1-Carbon Metabolism SNP

One-Carbon Metabolism SNP Chip Microarray


Per Sample

This is the MEGAEX microarray (illumina) containing over 2 million human SNPs including many related to one-carbon metabolism.


Non-UNC Users
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Service Description

This is the Infinium Expanded Multi-Ethnic Genotyping Array (MEGAEX®) array (illumina) containing over 2 million human SNPs.

Please Note: To download an Excel file containing all 2MM SNPs, go here.

We also run a customized version of this array that contains an additional 800 SNPs focused on the 1-carbon pathway.

Send DNA only, however if you only have blood or other body fluids and you need to have your DNA extracted, see our Genomic DNA Extraction recharge rate.

Procedure for Preparing DNA for the illumine MEGAEX® Array

Extract DNA with any standard method such as phenol-chloroform or a column-based method. We recommend a column-based method such as Qiagen’s QIAamp DNA Blood Mini Kit (Qiagen). The column methods are efficient, automatable, and have less chance of yielding samples with contaminants that could inhibit downstream applications. Per UNC Genotyping Core, DNA must be dissolved in 10 mM Tris-HCL pH 8.0, 1 mM EDTA (TE) (equivalent to Qiagen’s buffer AE).

Make sure that the DNA is of high quality (A260/280 ratio of ~1.8; a gel should be run to check integrity) and free from contaminating reagents (such as ethanol or phenol). To ensure the highest possible quality DNA, a column based method is recommended. Quantitate DNA using the Quant-iT™ PicoGreen ® dsDNA Kit (Invitrogen # P11496).

DNA Preparation Requirements for MEGA-EX SNP Genotyping:

  • Send samples in a 96 well plate (8 by 12).
  • Concentration*:  50 µl of DNA at a concentration of 50-100 ng/µl (2.5-5 µg total DNA)
  • Dilute purified genomic DNA in 10 mM Tris-HCL pH 8.0, 1 mM EDTA (TE).
  • Prepare a sample sheet with this information:  PLATE Name, POSITION, Sample Id, A260, A280, 260/280 ratio, DNA conc (ng/µL), DNA volume in plate (µL), and Total DNA amount (ng)
  • A sample sheet template will be provided.
  • One sample sheet for all the plates. Comma separated CSV, Excel or tab delimited txt format is acceptable.
  • Samples must be coded to ensure anonymity.
  • A copy of the IRB under which the samples were collected is required and methods must include processing and genotyping of samples.
  • Include an MGC Material Transfer Agreement signed by the PI named in your IRB approval.  MGC Material Transfer Agreement can be downloaded at:

Samples not following the above requirements will not be processed.

* Illumina recommends the Molecular Probes PicoGreen® assay for quantitation of dsDNA samples. We will use NanoDrop ND-1000 Spectrophotometer to double-check the DNA concentration.


Materials Transfer Agreement-Mammalian Genotyping Core

Please complete the Materials Transfer Agreement for Genotyping Services at the Mammalian Genotyping Core and return to the core.


Standard Operating Procedures

One-Carbon Metabolism SNP Chip Microarray-Standard Operating Procedures


Have Questions? Contact Us.

Saroja Voruganti, PhD
Core Director, Nutrigenetics Core
T: (704) 250-5009
E: saroja@unc.edu