Multiplex Genotyping
Overview
The CGF defines multiplex genotyping assays as any assay that produces more than one genotype per sample. Currently the CGF supports two custom multiplex assay types see below for their descriptions and requirements. Additionally, fixed content Whole Genome Association products are available.
Illumina® GoldenGate®
Recommended Use
GoldenGate® Custom Panels provide flexibility and high data quality for the scanning of specific genes or pathways. GoldenGate® Custom Panels are available in panels of 384–1,536 loci in multiples of 96.
Process
Panel design begins with the investigator supplying a list of genes and target SNPs that are of interest for the panel. All GoldenGate® assays are designed using publicly available sequence information to provide the most accurate assay design possible. Assays will be chosen according to investigator criteria and vendor design scores through an interactive process with the CGF Bioinformatics team.
Once a final design has been chosen and approved by the PI, the assay will be ordered from Illumina. The custom OPA (pool of all assay oligonucleotides) will take approximately 8 weeks to manufacture and ship to the CGF. Once in house, the assay will be validated using 90 samples from the HapMap panel, chosen based on the intended ethnic population, to check for concordant genotypes. All assays in the panel will be validated in this way prior to the genotyping of study samples.
Requirements
Samples must pass all Sample Handling and Pre-Genotyping QC criteria before they are considered for genotyping. Study samples must have at least 750 ng of total DNA with a concentration of at least 7.5 ng/µl as determined by PicoGreen® ("QDNA") to be included in GoldenGate® genotyping. Additional sample qualification based on phenotypic evaluation of the study will be performed and the PI will be informed of the results (see Pre-Genotyping QC section).
Each assay panel can genotype up to 94 samples per array (two wells on each plate are reserved for internal QC). Additionally, no plate can be processed with less than 48 samples. This must be considered when ordering for the project.
Due to the custom nature of the assay, the total number of samples to be genotyped must be stated at the time of order and the order will be directly billed to the investigator’s account at that time. The cost of GoldenGate® OPAs is mainly influenced by the total number of samples and SNPs to be genotyped on the OPA. Please contact the CGF for specific pricing information.
Reporting
Genotype reporting will follow the standard reporting scheme as listed in under the Post-Genotyping QC Reporting Data Delivery section.
Custom Infinium® BeadChip Assays (iSelect™)
Recommended Use
The Illumina® Custom Infinium® (iSelect)™ assays are for high density scanning targeted to specific regions or pathways. The Custom Infinium® BeadChip can be designed to genotype a minimum of 7,600 bead types to a maximum of 60,800 bead types (1 bead type is required for each A/G or C/T SNP and 2 bead types are required for A/T or C/G SNPs).
Process
Panel design begins with the investigator supplying a list of genes and target SNPs that are of interest for the panel. All iSelect™ assays are designed using publicly available sequence information to provide the most accurate assay design possible. Assays will be chosen according to investigator criteria and vendor design scores through an interactive process with the CGF Bioinformatics team. Special consideration must be taken when choosing A/T or G/C SNPs for inclusion in the iSelect™ assay as they require two bead types per SNP.
Once a final design has been chosen and approved by the PI, the assay will be ordered from Illumina. The custom chips will take approximately 12 weeks to manufacture and ship to the CGF. Once in house, the product will be evaluated using a portion of the HapMap panel, chosen based on the intended ethnic population, to check for concordant genotypes.
Requirements
Samples must pass all Sample Handling and Pre-Genotyping QC criteria before they are considered for genotyping. Study samples must have 500 ng of total genomic DNA at a concentration of 10 ng/µl as determined by PicoGreen® to be included in iSelect™ genotyping. Additional sample qualification based on phenotypic evaluation of the study will be performed and the PI will be informed of the results (see Pre-Genotyping QC section).
Pricing on these projects is sample size and bead type dependent. The iSelect™ assays genotype up to 12 samples per BeadChip and must be ordered with a minimum n=1,152 samples and n=7,600 bead types per project. The sample size can be increased in increments of 1,152 above the minimum sample size and the bead type can be increased in increments of 1,520 bead types above the minimum. This must be taken into account when ordering for your project. Please contact the CGF for specific pricing information.
Reporting
Genotype reporting will closely follow the standard reporting scheme as listed in the Post-Genotyping QC Reporting section. However due to the size and complexity of the genotyping data files, the CGF Analysis team will assist the investigator in the retrieval and export of genotyping data.
