Analytics
The CGF has expanded its analytic capabilities and developed tools for rapid analysis of genotype data, generated by the high throughput genotype platforms, such as the Illumina technology. To assist investigators, a service has been developed to accelerate the pace of research and to identify potential problems pre- and post-genotyping.
Given basic information pertaining to a study, the CGF will offer preliminary statistics along with the delivery of genotype data. In order to deliver these additional analyses, CGF will accept information on the identification of QC duplicate pairs or sets and case vs. control status for every individual genotyped or sample handled at the CGF. Because it is understood that the study information that is provided is of an extremely sensitive nature, it will be only used by trained CGF analysts and senior management ("dry lab" staff). The laboratory ("wet lab") staff will never have access to this information, because access to this data will be restricted to the dry lab staff.
Laboratory Staff Restrictions
- Storage of data will be in folders and databases to which laboratory staff do not have access privilege
- Linkage of genotype and subject information for analytic and QC purposes only
- Access to information will be restricted to analyst(s) responsible for performing the analyses on a study level-basis
- Preliminary analysis will only be shared with Principal Investigator of the study.
Value-added Reports and Analyses
- Completion rate per sample and assay
- Concordance among duplicates
- Discordances between reported and genotyped sex
- Tests for deviation from Hardy-Weinberg proportions
- Allele and genotype frequency distributions
- Basic contingency table association analyses
