Upstate is requesting proposals from qualified contractors (“Contractor” or “Bidder”) for the provision of Distributed Genome Sequencing and Exome Sequencing (“GSES”) Services. Genome sequencing and exome sequencing (“GSES”) identify nucleotide level changes, with respect to a reference genome, across the entire genome (including introns) or exonic regions of genes with known disease association, respectively. Either methodology is commonly employed in pediatric patients with unexplained congenital anomalies, autism spectrum disorders, developmental delays, and/or intellectual disability. These types of sequencing are often used in conjunction with chromosomal copy number microarrays (“CNM”) in such patients, as the array can identify regions of missing or gained genomic material that exceed 20 kilobases in size but cannot detect changes that are at the single nucleotide to several nucleotides level. Whole exome sequencing (“WES”) is ordered by a physician who is often also trained in Clinical Genetics and has ruled out a specific etiology for a patient’s clinical features. Genome sequencing can also be employed to identify copy number variations in lieu of CNM. Upstate does not currently conduct GSES and has the need for such testing. Instead of initiating a new validation for GSES, Upstate would like to pursue a distributed process of GSES by sharing responsibilities between Upstate and a selected New York State Department of Health (“NYSDOH”) approved vendor. Upstate laboratories will extract DNA from patient specimens and ship the DNA to the selected vendor. The vendor will subsequently conduct the wet bench laboratory preparation, sequencing, and bioinformatics required for GSES. Following the completion of the required wet bench and computational portion of the work, the GSES vendor will provide the associated data files (FASTQ, BAM, VCF) to Upstate in a HIPAA-compliant manner for Upstate to analyze in tertiary software against the reference genome and provide a clinical report. While the GSES vendor should already be approved to conduct GSES by NYSDOH, a validation that is approved by the NYSDOH of this distributed process will be necessary for Upstate. The scope of services (the “Scope”) outlined below has been established for the purpose of achieving and implementing program goals and objectives described in this document. Although the Scope is intended to serve as a reference in the preparation of the proposal, forthcoming proposals may offer additional services which support the goals of this RFP.
