GenoFIND Services for Microbiome

Full service clinical grade laboratory located in the United States.

Comprehensive staff of PhD and MD scientists.

Accreditations:

• CLIA - Clinical Laboratory Improvement Amendments
• CAP - College of American Pathologists
• State certified where applicable

DNA and RNA Extraction

Accept many sample types including:

• Saliva
• Whole blood
• Buffy coat
• Serum
• Buccal swabs
• And more

Fully validated standard operating procedures (SOPs) are used with a number of automated and manual extraction approaches to obtain the highest quality and yield of DNA regardless of sample type.

Every DNA extraction is accompanied by a number of standard quality controls to ensure accuracy of sample assessment and ultimately better success on downstream applications. Quality control measures include:

1. Quantitation – Fluorescent quantitation is commonly used to accurately determine the amount of double stranded DNA in a sample. We use a method involving the fluorescent dye PicoGreen to quantitate all samples that we extract.
2. Purity assessment - An A260/A280 ratio is commonly used to assess the purity of a DNA sample following extraction. This can be accomplished by determining the ratio of spectrophotometric absorbance of the sample at 260 nm to that of 280 nm. We perform this assessment using a NanoDrop instrument.
3. Integrity assessment - DNA integrity is critical for some downstream applications and to assess this agarose gel electrophoresis is performed to visualize the DNA before it can move on for further analysis. A single band with high molecular weight (>23kb) is an indicator of good sample integrity and a smear or otherwise lower molecular weight sample is an indicator of poor sample integrity.

Gel electrophoresis image demonstrating DNA samples with varying integrity. A single band showing molecular weight of 23kB or higher such as the first lane (1) show optimal integrity and suggest that the sample should be sufficient for most downstream applications. Smearing and decreasing overall molecular weight such as the samples in the remaining lanes (2-5) suggests lesser sample integrity. Samples with lesser sample integrity may not be sufficient for some downstream applications.

Other Services

• Whole Genome Amplification (WGA) – Allows you to amplify the DNA in a precious sample so that it can be used for many assays in the future without the requirement of re-collection.
• Aliquotting – Sample handling that allows you to have the sample distributed across multiple tubes and reduce or eliminate future freeze-thaw damage.
• Storage – Sample storage can be arranged for months or years depending on requirements in a CLIA accredited, environment controlled facility.

SNP Genotyping

Single Tube SNP Genotyping

Best for projects with:

• less than 1000 samples
• fewer than 50 SNPs
• Technology we use is TaqMan Single Tube assays. The TaqMan assay is an allele discrimination assay using PCR amplification and a pair of fluorescent dye detectors that target the SNP. One fluorescent dye is attached to the detector that is a perfect match to the first allele (e.g. an “A” nucleotide) and a different fluorescent dye is attached to the detector that is a perfect match to the second allele (e.g. a “C” nucleotide). During PCR, the polymerase will release the fluorescent probe into solution where it is detected using endpoint analysis in a real-time instrument.

Custom Arrays

Best for projects with:

• more than 1000 samples
• 50-500 SNPs
• Technology we use is TaqMan OpenArray. This system involves the custom printing of the SNPs of interest onto an array and subsequent automated processing of those arrays.

Commercial Arrays

Best for projects with:

• more than 100 samples (in some cases can be utilized with smaller sample numbers)
• thousands to millions of SNPs

Platforms available:

• Illumina
• Affymetrix

Custom Content Available

Fragment Analysis (INDEL, VNTR or CNV)

A technology used to assess insertions or deletions in the gene sequence. We use an approach including polymerase chain reaction (PCR) to amplify the region of interest followed by capillary electrophoresis to determine the length of the fragments amplified.

Fragment analysis allows for the investigation of:

• VNTRs – Variable number tandem repeats
• CNVs – Copy number variants
• INDELs – Insertions/deletions

Telomere Length Analysis (TLA)

This service is typically performed using a quantitative real-time PCR (qRT-PCR) method for absolute telomere length that can be found in O'Callaghan, N., V. Dhillon, P. Thomas, and M. Fenech. 2008 BioTechniques 44:807-809.

Other methods may be possible, please contact our Services Coordinator for more information.

Sequencing

We offer two types of sequencing technologies:

Next generation sequencing

• Performed using the Ion Proton and Ion PGM platforms
• Best used for targeted sequencing of large fragments of DNA (e.g. whole chromosome) and whole exome sequencing.

Sanger Sequencing

• Best used for targeted sequencing of small to midsized DNA fragments (i.e. 100-1,000bp).

What services does GenoFIND offer?

GenoFIND Services offers a wide variety of services including: nucleic acid extraction, genotyping, PCR- based assays, array-based assays and sequencing-based assays. In addition to extraction and downstream applications we also are able to offer a range of scientific consulting, bioinformatics and analysis services. We have access to a wide variety of platforms and qualified scientists with years of experience working with saliva samples so if you have any questions about a specific assay or analysis please contact your Sales Representative or the Services Coordinator for more information.

What should I do if I am not sure exactly what type of assay is the best choice for my project?

Contact your Sales Representative or the Services Coordinator for more information. Based on what you hope to accomplish we can usually recommend the most suitable technology for your project. If some background research is required a consulting scientist can review the literature from your field and make project recommendations.

I am not familiar with genomics. Can you help me to understand the data once my samples have been processed?

Our reports have been designed to be straightforward and easy to read. The Services Coordinator can also help you to understand the report and describe how to interpret it. If more in-depth analysis is required a consulting scientist can review your data and provide further interpretation.

How long will it take for my services to be performed?

The turnaround time for a project will vary dramatically depending on several factors including: number of samples, type of analysis and the queue at the lab. Typically most average sized projects can be completed within 4-5 weeks from the time that samples are received but if you require more rapid turnaround please let the Services Coordinator know. Remember the earlier you are in the queue the easier it will be to accommodate your timelines so always plan ahead.

What quality control measures come standard with your DNA extraction services?

We perform the following QC tests on all samples extracted:

• Fluorescent quantification of dsDNA using PicoGreen
• 260/280 Ratios by UV absorbance (to gauge purity)
• Agarose gels (to gauge DNA integrity)

More information under the Assays & techniques tab.

How do I ship my samples?

General Tips:

• Make sure all caps are secure for transport.
• Each sample must have a unique identifier written on the collection tube.

Oragene or ORAcollect saliva samples – Shipping recommendations

Buffy coat samples – Shipping recommendations

• For information on how to ship buffy coat samples at ambient temperature, please click here to learn about our HEMAgene•BUFFY COAT product.
• For more information on packaging of ambient temperature buffy coat samples, please refer to the following resources:
  • Shipping buffy coat samples - PD-WP-00034.pdf
  • IATA Guidelines
  • Your national biological sample shipping guidelines.
• If you are not using the HEMAgene•BUFFY COAT reagent or another means of ambient temperature stabilization, we recommend that buffy coat samples be shipped via overnight courier on dry ice.

Whole blood – Shipping recommendations

• Overnight ambient or cool temperature (4°C) is recommended for whole blood samples. It is important that the samples not freeze or get too hot to preserve the integrity of the sample.
• For more information on the packaging of whole blood samples please consult with your preferred courier and/or:
  • UPS - Shipping - Biological Substances
  • FedEx - Packaging Guidelines for Clinical Samples
  • IATA and ICAO Guidelines
  • An IATA trained shipping specialist.

Extracted DNA – Shipping recommendations

• We recommend that extracted DNA samples be shipped via overnight courier on dry ice.
• For more information on packaging of extracted DNA samples please refer to the following resources:
  • IATA Guidelines
  • Your national biological sample shipping guidelines.

What needs to be included on my manifest?

Manifest must list all samples using their UNIQUE identifiers

No extra spaces or punctuations (complete concordance between tube and manifest is required or batch will be put on hold until issues are resolved)

It is critical that all components of the unique identifier are addressed on the manifest including: leading and trailing zeros, initials or other alpha or numeric annotations.

Please click here to view a sample manifest.

Can you store my samples?

If required, short to mid-term storage of samples may be possible for your raw or extracted samples. Please contact the Services Coordinator for more information.

What will happen to my samples once the work is complete?

If you would like unused samples returned to you for storage and future analysis please ensure that you provide return shipping information including a courier account number at the time of contract signing.

Unless otherwise stated all samples that are not returned will be retained for 30 days past the date of project completion before being destroyed.

How long will my data be stored?

Unless otherwise stated, data will be retained for 1 year from the date of project completion on a secure server before being destroyed.

How long will it take for my services to be performed?

DNA Genotek’s privacy policy and practices have been created to comply with all Canadian Federal and Provincial based privacy legislation; particularly with regards to the Personal Information Protection and Electronics Documents Act (PIPEDA). DNA Genotek follows the following ten principals of personal information compliance;

• Accountability
• Identifying Purposes
• Consent
• Limiting Collection
• Limiting Use, Disclosure and Retention
• Accuracy
• Safeguards
• Openness
• Individual Access
• Challenging Compliance

If you have any questions about this policy or would like further information on the ten principles please contact: privacy@dnagenotek.com.

What is a SNP?

A SNP is a single nucleotide polymorphism and refers to a change in a single base at a specific location in the genome. These point changes in the genetic code may or may not result in changes in the phenotype of the donor. Referred to as a marker, it can be used to map inherited variation among individuals, often with reference to traits.

What is an rs#?

An rs# is the reference SNP ID number that is used to identify a specific location within the genome. The rs# is used to find primers and probes that specifically map to that location in the genome and will assist in determining the donors’ genotype at that position.

Where can I find SNP information?

SNPedia
dbSNP
DNA Genotek scientific publications

Dr. Ravinesh Kumar of the Conte Center for Computational Neuropsychiatric Genomics turned to GenoFIND for the analysis of collection samples for his pilot study. See why here.