Services

GeneSys - Industry-leading Genetic Analysis

Statistical Power:

Genizon combines the high call rates and accuracy of its Illumina genotyping platform with the power of GeneSys, an industry leading genetic analysis computing pipeline. Genizon will perform case-control or family trio analyses using individual SNPs and/or multi-marker haplotypes.

Initial Analysis Tools

From raw genotype data, Genizon will clean the data for genetic analysis resulting in SNPs and/or samples being removed from the dataset. Below is a list of initial analyses performed on the genotype data:
  • Minor allele frequencies are determined for all SNPs, removing those below a threshold (e.g. 5%)
  • SNPs not in Hardy-Weinberg equilibrium are detected
  • For trio data, SNPs that don't behave in a Mendelian manner are detected
  • SNPs with missing values above a threshold are removed
  • Call rates are determined for all samples, removing those below a threshold (e.g. 99%)

The figures below present 7-marker haplotype data from a Genizon genome-wide association study. The signal is at least 2 orders of magnitude greater with the Genizon process than with lower quality genotyping, demonstrating the power of Genizon's genotyping platform to distinguish signals from the background noise. The effect of missing data due to poor quality genotyping is evident. As little as 5% missing data can result in a significant signal reduction, and a corresponding increase in type I and type II error.


7 marker haplotype graph

Data Analysis Tools: These tools are part of Genizon's core technology and have been successfully applied to seven internal genome-wide association studies to date, resulting in the rapid discovery of multiple disease-associated genes and gene-based drug targets.
  • Phase Determination: For multi-marker analysis, a modified expectation-maximization (EM) algorithm is initially applied to determine phase for SNPs and to reconstruct haplotypes for adjacent SNPs. Where family trios are used, application of the modified EM algorithm follows initial phasing.
  • Haplotype Association Analysis: Single marker and haplotype frequencies are compared between case and control cohorts using proprietary haplotype association algorithms that use any number of markers, generally single markers and 3-, 5-, 7-, and 9-marker haplotypes. Analysis using longer haplotypes can also be performed as required by the study. Haplotype association algorithms have been optimized to identify signals from the genotyping and haplotype data.
  • Additional Analyses Available: Genizon can conduct permutation-based genome-wide or region-wide significance studies to identify the signals that rise above the genetic background noise of the data. Genizon's IT group has the capability to rapidly integrate additional analysis tools into the GeneSys pipeline.

Rapid Discovery: Candidate regions can be identified from genotyping data within 4 weeks of completion of genotyping.

IT Infrastructure: Genizon's IT department has established a state-of-the art IT infrastructure based on a combination of industry-leading commercial hardware and software solutions and in-house developed systems. The IT platform integrates and automates all systems to guarantee secure and reliable access to accurate data throughout the gene discovery process.

Electronic Data Access and Transfer: Genizon can deliver statistical analysis on electronic media in any standard format within 7 days of completion of the study. Long-term data storage is available and Genizon can provide the client direct electronic access to the data and customized data visualization through a secure portal.