Validation of Candidate Methylation Markers in Cervical Tissue and Cytology Specimens

The National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), plans to procure on a sole source basis services to measure the methylation levels of 11 top candidates from EpigenDX, Inc. 96 South Street, Hopkinton, MA 01748. This acquisition will be processed in accordance with simplified acquisition procedures as stated in FAR Part 13.106-1(b)(1). The North American Industry Classification System code is 541380 and the business size standard is $14.0 Million. Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price type contract. The period of performance is twelve (12) months from date of award. It has been determined there are no opportunities to acquire green products or services for this procurement. NCI/DCEG has been approved to continue with the study to determine the clinical utility of novel methylation markers for the early detection of cervical cancer. The specific objectives are to measure the methylation levels of 11 top candidates identified in a previously performed profiling assay using two methods, pyrosequencing and quantitative methylation specific PCR (qMSP) for 40 cervical tissue samples and pyrosquencing and qMSP for 114 liquid-based cervical cytology samples, including samples from women with normal cervical cytology and histology, cervical pre-cancer and cervical cancer and QC samples. Specifically, the three objectives are: (1) evaluate the level of methylation of the 11 genes in cervical tissue samples using pyrosequencing, comparing levels in women without cervical disease to those with cervical pre-cancer and cancer and (2) evaluate the level of methylation of the 11 genes in cervical cytology samples using qMSP and pyrosequencing, comparing levels in women without cervical disease to those with cervical precancer and cancer (3) compare the levels of methylation obtained from the two methods in cervical cytology specimens. The qMSP and pyrosequencing methods will be compared for clinical utility. DCEG will then select the top 5 candidate markers for further analysis using the superior method on up to 190 additional liquid-based cervical cytology samples. This contract requires a vendor who can develop qMSP and pyrosequencing assays for methylation markers and work with FFPE tissues and cytology specimens. Based on the Contracting Officer's Representative (COR), EpigenDx is the only vendor equipped with these capacities. Importantly, EpigenDx has already initiated a project on 5 markers and are therefore optimally positioned to continue this project examining additional markers on the same specimens. Contractor Technical requirements: - The contractor shall measure methylation levels of MAL, miR, ADCYAP1, MYOD1, TPEF, HS3ST2, DBC1, TMEFF2, SOX17, DBC1 and ATP10A in 40 cervical tissue including samples form women with normal cervical cytology and histology, cervical precancer and cervical cancer using pyrosequencing. - The contractor shall measure methylation levels of MAL, miR, ADCYAP1, MYOD1, TPEF, HS3ST2, DBC1, TMEFF2, SOX17, DBC1 and ATP10A in 114 cervical cytology specimens, including samples form women with normal cervical cytology and histology, cervical precancer and cervical cancer using pyrosequencing and qMSP - The contractor shall measure methylation levels of a select 5 candidates in 190 cervical cytology specimens, including samples form women with normal cervical cytology and histology, cervical pre-cancer and cervical cancer using qMSP. - The contractor shall summarize the measurements in an Excel sheet and send to NCI. Reporting Schedule: - The contractor shall provide an electronic report of the measurement results in Excel format. Deliverables: The deliverables include methylation levels MAL, miR, ADCYAP1, MYOD1, TPEF, HS3ST2, DBC1, TMEFF2, SOX17, DBC1, ATP10A, IGSF4, MOS, DCC, ASCL1 and SOX17 in 40 cervical tissue specimens and 114 cervical cytology specimens using pyrosequencing and qMSP and up to 190 specimens using qMSP. This notice is not a request for competitive quotation. However, if any interested party, especially small business believes it can meet the above requirement, it may submit a proposal or quote for the Government to consider. The response and any other information furnished must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can perform the requirement. Responses must be received in the contracting office by 11 AM EST, on August 14, 2014. All responses and questions must be in writing and faxed to +1 (555) 000-0000 or emailed to Reyes Rodriguez, Contracting Specialist via electronic mail at contact@example.gov. A determination by the Government not to compete this proposed requirement based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. No collect calls will be accepted. In order to receive an award, contractors must be registered and have valid certification in the Central Contractor Registration (CCR) and the Online Representations and Certifications Applications (ORCA) through sam.gov. Reference: N02CP42607-57 on all correspondence.