You’re setting up a new lab. How can you find the best genotyping tools for your research?

A researcher should determine the source and quality of their DNA samples before exploring genotyping products. For example, techniques such as PCR-based targeted genotyping may be more appropriate than high-throughput sequencing when dealing with damaged DNA recovered from historical materials. SNP arrays or NGS platforms like Illumina's NovaSeq may be preferred for large-scale population investigations; the quantity of samples also influences the decision. Researchers may choose TaqMan assays for targeted genotyping because of budgetary restrictions. Aligning the genotyping strategy with particular research objectives and resource constraints is crucial.

Setting up a new lab with the best genotyping tools for your research requires careful consideration and research. I would assess lab needs by defining your research goals: ? What type of genetic information are you interested in? (e.g., single nucleotide polymorphisms, copy number variations, mutations) ? What is the scale of your research? (e.g., number of samples, genome coverage) ? What is your budget? (e.g., instrument costs, reagents, sequencing costs) ? What is your timeline? (e.g., how quickly do you need results)

Identify the specific requirements of your research. Consider factors such as the type of samples you’ll be working with, the scale of your project, the level of resolution you need, and your budget.

When setting up a new lab, it's crucial to keep a close eye on your budget. Clearly outline how much will go into infrastructure and equipment, what's allocated for experiments and reagents, and how much is reserved for hiring new staff (technicians, Ph.D. candidates, postdocs, etc.). Don't get caught up in utopian claims, especially in genomics. Currently, any NGS platform is relatively expensive to both purchase and maintain, including services, upgrades, and replacing old models with newer ones.

Just like you'd choose the right pots and pans for your cooking style, think about the tools you need. Stay on budget; you don't want to break the bank. And here's the fun part: ask the experts, your fellow scientists, and the LinkedIn community for advice. It's like getting recommendations from friends about the best kitchen gadgets. Your lab is your creative space, so set it up with the tools that fit your scientific feast!

I would opt for the Next-Generation Sequencing (NGS) methods whenever possible. Sanger sequencing and microarrays are gradually fading into obsolescence. Everything has its own time... While the upfront costs may be lower with the latter, the results obtained are considerably distant from the output achievable through NGS.

Genotyping methods, like tools in a toolbox, come with unique strengths and limitations. PCR stands out for its speed and affordability but demands prior knowledge of the target sequence, potentially missing rare variants. RFLP is cost-effective and straightforward, yet limited to known polymorphic sites. SNP Arrays offer high-throughput, covering numerous samples and variants, but may be pricier and not cover all regions of interest. Microsatellites are versatile and reliable but require careful optimization and may not suit every scenario. Sequencing, a powerful and flexible option for any sample and variant, is time-consuming, resource-intensive, and may yield more data than necessary.

You can compare different methods by researching the available genotyping methods: Microarrays: Great for large-scale studies but limited to predefined variants. Real-time PCR: Accurate for specific loci but with limited multiplexing. Targeted sequencing: Precise for specific genome regions but can be expensive. Next-gen sequencing (NGS): Versatile for whole-genome or targeted analysis, requiring expertise. Digital PCR: Accurate for allele quantification but has limited throughput. Consider accuracy, sensitivity, throughput, cost, ease of use, and data analysis when making comparisons.

There are various genotyping methods available, including SNP genotyping, microsatellite genotyping, and sequencing-based methods. Each method has its strengths and weaknesses. For example, SNP genotyping is cost-effective and suitable for large-scale studies, but it may not provide the level of resolution needed for certain applications.

Once you’ve narrowed down the methods that might be suitable for your research, start evaluating specific products. Look at factors such as the cost, ease of use, throughput, and the level of technical support provided by the manufacturer.

Nevertheless, it might be an interesting proposal to approach companies like Illumina or PacBio and ask if they'd be willing to deliver a few sequencers to your lab for to see if you enjoy working with them or not.

Choosing genotyping methods is like selecting tools for a project. After deciding on methods, evaluating products is crucial. Consider features, performance, quality, and price. Seek reviews and recommendations. Evaluate ease of use, reliability, compatibility, vendor support, and budget alignment. This ensures seamless integration into your research journey, akin to selecting the right ingredients for a successful experiment!

Testing various genotyping products firsthand is valuable but not always practical. Pros include hands-on experience, direct comparison, and informed decision-making. However, the cons include high costs, time consumption, expertise requirements, and limited scope. Alternative approaches include a literature review for method comparisons, consulting with experts, attending workshops for the latest advancements, and collaborating on pilot studies. Opt for a combined strategy, tailored to research needs, budget, and resources. Seek help from experts, and stay informed about new technologies for effective decision-making in your genotyping endeavors.

If possible, test a few different products before making a final decision. This will give you a better idea of how each product performs in practice and whether it meets your specific needs.

I wouldn't suggest that testing NGS applications on different platforms is a common practice. Whether it's short-read sequencing or long-read sequencing, these methods are expected to work well with human (mammalian samples), plants, and possibly bacteria with some adjustments. But it all boils down to sample preparation. This is something you can experiment with on your own. For instance, you can test the isolation of cells/nuclei for your single-cell project. I can't imagine a situation where a sequencing company would lend you a sequencer to try out demo kits...

Other factors to consider might include the availability of reagents and consumables, the compatibility of the genotyping tool with other equipment in your lab, and the future research directions of your lab. It’s also worth considering whether the manufacturer provides regular software updates and improvements.

Sometimes, it's wiser to check if your research institute already has a genomics core facility or if there's a collaborative partner with one. Running a genomics lab independently can be super-expensive, so it might be worthwhile to discuss with management about supplementing lab operations with additional sources of funding to keep it running smoothly. Perhaps other research groups might also be interested in utilizing the lab for their omics projects.