The Translational Genomics Research Institute

Mayo Foundation for Medical Education and Research

John Carpten

David Craig

Mitesh J Borad

Michael Richard Barrett

George Vasmatzis

Sara Byron

Keith Stewart

Alan Bryce

Jessica Aldrich

David O Azorsa

Spyro Mousses

Winnie Liang

Jeffrey A Kiefer

Pia Huusko

Olli Kallioniemi

Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.

Targeted therapies for cancer

The present invention is directed to a method of detecting a genomic rearrangement in a nucleic acid sample with Long Insert Whole Genome Sequencing (LI-WGS). The method may include obtaining a nucleic acid sample and then fragmenting the nucleic acid sample (e.g., via sonication). In particular, the fragmenting may result in the production of a plurality of inserts. Thereafter, the method comprises purifying the plurality of inserts using magnetic beads and then amplifying the purified plurality of inserts. In addition, the method further comprises sequencing the purified and amplified plurality of inserts. In some aspects, the plurality of inserts have a length of between about 800 and about 1,100 base pairs.

Long insert-based whole genome sequencing

Methods of selecting a chemotherapy regimen for treatment of cancer in a patient are disclosed. A patient genetic sample from a bilary cancer such as cholangiocarcinoma is analyzed for a mutation in ERRFI1 and a chemotherapeutic agent is selected as a result of the analysis. If a mutation in ERRFI1 is present, treatment with an inhibitor of Epidermal Growth Factor Receptor (EGFR) is shown to have inhibitory effects on tumor growth. In this manner, the chemotherapy regimen is targeted to a given mutation in a patient's cancer.

The present invention provides compositions and methods of using the EPHB2 gene or its related signaling pathways to detect, prognosticate, assess the risk of, prevent, or treat cancers. Cancers amenable to the present invention include, but are not limited to, prostate cancer, breast cancer, and neuroblastoma. In one aspect, the present invention provides compositions which comprise an agent capable of eradicating or alleviating an abnormality in the EPHB2 gene or its related signaling pathways. This abnormality may cause or contribute to the development or progression of cancers. In another aspect, the present invention provides methods comprising detecting an abnormality in the EPHB2 gene or its related signaling pathways. The presence or absence of such an abnormality is indicative of the risk or disease status of cancer in a person of interest.

Compositions and methods for prognosis of cancers

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Phoenix, AZ, United States of America

John Carpten