of Adrenal Cortical Carcinoma Reveals Actionable Genomic Alterations and New Routes to Targeted Therapies Rand JV, Presta MJ, Wang K, Sheehan CE, Otto GA, Palmer G, Yelensky R, Lipson D, Chliemicki J, Palmer G, Ali SM, Morosini D, Miller VA, Stephens PJ, Ross JS. Presented at United States and Canada Association of Pathologists Annual Meeting 2014; 2014 Mar 1-7; San Diego, CA.

Comprehensive Genomic Profiling of Metaplastic Breast Carcinoma By Next Generation Sequencing Reveals Frequent Actionable Genomic Abnormalities and New Routes to Targeted Therapies Sheehan CE, Badve S, Wang K, Boguniewicz A, Otto GA, Palmer G, Yelensky R, Lipson D, Ali SM, Morosini D, Miller VA, Stephens PJ, Ross JS. Presented at United States and Canada Association of Pathologists Annual Meeting 2014; 2014 Mar 1-7; San Diego, CA.

Evaluation Of High Stage Skin Squamous Cell Carcinoma (SSCC) By Next Generation Sequencing (NGS) Opens The Door For New Routes To Targeted Therapies Al-Rohil RN, Tarasen A, Wang K, Sheehan CE, Carlson JA, Otto GA, Palmer G, Yelensky R, Lipson D, Ali SM, Morosini D, Miller VA, Stephens PJ, Ross JS. Presented at United States and Canada Association of Pathologists Annual Meeting 2014; 2014 Mar 1-7; San Diego, CA.

Evaluation Of Small Cell Undifferentiated Lung Cancer By Next Generation Sequencing Reveals Frequent Consistent Genomic Alterations Elkadi OR, Tarasen A, Foulke L, Sheehan CE, Wang K, Otto GE, Palmer G, Yelensky R, Lipson D, Ali SM, Morosini D, Miller VA, Stephens PJ, Ross JS. Presented at United States and Canada Association of Pathologists Annual Meeting 2014; 2014 Mar 1-7; San Diego, CA.

Evaluation Of Uterine Leiomyosarcoma By Next Generation Sequencing Reveals Actionable Genomic Abnormalities And New Routes To Targeted Therapies Huho A, Sheehan CE, Otto G, WangK, Palmer G, Yelensky R, Lipson D, Chiemlicki J, Ali SM, Morosini D, Miller VA, Stephens PJ, Ross JS. Presented at United States and Canada Association of Pathologists Annual Meeting 2014; 2014 Mar 1-7; San Diego, CA.

Targeted Next Generation Sequencing Of Osteosarcoma Reveals Frequent Actionable Genomic Abnormalities and Potential New Routes to Targeted Therapies Niu G, Al-Rohil RN, Vanushkina M, Sheehan CE, Nazeer T, DiCaprio M, Palmer G, Ali SM, Morosini D, Miller VA, Stephens PJ, Ross JS. Presented at United States and Canada Association of Pathologists Annual Meeting 2014; 2014 Mar 1-7; San Diego, CA.

Comprehensive next-generation sequencing-based genomic profiling identifies actionable genomic alterations in diverse pediatric tumor types: The Foundation Medicine (FMI) experience Hawryluk MJ, Wang K, Chmielecki J, Ali SM, Palmer G, Garcia L, White E, Yelensky R, Stephens PJ, Ross JS, Miiler VA. Presented at American Association of Cancer Research Annual Meeting 2013; 2013 April 6-10, Washington DC.

Next-generation sequencing (NGS) reliably identifies actionable genomic changes in common and rare solid tumors: The FMI experience with the initial 50 consecutive patients Palmer G, Miller V, Curran J, Ross J, Yelensky R, Stephens P, Lancelotta M, Lipson D. Proceedings of the 2012 American Society of Clinical Oncology Annual Meeting; 2012 Jun 1-5; Chicago, Illinois. ASCO; 2012. Abstract #10590.

Comprehensive Next-Generation Sequencing From Formalin Fixed Tissue Representing a Range of Specimen Ages and Tissue Types [abstract] Jarosz M, Juhn F, Brannan K, et al. Presented at Association for Molecular Pathology Meeting 2011.

Next-generation sequencing of FFPE breast cancers demonstrates high concordance with FISH in calling HER2 amplifications and commonly identifies additional clinically relevant genomic alterations Lipson D, He J, Yelensky R, Miller V, Sheehan C, Brennan K, Stephens P, Cronin M, Ross J. . Presented at CTRC-AACR San Antonio Breast Cancer Symposium 2012.

Posters and presentations from the 2013 American Society of Clinical Oncologists Annual Meeting. (12)

 
 

 

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Statements, including forward-looking statements, speak only to the date they are posted or provided (unless an earlier date is indicated), and Foundation Medicine does not undertake any obligation to publicly update any statements, including forward-looking statements, whether as a result of new information, future events or otherwise.