DNA analysis of breast milk

Contracting Office Address Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 6120 Executive Boulevard, EPS Suite 600, Room 6079, Rockville, MD 20852, UNITED STATES. Description The National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics DCEG plans to procure on a sole source basis with the University of Southern California, 1450 Biggy St. Los Angeles, CA 90033 for DNA analysis of breast milk. 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 621511 and the business size standard is $13.5 Million. Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price type contract. It has been determined that there is no opportunity to acquire Green Products or Services under this contract. The period of performance shall be twelve (12) months from date of award. Epidemiological data suggest that understanding biological changes during the "pregnancy-lactation cycle (PLC)" is important for increasing our knowledge of breast carcinogenesis. Giving birth for the first time before age 30 years is protective for breast cancer, whereas having a first birth at older ages increase risk. Lactation reduces risk slightly for breast cancer overall, but lowers risk dramatically for certain aggressive molecular tumor subtypes, such as basal breast cancers. Although giving birth reduces breast cancer risk over a woman's lifetime, pregnancy is associated with a short-term increase in breast cancer risk, and the tumors that develop are often aggressive. The purpose is to test whole milk to determine if the top genes specific for breast cancer in The Cancer Genome Atlas (TCGA) are methylated in DNA of breast milk using MethyLight. From an etiological perspective, there is strong evidence that the period from pregnancy through lactation and post-weaning remodeling influences breast cancer risk. Given that DNA methylation is pivotal in directing tissue differentiation and contributes to breast carcinogenesis, it is postulated that postpartum events influence DNA methylation patterns. The University of California (USC) is a leader in methylation analysis and is the developer of the MethyLight assay, including the breast cancer panel to be used in this project. USC also has unique experience applying and analyzing breast cancer methylation data generated with 450K Illumina platform. In contrast to readily available blood and tissues, the current project would test breast milk, including samples specifically processed for epithelial enrichment. The novelty of this project and the preciousness of the samples require a laboratory contractor with substantial expertise and the ability to adapt existing assays to a new sample type. USC is uniquely qualified by virtue of the TCGA experience. USC has also developed a method, called Digital MethyLight, capable of identifying single methylated DNA molecules present in the blood or possibly breast milk including women with breast cancer. This highly sensitive assay therefore permits testing of samples containing nanogram quantities of DNA, such as might be found in partially lysed frozen and thawed whole milk as is available from biopsied women in this project. USC has performed extensive analysis of primary breast tumors in the context of The Cancer Genome Atlas. A focus of USC is to identify candidate DNA methylation markers with high sensitivity for breast cancer detection that demonstrates cancer-specificity. Using TCGA data, this group has employed bioinformatics methods to identify the top 50 markers that were methylated in TCGA breast cancers, but not in blood from women without cancer. The specificity of these markers are likely applicable to milk because leukocytes represent the main non-epithelial cells in these samples. One candidate marker that was re-evaluated in serum from 24 matched case - control pairs (HB-080) achieved an ROC AUC of 0.9 for distinguishing women with late-stage breast cancer from controls and of 0.6 for early-stages cancers, using serum-based Digital MethyLight detection. Given that breast milk is derived directly from the affected organ, the performance characteristics of the assay may be better than for blood. Both the Digitial MethyLight Technology and the unpublished DNA methylation marker discovery represent unique resources not available elsewhere. This is not a solicitation for competitive quotations. However, if any interested party believes they can meet the above requirement, they may submit a statement of capabilities. All information furnished must be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the above unique specifications described herein. An original and one copy of the capability statement must be received in the NCI Office of Acquisitions on or before 11:00 AM EST on September 06, 2012. No electronic capability statements will be accepted (i.e. email or fax); an original and one copy must be sent to the NCI Office of Acquisitions to the address stated above. All questions must be in writing and can be faxed (301) 402-4513 or emailed to Miguel Diaz, Contract Specialist at miguel.diaz@nih.gov. A determination by the Government not to compete this proposed contract 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. In order to receive an award, contractors must have valid registration and certification in the Central Contractor Registration (CCR) and the Online Representations and Certifications Applications (ORCA) through SAM.gov. No collect calls will be accepted. Please reference solicitation number NCI-1201158-MD on all correspondences.