Next Generation Sequencing Automated Platform

This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding the availability and capability of all qualified sources to perform the potential requirement. This notice is issued to help determine the availability of qualified companies technically capable of meeting the Government requirement and to determine the method of acquisition. It is not to be construed as a commitment by the Government to issue a solicitation or ultimately award a contract. Responses will not be considered as proposals or quotes. No award will be made as a result of this notice. The Government will NOT be responsible for any costs incurred by the respondents to this notice. This notice is strictly for research and information purposes only. Background: The Functional Genomics Lab (FGL) efforts over the past five years have made a significant impact on the NIH Intramural Research Program (IRP). However, RNAi screening has its limitations, and newer technologies, in particular CRISPR/Cas9-based gene-editing approaches, can help address some of these limitations. The goals of the FGL are to: Collaborate with NIH investigators to perform genome-wide and targeted RNAi and CRISPR screening projects (assay development, screening and validation) to: Understand fundamental biological mechanisms. Accelerate target discovery for therapeutic development. Develop methods that advance the science of functional genomics screening and informatics. Perform education and outreach to increase awareness of TNRF tools and methods. Pursue new and complementary technologies for exploring gene function. Thus far, CRISPR screens have been performed primarily within an individual laboratory setting, where expertise exists — for example, when employing a pooled library approach with a simple phenotype such as cell survival. However, there is an increasing need for NIH IRP investigators to access robust, reproducible and flexible CRISPR/Cas9-based high-throughput screening (HTS) workflows that are compatible with the assessment of more complex phenotypic assays. Technical challenges associated with the development and implementation of these more complex screens are a barrier for most individual laboratories. Investment in CRISPR/Cas9-based screening platforms within the FGL will enable the NIH IRP community to access state-of-the-art functional genomic resources beyond RNAi. To address these needs, the FGL requires a flexible platform that is capable of being automated for existing RNAi workflows such as plate stamping, and that can also be utilized in a manual fashion for the development and optimization of next generation sequencing projects. Purpose and Objectives: The purpose of this request is for The National Center for Advancing Translational Sciences (NCATS) Division of Preclinical Innovation (DPI) to acquire a platform to support plate preparation for our Functional Genomics Laboratory (FGL). Product: Next Generation Sequencing Automated Platform (NGSAP) Project requirements: NCATS requires one (1) automated enclosed robotic platform including: Automated ambient storage for consumables (microtiter plates, tip boxes, others), robotic sample transportation HighResBio (HRB) Ambistore or equivalent Automated climate controlled storage for samples (microplates, etc) HRB Steristore, Thermo Cytomat, Liconic or equivalent Two (2) Beckman Coulter Biomek i7 capable of supporting next generation sequencing (NGS) workflows B87585 Biomek i7 Hybrid (MC + Span-8) One system will be integrated within the automated enclosed robotic platform, while another will be used for offline assay and process development tasks Plate sealer Agilent PlateLoc or equivalent Plate seal remover Azenta Plate Seal Remover or equivalent Plate centrifuge Agilent VSpin or equivalent Scheduling software to create custom workflows with the ability to integrate with other peripheral pieces of equipment involved in RNAi screening and NGS assays as required Salient Characteristics: The vendor shall be responsible to provide equipment that fulfills the following requirements: The NGSAP must be fully enclosed to prevent contamination of cells and siRNA samples. The NGSAP must include integrated ambient and climate-controlled storage system that fits microtiter plates and pipette tip boxes for the Biomek i7. The integrated ambient storage system must be random access. The storage carousels must have - High Speed Plate Storage: the system needs the ability to retrieve and store plates in 12 seconds. Also, storage needs the ability to quickly inventory all plate types within 60 seconds. This inventory process must include the exact location of each piece of labware and its associated barcode. There must be at least 24 additional hotel type storage locations for various pieces of labware. These must be individual stations and not a stack type configuration. The integrated ambient storage system must hold a minimum of 300 pieces of labware to accommodate the entire library collection of 189 plates plus pipette tips, multiple destination plates and also leaves room for future expansion. The NGSAP must have quick delidding and lidding capabilities. The NGSAP must run from a dynamic scheduling software and be able to optimize throughput in order to run as many samples as possible and minimize evaporation. The scheduling interface must be user-friendly such that a biologist can potentially create and run their protocol. The scheduling software requires the ability to run custom scripting components in order to track source and destination plate association as well as correlation of aspirations and dispenses from and to specific wells. The scheduling software must be able to fully recover from errors that may occur during a run. The robotic arm used on the NGSAP will need to have access to all devices specifically with a horizontal reach of 450mm and a vertical reach of 750mm. The tolerance shall be + or – 25mm. There must be a redundant robotic arm included with the system in the event of a hardware failure to quickly swap out if necessary to recover as quickly as possible. The robotic arm will need to be taught all system positions using a quick and simple process such that a biologist could potentially handle this task. The robotic arm and more specifically gripper must be able to pick and place labware very reliably to avoid losing expensive samples/experiments due to poor accuracy. The NGSAP must be able to have all peripheral devices integrated into a unified scheduling software. It is extremely important that the NGSAP be capable of handling, tracking, and associating all source plates to as many destination plates required in a single run. Robot envelope: provides user with the exceptional reach and range in both the x, y and z-axis. The minimum z-axis travel must be 745 mm. The NGSAP must have - Product accessibility: full access to all devices using a turntable or sliding shelves to access devices with simplistic cable management is required. The NGSAP must have - Modular system design: the ability to easily reconfigure the system in less than 60 seconds. Software must have - User Experience: the software incorporates the latest software technologies to ensure that whether designing protocols, or launching an order, the focus is always on a user-friendly interface, backed up by the highest levels of application reliability. Software must have - Order Interleaving and Scheduling: can run multiple orders in parallel and supports injection of new orders with time or event-based control. Software must have - Gantt Chart Simulations: Fast Gantt Chart simulations with accurate protocol timing data that allows operators to use detailed sample treatment and resource utilization statistics to quantitatively optimize their orders before run-time. Software must have - Sample Input Control: A wide range of sample input control mechanisms can be used to balance throughput and sample treatment for the required application. Software must have - Device Pooling: Supports a wide range of pooling options for all classes of device, even complex liquid handlers. Strategies including “first available”, “round robin” and “fail over” can be defined during protocol design and then dynamically adjusted while orders are live on the system. Software must have - Scripting Components: allows operators to run custom scripting components not embedded into the software. Multiple languages must be supported (for example, Java, VB or .NET), scripts must have access to a number of run time variables including plate number and barcode. Software must have - Ability to be controlled via a restful API. Software must have - Decision Nodes: using the results of a custom script execution to alter a plate’s processing pathway mid-run. Software must have - Plate processing manipulation provides the ability to manipulate assay handling parameters of a specific plate mid-run. Software must have - Device Control: the ability to remove a device from the system during a run to use in standalone mode and then, once action is complete, return the device back into active use on the platform is required. This action must not allow stoppage of the protocol. Anticipated period of performance: Approximately 16-24 weeks ARO. Buy American Clauses: FAR 52.225-2, Buy American Certificate (Feb 2021) FAR 52.225-6, Trade Agreements Certificate (Feb 2021 Capability statement /information sought. Companies that believe they possess the capabilities to provide the required services should submit documentation of their ability to meet each of the project requirements to the Contracting Officer. The capability statement must specifically address each of the project requirements separately. Additionally, the capability statement should include 1) the total number of employees, 2) the professional qualifications of personnel as it relates to the requirements outlined, 3) any contractor GSA Schedule contracts and/or other government-wide acquisition contracts (GWACs) by which all of the requirements may be met, if applicable, and 4) any other information considered relevant to this program. Capability statements must also include the Company Name, Unique Entity ID from SAM.gov, Physical Address, and Point of Contact Information. The response must include the respondents’ technical and administrative points of contact, including names, titles, addresses, telephone and fax numbers, and e-mail addresses. Interested companies are required to identify their type of business, applicable North American Industry Classification System (NAICS) Code, and size standards in accordance with the Small Business Administration. The government requests that no proprietary or confidential business data be submitted in a response to this notice. However, responses that indicate the information therein is proprietary will be properly safeguarded for Government use only. Capability statements must include the name and telephone number of a point of contact having authority and knowledge to discuss responses with Government representatives. Capability statements in response to this market survey that do not provide sufficient information for evaluation will be considered non-responsive. When submitting this information, please reference the solicitation notice number. One (1) copy of the response is required and must be in Microsoft Word or Adobe PDF format using 11-point or 12-point font, 8-1/2” x 11” paper size, with 1” top, bottom, left and right margins, and with single or double spacing. The information submitted must be in an outline format that addresses each of the elements of the project requirement and in the capability statement /information sought paragraphs stated herein. A cover page and an executive summary may be included but is not required. The response is limited to ten (10) page limit. The 10-page limit does not include the cover page, executive summary, or references, if requested. All responses to this notice must be submitted electronically to the Contract Specialist and Contracting Officer. Facsimile responses are NOT accepted. The response must be submitted to Morgen Slager, Contract Specialist, at e-mail address [email protected]. The response must be received on or before April 27, 2023, at 2:00 pm, Eastern Standard Time. “ Disclaimer and Important Notes: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a presolicitation synopsis and solicitation may be published in www.sam.gov. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).”