We have completed a genome wide linkage scan using >5700 informative single-nucleotide polymorphism (SNP) markers (Illumina IV SNP linkage panel) in 642 Caucasian families containing affected sibling pairs with rheumatoid arthritis (RA), ascertained by the North American Rheumatoid Arthritis Consortium. The results show striking new evidence of linkage at chromosomes 2q33 and 11p12 with logarithm of odds (LOD) scores of 3.52 and 3.09, respectively. In addition to a strong and broad linkage interval surrounding the major histocompatibility complex (LOD>16), regions with LOD>2.5 were observed on chromosomes 5 and 10. Additional linkage evidence (LOD scores between 1.46 and 2.35) was also observed on chromosomes 4, 7, 12, 16 and 18. This new evidence for multiple regions of genetic linkage is partly explained by the significantly increased information content of the Illumina IV SNP linkage panel (75.6%) compared with a standard microsatellite linkage panel utilized previously (mean 52.6%). Stratified analyses according to whether or not the sibling pair members showed elevated anticyclic citrullinated peptide titers indicates significant variation in evidence for linkage among strata on chromosomes 4, 5, 6 and 7. Overall, these new linkage data should reinvigorate efforts to utilize positional information to identify susceptibility genes for RA.

Rheumatoid arthritis (RA) is an inflammatory disease with a complex genetic component. An association between RA and the human leukocyte antigen (HLA) complex has long been observed in many different populations, and most studies have focused on a direct role for the HLA-DRB1 "shared epitope" in disease susceptibility. We have performed an extensive haplotype analysis, using 54 markers distributed across the entire HLA complex, in a set of 469 multicase families with RA. The results show that, in addition to associations with the DRB1 alleles, at least two additional genetic effects are present within the major histocompatibility complex. One of these lies within a 497-kb region in the central portion of the HLA complex, an interval that excludes DRB1. This genetic risk factor is present on a segment of a highly conserved ancestral A1-B8-DRB1*03 (8.1) haplotype. Additional risk genes may also be present in the HLA class I region in a subset of DRB1*0404 haplotypes. These data emphasize the importance of defining haplotypes when trying to understand the HLA associations with disease, and they clearly demonstrate that such associations with RA are complex and cannot be completely explained by the DRB1 locus.

Summary This project grew out of the need for automated systems to enable the collection, preparation and storage of DNA and other blood derived elements from several hundred thousand human subjects. These subjects are being entered into a large longitudinal cohort study, the New York Cancer Project. Over the last 4 years, the North Shore LIJ Biorepository has designed and implemented robotic and information systems to support this project. The system is currently capable of automated storage and retrieval of approximately 250,000 specimens of genomic DNA with precise control of volume, concentration, and specimen tracking, in a 96 well format that is suitable for high throughput genotying. The operations of the NS-LIJ Biorepository implement the latest technologies available for specimen processing and data management and is organized around various integrated systems, including Lab Processing Systems, Storage Systems, Lab Processing Systems, Inventory Systems, and Information Management Systems. A flexible modular robotics platform provides for dynamic robot protocol development and deployment to allow modifications in response to changing laboratory requirements. The system consists of the following components: a CRS robotic track arm which moves specimens to different processes along its table, a TECAN Genesis liquid handling workstation, a TECAN SpectraFluor Plus plate reader for specimen analysis via Fluorescence or UV spectroscopy, a CRS Storage Carousel, an Abgene ALPS100 plate sealer, a TECAN / GIRA MOLBANK, and other ancillary devices both purchased and custom designed. A Supervisory Control And Data Acquisition (SCADA) System provides freezer monitoring and data-logging services for all freezers at the NSHS - LIJ Biorepository, the MOLBANK, and the environments in which they are maintained. In the event of a freezer or environment discrepancy / failure, the system is capable of several programmable actions including, automatic voice phone alert system, pager alert system, fax alert system, and other application program launch via its connected computer and network. The principle components of the Information Management System utilizes a A Dell Power Edge Server - Redundant Independent Array Disks (RAID) system. Both a RAID 1 (disk mirroring) and RAID 5 (disk striping) disk management system have been setup to create disk redundancy in order to prevent data loss due to disk failure. The system also features a triple power supply and is powered by separate UPS systems and back-up power. A Microsoft SQL enterprise database receives data from robots, instruments, and laboratory technicians. Custom user applications and instrument interfaces are constructed from high-level languages "C", "Visual Basic", "RAPL-3", and the Microsoft Visual Studio development suite. Microsoft IIS web server and user web services interfacing are currently being implemented in order to provide customized, web-based data access solutions for a variety of users.