Affymetrix 10k, 100k and 500k Genotyping | FAQs

Affymetrix 10k, 100k and 500k Genotyping

 

Tell me about these three products

The Affymetrix GeneChip Human Mapping SNP arrays are a fast, economic and powerful SNP-based genetic mapping tool.

The 10K single array product provides data on over 11,000 SNPs distributed across the genome. The 100K set is comprised of a set of two 50K arrays each with 50,000 SNPs and together, they provide data on over 100,000 SNPs across the genome. The 500K Array set is comprised of two 250K arrays, each capable of genotyping on average 250,000 SNPs. Please see below for a snapshot comparison of the 10K, 100K and 500K SNP coverage. In addition, you also have the flexibility to choose to use single 50K or 250K arrays.


FAQ affymetrix 1


Figure 4:  A snapshot comparison of 10k, 100k, 500k SNP.

We can offer contract research with all Affymetrix SNP genotyping products.

What are the advantages of using SNP array?

  • The SNP density enables highly powered whole genome studies.
  • It allows you to stay in charge of your budgets. A complete data set is generated from each DNA sample. This gives you the flexibility to select those samples that will be the most informative in your sample set. You can type them first, analyse your genome wide data and then decide if you need to do more.
  • The assay uses just 250ng of genomic DNA per chip - only as much as is used up on just 50 microsatellites.
  • Source BioScience LifeSciences has set up a high-throughput mode of operation with multiple samples processed in parallel. Typically, you will get data about 2 weeks after we start processing.

 

How do I get started?

Using our experience and expertise from years of RNA expression analysis on the Affymetrix platform, Source BioScience LifeSciences will process your DNA samples efficiently, accurately and economically (of course, we cannot guarantee that every project will give a significant LOD score: this depends on mode of inheritance, family structure and map location). We have kept costs as low as possible with prices starting at about £400 per sample (inclusive of chip, consumables and processing costs). Discounts may be given for large projects. We offer free advice regarding projects and data analysis. Contact us now to confirm pricing and to get a custom proposal of work.

 

How should I supply my DNA?

The precise amount of DNA required for each sample will be a minimum of 10ul at 50 ng /ul using reduced EDTA TE buffer (0.1 mM EDTA, 10mM Tris HCl, pH8.0). Each array requires 250ng of DNA that has preferably been tested by you for its integrity. If this is not possible please send OD260/280 ratios of samples to confirm ratio >1.8 for each sample. Samples may be accepted of a lower quality at the discretion of Source BioScience LifeSciences but risk a higher chance of poor quality PCR.



Sample IDs should be provided in Excel format. Samples to be tested should be sent in a 96-well format on dry ice.


Please contact us to discuss your project and confirm your despatch arrangements for samples.


 

What if my samples don't pass the post PCR quality control stage?

Samples that fail the PCR QC stage will be withdrawn from the process at a cost of £100 per sample to cover consumable costs to this point, unless instructed to continue at customers risk. We would also offer customers the option of performing whole genome amplification to "rescue" their samples. It is a very successful method to obtain enough good quality DNA for further downstream processing (more info).

 

When can you start my project?

We will only order chips and schedule your project on acceptance of your personal quotation and receipt of the following details:

  • a signed copy of agreed quotation
  • a signed copy of terms and conditions
  • your details including purchase order with VAT exemption if it applies.

 

We can only order chips and schedule your project on receipt of these details.

 

When will I have to pay for the project?

For large projects you will be billed at the start of the project for the Affymetrix GeneChip Mapping arrays since they need to be ordered well in advance. You will be invoiced for the balance upon completion of the project and delivery of results. You will be notified in your proposal whether up-front payment for GeneChips is required.

 

How will I receive the data?

Source BioScience LifeSciences will supply you with the data from the samples on CD in strict confidence using Affymetrix software in Excel format. For example:

SNP ID

TSC ID

dbSNP RS ID

Chr

Chr Location (deCODE map)

pp1 control 10xba 220503

Call 1

Call 2

Zone

SNP_A 1513509

tsc 111

rs 0713055

6

161960064

173.2

B

B

0.05

SNP_A 1513556

tsc 112

rs 0713056

6

161960122

173.2

A

A

0.53

SNP_A 1518411

tsc 256

rs 0949459

7

42288671

64.7

A

B

0.08

SNP_A 1511066

tsc 864

rs 0713298

10

67254514

83.4

A

A

0.21

 

 

This all looks great but I still would rather do microsatellites

We continue to provide contract research using microsatellites and have successfully completed more than 30 genome scans using microsatellites.

 

 

I still have some questions, who can I speak to?

If you are interested in using the Affymetrix GeneChip Human Mapping Arrays or have any queries please contact us with full details of your study including the number of samples. We will return a customised project proposal, and we can schedule your work as soon as possible. Scheduling will only be arranged on receipt of a valid purchase order number.