Technology for genotyping
The Biobank Genomics Core at Personalized Medicine provides flexible, high-quality, high-throughput SNP genotyping to the Mass General Brigham research community. We offer Taqman genotyping as well as genome-wide methylation and genotyping assays on our Illumina iSCAN platform. We employ state-of-the-art automation, including Biomek FX, Perkin Elmer Janus, a QuantStudio5 Sequence Detection System and an Illumina iScan system.
For Taqman, all requested assays must be available on demand from Thermo Fisher, as we do not carry out assay design and optimization.
For Illumina Infinium, we stock the Global Diversity Array (GDA), Global Screening Array (GSA) and the Human Methylation 850 EPIC array. We can run any of the commercial arrays available from Illumina, with the exception of Infinium XT products. Please order reagents and arrays directly from Illumina and have the reagents shipped directly to our lab.
New chip types may require additional processing time for clustering and allele calling on completion of wet lab work. Please ask if TAT will be impacted.
Specimen requirements per technology:
Technology |
SNP Info |
DNA |
Concentration |
Quantitation |
Minimum Volume |
---|---|---|---|---|---|
Illumina Infinium Genotypes | Fixed Panels |
Genomic DNA Only |
50 ng/ul |
Picogreen |
20 ul |
Taqman |
RS# or customer-provided sequence information |
Genomic or WGA DNA |
5-10 ng/ul |
Picogreen |
30 ul |
Illumina Infinium Methylation |
Human/Mouse |
Genomic DNA or Bisulfite-Converted DNA |
50 ng/ul of Genomic DNA |
Picogreen |
40 ul |
Quality control
All DNA plates delivered to the lab for genotyping will be quantitated by picogreen to ensure the concentration of the DNA is at the required 50 ng/ul. Those samples with lower concentrations or high amounts of degradation will only be genotyped with permission from the principal investigator, with the understanding that Personalized Medicine is not responsible for drop in data quality. If concentrations are greater than required by the technology, then we are able to normalize the concentration in-house for a charge, or the plates can be returned to the customer for normalization.
Please note that normalization will increase turnaround time. You may waive the option of quality control, but then no guarantee is given to the quality of the genotypes and all costs will be passed onto the customer regardless of quality of data. WGA DNA is not recommended due to decreased call rate and amplification of allelic bias present in the original WGA sample.
For samples extracted outside of our lab, we suggest each plate contains 95 samples which will be genotyped alongside a positive control sample. The resulting genotypes from the positive control sample will be compared over time to ensure reproducibility and performance of our lab process.
Turnaround time
We work on a first-come, first-served basis. Our expected turnaround time depends on our queue at the time we receive your samples. Once receiving the reagents, processing takes two to three weeks for up to five plates. Larger projects may require additional processing time.
Ordering and pricing
Before genotyping can be carried out, please visit our order entry page to place a GIGPAD batch order. For quotes and customer inquiries, please email us.