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  • Data Release Policies

    The following sections describe the policies currently in place for public release of PhAT SNP discoveries and Case-Control genotyping results. NIH policy mandates a maximum of 60 days between discovery and publication. In practice, the delay between discovery (dated from completion of quality control) and publication on the public website is currently of the order of 10 to 20 days for both SNP and genotype data.

  • SNP discovery data release policy

    Following quality control review, raw data from sequencing and SNP identification is transferred from the sequencing facility in Tucson to the Bioinformatics group in Boston, where it is processed through the PhAT Bioinformatics pipeline and published in detail on the private website for review by all PhAT investigators.

    The reference sequence, raw genotype data for each subject sequenced and SNP flanking sequences, sample specific tables of allele and genotype frequencies and counts are prepared and published for review within a few hours of transfer of the raw data from the Sequencing facility. Haplotype inference and pairwise LD estimation involve substantial computing time and may take several days to complete. These are published for review as soon as they become available.

    Within one week of internal review release, all material is made available on the public website

    To ensure that visitors can quickly locate newly published material, the public site home page is automatically updated to show all SNP released within the previous 30 days. A wide range of prepared reports are available for all published SNP, but in order to ensure that visitors can obtain SNP data in formats which suit their individual needs, we make a dynamic web application available which permits site visitors to tailor their own reports. Visitors may choose a variety of report formats and may limit the output to one or more samples and exclude SNP below arbitrary minimum allele frequencies. Like the prepared reports, outputs from these visitor-specified reports may be viewed as web pages or downloaded as text or spreadsheet files.

    Software to prepare material for submission of SNP discoveries to dbSNP is nearing completion. SNP discoveries will be submitted to dbSNP as soon as practicable.

  • Case-control genotyping data release policy

    As soon as genotyping quality control activities are completed, genotype and phenotype data are extracted from the Laboratory Information System Oracle database in the form of SAS and other analysis format files. SAS and other statistical analysis programs are immediately commenced and the outputs sent to the Statisticians for review as soon as they are available.

    Case-control genotyping summary and detailed reports are immediately released on the public site after review and approval.

  • Citation guidelines for users of PhAT published data

    Published data are freely available, but users are asked to appropriately cite the PhAT project as the source if they make use of the material. The website has a link to the document which sets out in detail the style and details of citation and acknowledgements requested for use of any data published on the PhAT website. The contents of that document were developed from a model document provided by the PGA Coordinating Committee.

  • Disclaimer of Liability for PhAT published data

    Every web page on the PhAT site has a link (at the end of the page) to a formal disclaimer of liability. This document indicates that while every care is taken to ensure that the material is accurate and complete, no guarantees are given and no liability will be accepted for damages arising from any use of the material.