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DATABASE FOR STORAGE AND ANNOTATION OF GENETIC VARIANTS

(contract last updated 02/14/2014)

SCOPE: Contract for the purchase of  specialized database for the storage and annotation of genetic variants. 

 

The University looking for a commercially available platform that not only allows for storage and annotation of genetic variants, but also provides a provider/laboratory interface for the purpose of supporting updated clinical information.  The University is seeking a database software/service that is appropriate for storing genetic information from multiple sequencing and genomics platforms for human translational research and clinical testing.  The software will need to be installed at multiple sites at the UW, including the Wisconsin State Laboratory of Hygiene, UW Biotech center, UW Hospital and Clinics, and possibly the Morgridge Institute


CONTRACT # DESCRIPTION
14-5513 DATABASE FOR STORAGE AND ANNOTATION OF GENETIC VARIANTS
CONTRACT ORIGIN: ADDITIONAL INFORMATION:
UW-Madison
Purchasing Services
21 N Park St, Ste 6101
Madison, WI 53715-1218
UW-Madison users contact:
Unassigned
608-262-1526 / FAX (608) 262-4467
purch@bussvc.wisc.edu and ask to have your request assigned to an agent
  Non-UW-Madison users contact: Vendor Representative
COOPERATIVE PURCHASING: YES
CONTRACT TERM: February 15, 2014 through February 14,   2019, unless amended, cancelled or rebid.

Vendor(s)
140221
Cartagenia Inc
485 Massachusetts Ave  Ste 300
Cambridge  MA  02139
     
Sales Representative: PHONE #  
Drew Arnold 507-202-4002  
E-mail: drew.arnold@cartagenia.com
  PHONE #  
Ordering/Expediting: 617-475-5015  
Supplier Diversity Reporting: 857-453-0425  
Website:www.cartagenia.com
Federal Employee ID # (FEIN) 80-0809682
Commodity Code 175-23
208-37
209-38
490-43
F.O.B.

“I” F.O.B. DESTINATION AND INSTALLED
“V” F.O.B. SERVICE/MAINTENANCE

Additional charges for extending the contract would volume based.  Volume discounts are built into the pricing.
Terms: N/30
Invoicing: Invoices shall reflect contract pricing.
Pricing Information: SEE BELOW

ITEM

DESCRIPTION

COST

1

Software Licenses

$85,625.00

2

Implementation & Configuration Costs

$10,000.00

4

Training Costs

$15,000.00

5

Other, if any

$12,844.00

6

Annual Cost after purchase: Annual Software Maintenance & Support Cost

$12,844.00

7

Annual Cost after purchase

$85,625.00

SPECIFICATIONS

 

1.       The system must meet all CAP requirements for LIS functions, or provide evidence of compliance if it is not locally hosted.

2.       Adequate security measures to ensure confidentiality of patient data including:

         * Ability to control an individual’s access to those functions/data they are authorized to access;
         * Audit system to identify all persons who have added, modified, and accessed patient data.

3.       The system must contain well documented APIs, or other methods to export of data in standard formats (i.e. HL7, VCF).

4.       The system must support complex queries across multiple data fields including the following:

         * Queries must also be appropriate for the individual’s security level (i.e. exclude or include PHI as appropriate);
         * Ability to export queried data.

5.       The system must support simultaneous user login from multiple physical locations including:

         * Full audit trail for access;
         * Ability to restrict access down to specific servers/workstations;
         * The system must Interface with other LIS/EMR systems:  EPIC and WindoPath (Psyche systems).

6.       The system must be able to store or access patient related information for the following:

         * Requesting laboratory’s contact information;
         * Patients MRN or other affiliated IDs;
         * Dates samples were received, transferred, and reports sent.

7.       The system must be able to store sequencing related data, including:

         * Track multiple samples per patient; multiple tests per sample; multiple genes per test;
         * tore variant data from NGS and Sanger platforms;
             * Distinguish the source of the data;
             * Track which variants are supported by multiple sources;
         * Store information related to the interpretation of variants
             * Journal articles or references;
             * Geneticist notes;
             * Results from interpretation programs;
             * Store multiple forms of supplemental data.

8.       The system must be able to store and track information related to variant pathogenicity, including the following:

         * Molecular nomenclature (nucleotide description);
         * Protein position;
         * Gene;
         * Chromosome location;
         * Genome coordinates.

9.      The system must be able to store and track notes at multiple levels including:

         * Patient;
         * Sample;
         * Test;
         * Gene;
         * Variant;

10.    The Contractor must provide staff training and formal system testing including:

         * Installation- The installation must include significant training (up to 100 hours) for users. A manual must be provided;
         * Software Upgrades must be included in the annual maintenance costs.

11.    Contract or must provide ongoing customer support and maintenance, with the following requirements:

         * Critical issues must be resolved within 24 hours of the time they are reported to the provider;
         * Support may be requested by authorized users.

12.   Contractor must provide annual licenses:

         * Must be available as a year-to-year license with access to all upgrades and with the option for periodic development of new features as the project evolves.

13.   The system must provide the following access:

         * The system must be accessible via a web-based interface available to all users regardless of computer platform. The system must allow a scalable number of users to be logged in at the same time.

Additional features
14.    The system must have the ability to store deletion/duplication related data including the following:

         * aCGH results;
         * FISH results;
         * Q-PCR.

15.   The system must be able to combine all stored data into a single report.

16.   The system must be able to track statistics to aid interpretation of future variants including:

         * Number of times the variants has been identified;
         * Number of times the region containing the variant was interrogated.

17.  The system must have the ability to link and/or group cases based on pedigree

18.   The Contractor must be able to include provider linkage offering access to clinical reports and variant annotation
updates.


Revision History

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