Nucleic acid sample quality and quantity specifications

Whole Genome Arrays

	Minimum DNA volume*	Required DNA concentration**	Minimum number of samples^
Affymetrix 6.0	30uL	50ng/uL	95
Infinium Omni1quad	30uL	50ng/uL	95
Infinium OmniExpress	30uL	50ng/uL	95
Infinium Omni2.5quad	30uL	50ng/uL	95
Infinium Omni2.5-8 sample	30uL	50ng/uL	95
Infinium Omni5M-quad	35uL	50ng/uL	95
Infinium OmnExpress + Exome Array	30uL	50ng/uL	95
Illumina Infinium Methylation 450K	50uL	50ng/uL	95

Custom Content Genotyping

	Minimum DNA volume*	Required DNA concentration**	Minimum number of samples^
Illumina iSelect	30uL	50ng/uL	95-standard panel (e.g. Metabochip, Immunochip, Exome chip)
Illumina GoldenGate	30uL	50ng/uL	480 samples
Illumina BeadXpress	30uL	50ng/uL	480 samples
Sequenom iPlex MassArray	20uL + 5uL per pool	5ng/uL	100,000 genotypes (samples x SNPs); pools up to 7 SNPs
Sequenom hME MassArray	20uL + 5uL per pool	2.5ng/uL	100,000 genotypes (samples x SNPs); pools up to 36 SNPs

RNA requirements for Gene Expression

	Minimum RNA volume*	Minimum RNA concentration**	Compatibility, number of samples and notes***
Affymetrix 3' IVT Express	20uL	50ng/uL	Affy, 30 samples, Good quality total RNA
NuGen Ovation V2	20uL	10ng/uL	Affy, 30 samples, partially degraded, limited RNA
NuGen Pico	20uL	1ng/uL	Affy, 30 samples, Partially degraded, very limited RNA
Ambion Illumina Total Prep	32uL	50ng/uL	Illumina WG, RF and HT, 24 samples, Good quality total RNA
Illumina WG DASL	20uL	80ng/uL	Illumina, 24 samples, FFPE/ degraded samples

* Includes volume needed for Biological Samples Platform and for arrays.
**DNA concentration as measured by PicoGreen method. Spectrophotometry (A260) is not a recommended quantification method for these platforms.
***All RNA quality must be assessed using a bioanalyzer chip (except FFPE samples) prior to running expression arrays.
^Minimum number of samples applies to external collaborators; contact us if you are a Broad affiliate.

General Considerations

All samples to be used on our genotyping platforms must come to GAP through the Biological Samples Platform (BSP). BSP is responsible for sample registration, sample handling and quality control of all samples (e.g., concentration measurement by PicoGreen). The volumes in the table above include what is the total DNA required for both BSP and GAP.

Please note that samples for expression analysis do NOT need to be sent to us through BSP. RNA samples can be sent directly to the project manager handling your study. Please coordinate with your project manager to get your RNA samples to our expression platform. RNA must be provided in a 96-well plate (not individual tubes).

DNA isolation

We suggest using an appropriate Quiagen kit (e.g., QIAGEN QIAamp™ DNA Blood Maxi Kit) or DS/ProK digestion followed by phenol-chloroform extraction and Millipore Microcon™ or Centricon™ ultra-purification and concentration for DNA isolation purposes. Other methods may work as well as long as the DNA is eluted/resuspended in either water or a low salt buffer (e.g., TE with reduced EDTA (10 mM Tris, pH 8.0; 0.1 mM EDTA)).

Higher salt concentrations can have adverse effects in both GAP and BSP processing. If you have concerns about your DNA isolation method please contact us.

RNA isolation

We suggest using either TRIzol® Reagent by Invitrogen or Quiagen RNeasy kits for RNA isolation but other methods can work as well. Please contact us if you plan to use FFPE samples for your expression study because these samples require special isolation methods and it is critical that we make sure the isolation kit is compatible with the arrays.