We are planning to perform genome-wide genotyping. We are doing diabetic retinopathy related research where we will analyze 50 subjects. We are trying to decide on a suitable platform, array and software. Can you please give us recommendations?
If you want to stay in one ecosystem then looking at Illumina's portfolio may be good place to start: https://www.illumina.com/techniques/popular-applications/genotyping/whole-genome-genotyping.html
You should be able to find everything you need there all the way to software.
Indeed I was looking at their GenomeStudio Software. So basically the lab that would be doing genotyping for me would need to decide on Array and Library Prep Kit using this selector: https://www.illumina.com/library-prep-array-kit-selector.html?tags=web%3Aareas_of_research_focus%2Fcomplex-disease-genomics%2Cweb%3Akey-use%2Fgenotyping%2Cweb%3Amethod%2Fwhole_genome_genotyping_array%2Cweb%3Aspecies%2Fhuman
( I am not very familiar with this process) ...and is there is any array that is preferred for Human population?
That will depend on what you hope to get from the data and the budget you have available. Ask the lab you are planning to work with for assistance.
I am trying to see what would be the ideal scenario for selecting genotyping methods/tools for my study hypothesis (described in the comment bellow) and when I know that I will find a lab that can perform it. Can you please advise?
Which questions do you want to answer? That may strongly influence the choice of platform. Maybe something sequencing-based rather than arrays.
We hypothesize that the genetic basis of the interindividual transcriptional response to glucose differs between individuals with and without diabetic retinopathy and contributes to differences in susceptibility to diabetic retinopathy.
This disorder is likely polygenic? If you have a lot of samples the SNP arrays will be more cost effective but otherwise doing exome sequencing (or even genome) may be an option to look at.
I will most likely have 50 samples. Does that qualify as a lot of of samples or?
For example Illumina Omni arrays are between $200-$500 (example LINK). Large sequencing companies have specials for WES for ~$350-400 per sample. Both may require minimum samples but at at 50 you may be able to qualify. Informatics burden would be very different for the two technologies.
I have reached to Thermo Fisher and this is what they are offering. Can you please tell me would you go for any of these ones they recommend or Illimina Omni? (in particular Infinium™ Global Diversity Array) Unfortunately link you shared doesn't work.
For Thermo Fisher:
The first option would be, Axiom our signature genotyping assays with a semi-automated solution. The Axiom Precision Medicine Research Array (PMRA) is a broad and powerful genotyping resource for researchers driving deeper scientific insights into a variety of important health questions related to common and rare inherited diseases, genetic risk profiling, immune response, pharmacogenomics research, and many other areas associated with precision medicine. This array kit includes the 1x96-format array plate, as well as an Axiom 2.0 Reagent Kit and Axiom GeneTitan Consumables Kit.
• Genome-wide association study (GWAS) variants
• Clinically actionable variants
• Variants to cover immune function, autoimmune diseases, and inflammatory diseases and response
• Pharmacogenomic variants
• Functional variants
• Cancer common variants
• Blood phenotype variants
• Fingerprint/sample tracking variants
The second option, the Genome-Wide Human SNP Array 6.0 features 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNP Array 6.0 is the only platform with analysis tools to truly bridge copy number and association, including a new, high-resolution reference map and a copy number polymorphism (CNP) calling algorithm developed by the Broad Institute. The SNP Array 6.0 demonstrates industry-leading performance and represents more genetic variation on a single array than any other product, providing maximum panel power and the highest physical coverage of the genome.
Talk to the core and request the platforms they support. Request for their input in the context of your research and publications/literature of any help in your research context (from core or the core customers).
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