Genomic Directed Salvage Chemotherapy With Either Liposomal Doxorubicin Or Topotecan

Inclusion Criteria: * Must have history of histologically or cytologically confirmed epithelial ovarian cancer with recurrence. * Must have measurable disease, defined as at least one lesion that can be accurately measured in at least one dimension (longest diameter to be recorded) as \>20 mm with conventional techniques or as \>10 mm with spiral computed tomography CT) scan. * May have had only 2 prior chemotherapy regimens, with at least one regimen containing platinum, and disease recurrence or progression occurring between 0 to 12 months (1 to 365 days)from the platinum-containing regimen. Patients who have been treated with consolidation treatment are allowed and the consolidation will not be considered a separate regimen. Hormonal therapy and immunotherapy will not be considered a prior chemotherapy regimen. Hormonal therapies given to treat the patient's cancer should be stopped at least 30 days prior to dosing on this trial. Typical low-dose hormone replacement therapy to treat postmenopausal symptoms may be continued at the treating physician's discretion. * Life expectancy \>6 months. * ECOG performance status 2 or less (Karnofsky 60%). * Must have normal organ and marrow function as defined below: * leukocytes 3,000/microL * absolute neutrophil count 1,500/ microL * platelets 100,000/microL * total bilirubin ≤1.5 X institutional upper limit of normal(ULN) aspartate aminotransferase \[AST(SGOT)\]/alanine aminotransferase \[ALT(SGPT)\] ≤2.5 X ULN creatinine within normal institutional limits OR creatinine clearance 60mL/min/1.73m2 for patients with creatinine levels above institutional normal * Ability to understand and willingness to sign a written informed consent document * Measurable disease on CT must be considered amenable to biopsy by Core methods (core biopsy may be radiographically or non-radiographically performed). Potential ability to obtain core material must be reviewed by Principal Investigator (PI) and/or his designates prior to enrollment. * Must consent to biopsy as part of enrolling into trial. * Patients with reproductive potential must use an adequate contraceptive method (e.g. abstinence, intrauterine device, oral contraceptives, barrier device with spermicide or surgical sterilization) during treatment and for three months after completing treatment. * Must have a Multiple Gated Acquisition (MUGA) scan or 2-d echocardiogram indicating an ejection fraction of \> 50% or institutional standards within 42 days prior to first dose of study drug. The method used at baseline must be used for later monitoring. Exclusion Criteria: * Patients who have had chemotherapy or radiotherapy within 4 weeks (6 weeks for nitrosoureas or mitomycin C) prior to entering the study or those who have not version 13, 01/10/08 MCC 15042 16 recovered from adverse events due to agents administered more than 4 weeks earlier. * May not be receiving any other investigational agents concurrently. * Patients with known brain metastases should be excluded from this clinical trial because of their poor prognosis and because they often develop progressive neurologic dysfunction that would confound the evaluation of neurologic and other adverse events. * History of allergic reactions attributed to compounds of similar chemical or biologic composition to liposomal doxorubicin or topotecan. * Myocardial infarction within 6 months. History of cardiac disease, with New York Heart Association Class II or greater, or clinical evidence of congestive heart failure. * Uncontrolled intercurrent illness including, but not limited to, ongoing or active infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social situations that would limit compliance with study requirements. * Women who are pregnant. * Women who are breastfeeding should discontinue breastfeeding. * Human Immunodeficiency Virus (HIV)-positive patients receiving combination anti-retroviral therapy are excluded from the study because of possible pharmacokinetic interactions and increased toxicity. * Patients may have had no other malignancies in the prior 5 years other than non-metastatic, locally-controlled, non-melanomatous cutaneous cancers. * Patients who have received radiation to more than 25% of marrow-bearing areas.