Immune Response to Antigens

Overview

About this study

The purpose of this study is to sequence patient germline and tumor samples, and nominate top neoantigen candidates using an in-house developed bioinformatics pipeline, and to validate the neoantigen candidates by laboratory assays using patient peripheral blood immune cells or serum.

Participation eligibility

Participant eligibility includes age, gender, type and stage of disease, and previous treatments or health concerns. Guidelines differ from study to study, and identify who can or cannot participate. There is no guarantee that every individual who qualifies and wants to participate in a trial will be enrolled. Contact the study team to discuss study eligibility and potential participation.

Inclusion Criteria:

  • Age > 18 years
  • For cancer patients:
    • 100 samples from different cancer types, solid or blood tumors. We expect we’ll have the largest number of breast cancer patients as mentioned above.
    • Stages II, III, or IV disease.
  • Provide written informed consent.
  • Willingness to provide blood samples for neoantigen validation and T-cell activity assays.

 

Exclusion Criteria:

  • Immunocompromised patients including patients known to be HIV positive.
  • Patients receiving systemic steroid therapy or any other immunosuppressive therapy ≤ 30 days prior to registration. NOTE: Inhaled steroids, low-dose corticosteroids (e.g. equivalent to or less than oral prednisone 10 mg daily), and steroid use for primary prevention of nausea per institutional guidelines are allowed.
  • Patients who received radiation therapy to the planned biopsy site within 6 months.
  • Recent chemotherapy is not an exclusion criterion.
  • Patients will also be excluded based on tissue/RNA/DNA quality and quantity
    • If any of the following quality and quantity thresholds are not met, the patient will be excluded:
      • Tumor tissue cellularity equal to or greater than 30%;
      • There are ≥ 2 cores with passing cellularity;
      • ≥ 30% of tumor RNA with fragment sizes are ≥ 200 base pairs;  
      • < 10% of DNA fragments are smaller than 1 kb; and
      • Sufficient amount of both DNA (blood and tumor) and RNA (tumor) for exome sequencing and standard RNAseq according to the Mayo sequencing core (note: kits and technologies change overtime, so these are not fixed numbers). Note that since long-read RNAseq is optional, poor long-read RNAseq data (if generated) quality is not an exclusion criterion.
  • Pregnant women will not be allowed to enroll on this study.
  • Patients will either have the archived frozen tissue or consented to give fresh tissue biopsy and blood samples to the study.  Alternatively, if tumor sequence data is already available from 14-004094, that data can be used in the place of a newly collected or archived frozen sample.  However, fresh blood must still be collected.

Note: Other protocol defined Inclusion/Exclusion criteria may apply.

Eligibility last updated 11/15/22. Questions regarding updates should be directed to the study team contact

Participating Mayo Clinic locations

Study statuses change often. Please contact the study team for the most up-to-date information regarding possible participation.

Mayo Clinic Location Status Contact

Jacksonville, Fla.

Mayo Clinic principal investigator

Yan Asmann, Ph.D.

Open for enrollment

Contact information:

Yan Asmann Ph.D.

(904) 953-6717

asmann.Yan@mayo.edu

More information

Publications

Publications are currently not available
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