Tumor Specific Plasma DNA
Tumor Specific Plasma DNA
In 2011, there was an estimated 233,000 cases of invasive breast cancer, and 39,970 deaths
 from breast cancer in the United States. The vast majority of patients are diagnosed with
 Stage I-III resectable and potentially curable disease, and for these patients, the most
 pressing questions are whether adjuvant endocrine or chemotherapy are indicated, and if so,
 how to determine whether these treatments are working. Adjuvant systemic therapy reduces
 relative recurrence rates by 30-50%, depending on the age of the patient and tumor
 characteristics. However, patients with early stage disease often do not bear measurable
 markers of disease such as an elevated cancer antigen 27-29 (CA27.29) or circulating tumor
 cells. Patients with early stage breast cancer are typically treated with adjuvant therapy
 based on historical evidence showing that such therapy prolongs survival in this population.

 Lung cancer is the most common malignancy and the leading cause of cancer-related death in
 the U.S. Approximately 220,000 new cases of lung cancer are diagnosed in the U.S. every year.
 Unfortunately, lung cancers are often diagnosed at later stages than breast cancer, due in
 part to little/no effective screening for lung cancer. As with breast cancer, patients are
 commonly treated with chemotherapeutic agents, but treatment regimens can take several weeks
 to months to elicit clinically detectable anti-tumor effects. A biomarker to assess early
 tumor response to therapy would benefit this patient population.

 The contents of dying tumor cells can be detected in the bloodstream, and this may be
 enhanced by the leaky vasculature of solid tumors. Protein biomarkers of tumor cell death are
 difficult to detect due to the complex nature of plasma and the lack of technical
 sensitivity. In contrast, DNA is easier to detect through polymerase chain reaction (PCR)
 amplification. Indeed, circulating tumor DNA has been detected in plasma from patients with
 osteosarcoma, breast cancer, and colorectal cancer. Until recently, it was impractical to
 develop an assay to routinely quantify circulating tumor DNA due to heterogeneity between
 patients and tumors. Advances in genomic technology now permit sequencing a tumor genome to
 identify patient-specific genomic aberrations. Major genomic alterations (i.e., insertions,
 amplifications, deletions, inversions, translocations) can be readily detected using PCR
 primers which will recognize tumor DNA but not normal DNA.

 While this strategy may be generally applicable to diverse types of solid tumors, two issues
 are apparent in breast cancer. Firstly, the incidence of chromosomal rearrangements varies
 widely. Whole-genome sequencing of 15 breast tumors revealed a range of 1-231 major genomic
 alterations (mean= 68), where 2 tumors had 1 alteration, and 9 tumors had > 20 alterations.
 Single-base point mutations are more common but difficult to reliably detect using PCR.
 Therefore, the investigators must consider that a small subset of patients may have a limited
 number of genomic alterations available for this assay. Secondly, intratumoral heterogeneity
 may mean that some genomic alterations are not present in every tumor cell. Such
 heterogeneity has been inferred from FISH and immunohistochemistry (IHC) studies for many
 years, and is now being verified at the genomic level. The investigators must consider that
 only a subpopulation of tumor cells may be sensitive to cytotoxic therapy, so changes in the
 levels of circulating tumor DNA may only be reflected with analysis of genomic alterations
 specific to the sensitive cells.
Inclusion Criteria:

 Women or men > age 18.

 Ability to give informed consent

 Archived tumor tissue must be available for genetic analysis.

 Patients with early-stage breast cancer

 Histologic documentation of invasive breast cancer by core needle or incisional biopsy.

 The invasive cancer must be either:

 -  triple-negative with both estrogen and progesterone receptor staining present in fewer
 than 10% of invasive cancer cells by IHC, and HER2-negative defined as IHC 0-1+, or
 with a FISH ratio of <1.8 if IHC is 2+ or if IHC has not been done.

 or

 *HER2-positive with IHC 3+ or a FISH ratio of >2.2.

 Clinical Stage II-III invasive breast cancer with the intent to treat with:

 -  pretreatment mammography, ultrasound, and breast MRI for staging

 -  pretreatment axillary staging

 -  neoadjuvant treatment with DNA-damaging chemotherapy (with or without HER2- directed
 therapy)

 -  post-chemotherapy breast MRI

 -  surgical resection of the primary tumor with an axillary dissection for one or more
 positive nodes after neoadjuvant chemotherapy

 Patients with multicentric or bilateral disease are eligible if the target lesion(s) meet
 the other eligibility criteria.

 No prior chemotherapy, endocrine therapy, or radiotherapy with therapeutic intent for
 treatment of a prior malignancy is allowed.

 Patients with locally advanced or metastatic breast cancer Histologic documentation or
 history of invasive breast cancer by core needle or incisional biopsy, or by surgical
 resection.

 ER/PR/HER2 status may be determined using any breast tumor specimen acquired at any point
 during a given patient's disease history (i.e., archived tumor). The invasive cancer must
 be either:

 *triple-negative with both estrogen and progesterone receptor staining present in fewer
 than 10% of invasive cancer cells by IHC, and HER2-negative defined as IHC 0-1+, or with a
 FISH ratio of <1.8 if IHC is 2+ or if IHC has not been done.

 or

 *HER2-positive with IHC 3+ or a FISH ratio of >2.2.

 Clinical Stage III-IV invasive breast cancer not amenable to curative surgical resection,
 with intent to treat with:

 -  if tumor is triple-negative, treatment with DNA-damaging chemotherapy as per standard
 of care in the first-line setting for advanced/metastatic disease.

 -  if tumor is HER2+, treatment with DNA-damaging chemotherapy, HER2-directed therapy, or
 a combination as per standard of care in any setting for advanced/metastatic disease.

 -  CT of chest, abdomen, and pelvis and bone scan or PET-CT for staging to assess
 response (by RECIST) approximately every 8 weeks or as clinically indicated with the
 primary course of DNA-damaging chemotherapy. The bone scan will not need to be
 repeated if the baseline bone scan is negative.

 Patients with newly diagnosed non-small cell lung cancer (NSCLC) Histologic documentation
 of NSCLC by core needle biopsy or a fine needle aspirate.

 Clinical Stage II or III lung cancer with the intent to treat with:

 -  pretreatment chest CT and or PET/CT

 -  induction (neoadjuvant) therapy with DNA-damaging chemotherapy

 -  post-chemotherapy lung chest CT and or PET/CT

 -  surgical resection of the primary tumor(s) after induction (neoadjuvant) chemotherapy
 No prior chemotherapy or radiotherapy with therapeutic intent for treatment of a prior
 malignancy is allowed.