Affymetrix SNP Genotyping

Starting from very small quantities of total DNA (from 30 ng), we can apply very robust and cost effective protocols to give you the confidence and turnaround times critical for  successful experiments.

A) Sample reception

Incoming samples. All samples received are labeled with a unique internal ID number and recorded in a validated electronic laboratory system management database. They are checked to confirm package/sample integrity, appropriate shipping conditions (frozen samples/dry ice, where appropriate), and a confirmation of sample identity against the shipping manifest is sent by e-mail on the  day of reception.

B) DNA extraction and QCs

If needed, DNA is extracted from any eukaryotic (animal or plant) samples (see Nucleic Acid Extraction in DNAVision)

Quantification and estimation of DNA purity is performed using Nanodrop spectrophotometer readings at 260 and 280 nm. (depending on the GeneChip chosen, a minimum of 250 ng or 500 ng of total DNA is required) *

DNA integrity is checked on a 1% or 2% agarose gel. High quality genomic DNA appears as a major band at approximately 10-20 kb on the gel without smear

* If the minimum quantity is not reached, a amplification can be performed using the Qiagen Repli-G® Kit from 30 ng

C) Labeling / hybridization and scanning

• Restriction/ligation/amplification of the gDNA
• Check of PCRs reactions on agarose gel
• Purification of PCRs products
• OD measurement (1.0 to 1.2 is required)
• Fragmentation and terminal labelling
• Check of fragmentation on agarose gel
• Array hybridization, washing and scanning

NOTE that DNAVision is also equipped fore Targeted Genotyping using the Affymetrix MIP system (Molecular Inverted Probes).

D) Quality Control and Deliverables

Extraction of the data using the Genotyping Console. As recommended by Affymetrix, several quality controls (QCs) are performed while processing the samples. These QCs include visualization of the GeneChip, QC contrast , % of call rate, crosscheck with the gender, if available, ...

As part of our Affymetrix SNP Genotyping service, you will receive:

• Raw data files
  • .xml / grp / jpeg and .Cel files
• Extracted data files from Affymetrix Genotyping Console software:
  • file including all the QCs
  • file including the genotypes, intensities and confidence scores
  • file including the annotations provided by SNP
• Project report :
  • Project description
  • DNA assessment data
  • Affymetrix assessment data
  • Conclusions of the analyses if required (see below)

E) Biostatistical and Bioinformatical analyses

In addition to  the core service activities carried out in a high quality environment, we can also provide you with basic to in-depth data analysis to extract  the relevant information from your data. For  more details please go to Bioinformatics in DNAVision.

• Copy Number Variation (CNV) aberrations analysis
• Lost of Heterozygosity (LOH) analysis
• Analysis of pedigree including homozygosity mapping with HR Finder
• Genome wide association studies

All  data are provided in an electronic form on a DVD. Encryption is available on request. Data may also be delivered via a secure dedicated web site.

F) Available and Custom Catalog Arrays

We can provide you with any GeneChip Array available on the Affymetrix website (including the DMET Array) (http://www.affymetrix.com/products_services/index.affx). According to the availability, we can also provide you with any custom Microarrays.