High-throughput genotyping is useful for identifying, assessing and validating genetic diversity of individuals and populations and for elucidating the relation of genetic variants to diseases, including single nucleotide polymorphism (SNPs), insertion/deletions and copy-number variations.  Typically, these studies are conducted to discern genetic differences between case and control groups for a disease or condition. Genotyping studies have been performed on a wide variety of diseases, including Parkinson’s, Crohn’s disease, obesity, diabetes, bipolar disorder, arthritis, hypertension, cancer (prostate, colorectal, breast), Alzheimer’s, multiple sclerosis, ALS and glaucoma.  Increasingly, genotyping is used to validate the results of  genome sequencing, such as exome sequencing, whole genome sequencing and targeted sequencing.  Some genotyping arrays have been used for diagnosing diseases and for disease risk assessments.

High-throughput genotyping has also been extensively used for population genetics and genomic ancestry studies as well as animal and plant breeding.

Methods

Genotyping studies may involve single samples up to thousands, usually collected from clinical settings where detailed information is gathered relating to disease etiology, family background, etc.  Patient samples are taken from cheek swabs, blood, paraffin imbedded tissue samples or saliva. Then, DNA is extracted and applied against test slides where hybridization is carried out against several thousand to millions of target regions.

Challenges

In large genotyping studies, samples are often collected from multiple sites over a significant duration. Hence, maintaining sample identification integrity and computerized sample tracking is essential. Centrillion has many years of experience in working with large sample sets and we have applied our experience to maintaining rigorous sample tracking. Starting with shipment of barcoded sample plates ready for customer samples, Centrillion utilizes robotic processes for sample processing and a custom Laboratory Information Management System (LIMS). We send you our SOP for shipment and maintain LIMS tracking at every step for every sample.

Patient DNA samples may not always be of the highest quality.  Fortunately, with experience and careful execution, modern genotyping technologies can generate good quality data from imperfect samples.  While genotyping technologies have become quite reproducible, plate-to-plate variations can happen. Therefore, in our genotyping process, we always genotype a process control sample so we can determinate plate-to-plate reproducibility and accuracy.  The control sample genotyping data are provided to our customers free of charge.

How Centrillion Can Help Your Large-Scale Genotyping Studies

Centrillion is expert in genotyping platforms enabling simultaneous, high-throughput SNP genotyping and sensitive copy-number variation analysis. For certain research programs, it may be advantageous to utilize a targeted genotyping approach via a custom genotyping solution. By this approach you may select and interrogate a set of custom SNPs of your choosing. We can help you leverage this approach to target the specific SNP set of interest for your study by designing the assays, performing the lab work and helping you to analyze the results.