Frequently Asked Questions

Genomics Platform FAQs

Genotyping & Arrays FAQs

Genomics Platform FAQs

How do I initiate a project with the Genomics Platform?

Please use the inquiry form to contact us.

Is the Genomics Platform a "fee-for-service" or core facility?

We work collaboratively with scientists both at the Broad and around the world to utilize these tools to address cutting-edge questions and major projects that are beyond the scope of a single laboratory. We typically work under a collaborative model where we have scientific engagement in the design, execution, and analysis of a study; however, we do accept qualified "fee-for-service" projects from outside the Broad, as capacity allows.

How much will my project cost?

To inquire about current pricing, please use the inquiry form.

Do you have any minimum requirements for new projects?

Yes. We have minimum project requirements for external users. Please see the Genomics Platform technologies and the nucleic acids quality and quantity specifications pages for details on the minimum requirements for each platform. These minimum requirements allow us to recoup our costs, as required by Specialized Service Facilities.

I have an active IRB (Institutional Review Board) application at my home institution. Does my IRB have to be approved at the Broad?

Your designated project manager here at the Broad will work with you to complete the proper forms needed to obtain approval from the Broad's IRB. Please note that we must have IRB approval of your project before your samples can be analyzed.

How do I get my samples to the Genomics Platform?

We will send you tube kits for your samples. These kits contain individual barcodes for each sample, which allow us to track your samples throughout course of the project. We will also handle, store and plate all of your samples and perform QC steps (e.g., concentration analysis using PicoGreen).

What is your policy on sample re-runs?

If we made a processing error that results in the failure of an assay, then we will re-run the sample at no additional cost. If a sample needs to be re-run for other reasons (e.g. poor sample quality) then the re-run is the investigator's responsibility.

How long will the process take?

Your project manager will be able to give you a specific estimate of how long your genotyping or expression study will take once your funding is in place.

Are discounts available for Broad affiliates?

Unfortunately, we cannot offer discounts to anyone, regardless of their affiliation. The rules governing the Broad platforms' Specialized Service Facilities require that every project is charged the published rate. SSF prices are set at a rate that covers the labor, materials, and indirect costs of the particular assay, with no profit margin.

Genotyping & Arrays FAQs

What are the guidelines for sample preparation?

Please see our nucleic acids quality and quantity specifications page.

How do I extract my DNA?

Recommended DNA extraction methods include: 1. SDS/ProK digestion followed by phenol-chloroform extraction and Millipore Microcon(tm) or Centricon(tm) ultra- purification and concentration. 2. QIAGEN QIAamp(tm) DNA Blood Maxi Kit or other appropriate Qiagen kits.

How do I extract my RNA?

TRIzol reagent and Qiagen RNeasy kits both provide high-quality RNA. Please contact us if you are planning on using FFPE samples as they require specific isolation methods.

How do I send my RNA?

Please put your RNA samples in the following 96-well plate: (ABGene 96w skirted PCR plate, MSP9601). You can either bring your samples to the Broad or ship them to us. Please coordinate with your Broad project manager when you are ready to send your samples.

What can I elute/resuspend my DNA in?

Ideally, samples should be sent to us in water. Low salt buffers such as TE with reduced EDTA (10 mM Tris, pH 8.0; 0.1 mM EDTA) are also fine.

How much DNA/RNA should I send?

Please see our nucleic acids quality and quantity specifications page for details on the volumes and concentrations needed for each platform.

What genotyping platform is best for my project?

The appropriate genotyping platform depends on the scope of your project. Please use the inquiry form to contact us and a member of our team will gladly discuss any study design questions you might have.

Can I use WGA'd DNA?

WGA (whole genome amplified) DNA gives roughly equivalent results on the lower-plex genotyping platforms (Sequenom, GoldenGate). However, we have observed suboptimal results with WGA DNA on whole genome platforms and do not recommend WGA prior to Affymetrix or Infinium genotyping.

Do I need to clean up my WGA'd DNA for platform X?

If the whole genome amplified (WGA) material is destined for an Illumina Golden Gate or BeadXpress project, we recommend cleaning up the WGA reaction. Although WGA cleanup does not have any adverse effects on genotype performance, it can improve call rates on Sequenom.

I measured DNA concentration with the NanoDrop; will that be OK?

Our protocols are optimized for DNA concentrations as measured by PicoGreen. We frequently find that a Picogreen concentration is approximately half or less of that measured by NanoDrop. Therefore, we require PicoGreen derived concentrations for all DNA applications. We also require that samples be measured here at the Broad.

Why are DNA requirements for Illumina expression projects in multiples of 6?

The Illumina Ref-6 arrays assay 6 samples per chip. To maintain the lowest cost possible, we only run full arrays, meaning projects with multiples of 6. Likewise, for the Ref-8 arrays (8 samples per chip), multiples of 8 are required.

How will I retrieve my data, and in what form(s) will they be?

Data can be downloaded using the Arrays project management interface, using the GAP portal. If you have a small amount of data, we may be able to attach the data and send via e-mail. If you have a very large dataset, we may need to send it to you on a hard drive. Contact your project manager to discuss the best solution for your analysis needs. Genotyping data are available in raw data files (.cel for Affymetrix, .idat for Illumina) and in .ped files already formatted for downstream applications (all platforms). Expression data are available in raw data files (.cel for Affymetrix, .idat for Illumina).

How do you choose proxy SNPs or redundancies to get higher plex assays?

SNAP is a web server for finding and annotating proxy SNPs (single nucleotide polymorphisms) based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.

What is Birdsuite/Birdseed and how do I access it?

Birdsuite is a fully open-source set of tools to detect and report SNP (single nucleotide polymorphism) genotypes, common copy number polymorphisms (CNPs), and novel, rare, or de novo copy number variants (CNVs) in samples processed with the Affymetrix platform. Birdseed is a tool that preceded Birdsuite and reports SNP genotypes. You can access Birdsuite through the Broad Institute's software page. If possible, we will run all genotyping data through Birdsuite before providing it to you.

How do I access genetic variation software such as SNAP, PLINK and Haploview?

Please visit the Broad Institute's software page for access to these software tools.

Why don't my 36 SNPs fit into 1 Sequenom pool?

In designing a multiplex assay, Sequenom design tools group together as many genotyping assays as it calculates are likely to be successful in combination, as some sequences can interfere with one another. The highest pooling efficiency occurs with large SNP lists; it would be extremely unlikely to ever group a list of 36 SNPs into one pool. If it were possible to design a pool of 36 SNPs, some SNPs in the pool might not perform optimally when we try to multiplex 36 reactions.

Do I *have* to have my samples fingerprinted before whole-genome genotyping?

Yes, it is part of our standard quality assurance protocol. We frequently find some percentage of samples destined for GWAS (genome-wide association studies), which are revealed to have genders that are inconsistent with their clinical data, and/or Mendelian inconsistencies suggesting a potential sample mix up. Fingerprinting can also reveal poor DNA quality in specific samples. These samples, which are thus uninformative for GWAS, can be excluded prior to spending the money on the whole genome genotyping array. After GWAS, we again check the concordance of the fingerprint genotypes against the whole genome array genotypes. Fingerprinting is therefore critical for filtering samples before GWAS and as a process QC.

What control(s) do you include when plating?

For our whole genome arrays, DNAs from a HapMap trio (one trio member's DNA per plate) are plated in rotation onto production plates.

Can you provide me with control genotype data?

We cannot share genotype data generated by one group of users with investigators outside that project. However, many genotyping studies performed at the Broad (including controls) have been submitted to dbGaP where they can be downloaded by outside researchers.

What is your policy on sample re-runs?

If we made a processing error that results in the failure of an assay, then we will re-run the sample at no additional cost. If a sample needs to be re-run for other reasons (e.g. poor sample quality) then the re-run is the investigator's responsibility.

How long will the process take?

Your project manager will be able to give you a specific estimate of how long your genotyping or expression study will take once your funding is in place.

Are discounts available for Broad affiliates?

Unfortunately, we cannot offer discounts to anyone, regardless of their affiliation. The rules governing the Broad platforms' Specialized Service Facilities require that every project is charged the published rate. SSF prices are set at a rate that covers the labor, materials, and indirect costs of the particular assay, with no profit margin.