Affymetrix Human SNP 6.0 Genome-Wide Genotyping Services
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation
and represent over 80% of the genetic variation between individuals. SNPs are ideal
candidates for research correlating phenotype and genotype. Since some SNPs predispose
individuals to a certain disease or a trait or cause an altered reaction to a drug,
they are proving to be highly useful in diagnostics and drug development.
With more than 1.8 million genetic markers, Affymetrix’ SNP 6.0 array provides high-performance,
high-powered and low-cost genotyping. It is now available from Asuragen. In combination
with Asuragen’s service expertise you have the tools to carry out a whole-genome
study and bring power to your research. Asuragen performs hundreds of Affymetrix
profiling jobs per month, and was the only commercial service provider participating
for the Affymetrix platform in the pivotal MAQC study. Our validated procedures and optimized processes
give you the quality and turn-around time critical for a successful experiment.
Learn more about how we qualify our methods and staff.
Description of Services
Asuragen provides services using the Genome-Wide Human SNP Array 6.0, a single array
with more than 1.8 million markers of genetic variation, including more than 906,600
SNPs and more than 946,000 non-polymorphic probes for the detection of copy number
variation. The SNP Array 6.0 demonstrates excellent performance and represents more
genetic variation on a single array than any other product, providing maximum panel
power and the highest physical coverage of the genome (median marker spacing of
680 bases).
The SNPs were chosen from the public and Perlegen SNP databases and are represented
on this array based upon reproducibility, call rate, accuracy and concordance with
genotypes from the International HapMap Project (for more information on SNP selection
– link to Affymetrix website). Of the 946,000 non-polymorphic copy number probes
contained on the Array, 202,000 probes were selected based on known copy number
changes reported in the Toronto Database of Genomic Variants (DGV). The rest of
the probes were chosen to be evenly spaced along the genome to enable the detection
of novel copy number variation.
Workflow for SNP 6.0 genotyping services:
- Incoming DNA QC (click here for
sample prep services):
- Target preparation, followed by Affymetrix recommended in-process
QC
- Array hybridization, washing, and scanning followed by array QC
- Data summarization (see Deliverables Section)
Target preparation:
For target preparation Asuragen uses the Affymetrix validated Genome-Wide Human
SNP Nsp/Sty Assay. In short, 500 ng of total genomic DNA is digested with Nsp I
and Sty I restriction enzymes creating cohesive 4 bp overhangs. Universal adaptors
are then ligated to all fragments resulting from restriction enzyme digestion, regardless
of size, via these cohesive 4 bp overhangs. A generic PCR primer that recognizes
the adaptor sequence is used to amplify adaptor-ligated DNA fragments from both
restriction digests. The PCR conditions have been optimized to preferentially amplify
fragments in the 200 to 1,100 bp size range. PCR amplification products for each
restriction enzyme digest are combined and purified using polystyrene beads. The
amplified DNA is then fragmented, labeled, and hybridized to a SNP Array 6.0 (see
Figure below).
Deliverables
Included in the price of SNP genotyping, you will receive:
Analyses performed are:
- Genotype calls produced using the Birdseed v2 algorithm, developed
by the Broad Institute
- Copy number variation analysis based on the Canary algorithm listing
NC state calls. Annotations listed from the DGV
Affymetrix SNP 6.0 Deliverables:
- Affymetrix Raw Data Files
- Analysis Report (in MS Excel Format, unless table dimensions exceed
MS Excel capabilities, in which case .txt files will be provided)
- Project Description
- Intensity QC
- Genotype Summarys
- Filtered SNP List
- SNP Summary Statistics
- Copy Number QC
- Copy Number Segment Summary
- CHP, CNCHP, CNVCHP files
- Figures:
- Karyoview of each sample representing cytobands depicting gains and
losses for each chromosome (.pdf format)
To ensure security, all information is provided in an electronic form on a DVD.
Encryption is available on request. Data may also be delivered via an FTP site or
e-mail.
During our processes, we monitor many QC checkpoints as recommended by the Affymetrix
procedures. We utilize in-process sample controls, and process or reagent batch
controls. Should any sample-specific QC measure result in an “alert” or “fail” reading,
we will contact you to discuss available options.
Asuragen’s rigorous procedures enable Asuragen to be the only service provider to
offer a Data Quality Guarantee:
If, for any reason, a qualified sample does not pass our process control specifications,
we will re-run the sample at no additional charge.
Read more about our
commitment to the best possible data quality, or read about our contributions to
in-process controls and
standardization.
Sample Handling and Processing
All samples are received and entered into the analysis queue under a controlled
SOP to confirm package/sample integrity, appropriate shipping conditions (frozen
samples/dry ice, as appropriate), and individual confirmation of sample identity
against the shipping manifest and sample submission form and instructions.
Most projects are completed in two weeks or less. If you have a critical time requirement,
we can often meet your need for no additional charge.
Read more about our commitment to prompt turn-around times.
Additional Services Available from Asuragen
Available Genome-wide SNP Arrays
Human SNP Array 6.0
Catalog Numbers for Affymetrix SNP 6.0 Services
|
CA0068
|
QC, Nanodrop and Agarose Gel, for DNA applications
|
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CA0092
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Target Preparation, Affymetrix SNP 6.0
|
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CC0380
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Affymetrix Genome-Wide Human SNP Array 6.0
|
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CA0093
|
Array Processing and Scanning Affymetrix SNP 6.0; per sample
|
*Asuragen supports a broad range of arrays from Affymetrix. Contact Asuragen for
more detail.
Sample Input Requirements for the services listed above are found in the Sample Submission Form and Shipping Instructions