Genomics
Service Providers
Genomic sequencing services are available at numerous local labs. There are several DNA sequencers spread out across the country. These facilities offer high-quality data generation and analysis capacity, with expert assistance at competitive prices. Contact our help centre or the providers in your area to discuss your needs.
It has become a requirement of publication to make the data generated for publication, publicly available. There are several genomic data repositories for data deposition. These data are processed, compiled, and made accessible via genome browsers. Omics experiments often rely heavily on available data as a starting point. Sometimes it may even be possible to make use of existing data rather than needing to generate new data. The first step in any Omics experiment is therefore to check what data are available.
The two primary genomics databases are the NCBI Genome Database and the Ensemble Genome Database. These databases contain genomes across all kingdoms of organisms. Most of the sequences, though are focused on model organisms. There are already thousands of organisms for which we have genomic sequences, as well as thousands of human genomes. There are also several databases for specific purposes like the cancer genome databases, that focus on genomes of a variety of cancers.
Data Generation
Depending on the amount of information required, there are a variety of ways to generate genomics data. If a small specific area of the genome such as a gene or control sequence needs to be studied, the region is amplified by polymerase chain reaction (PCR), quantitated and characterised. Recently this has been shown to be useful in identifying infection by SARS-CoV-2 in the COVID-19 pandemic.
If more global information about the genome is required, commercial or custom DNA microarrays are available to determine the prevalence of known genomic variances. Sanger sequencing used initially to sequence the human genome, has been automated using fluorescent tags to allow high throughput applications. Small genomes are easily sequenced by Sanger sequencing. Next-generation sequencing (NGS), which covers a variety of modern parallel sequencing techniques, allows sequencing of an entire human genome within a day. Depending on the information required, NGS is used to sequence the whole-genome or just the exomes.
Analysis Tool Collections
Genomic sequencing produces a large amount of data and the data analysis consists of multiple steps. To ensure that data is processed in a consistent manner H3ABioNet and others have compiled several trusted tools and workflows. Due to the large amount of data needing to be processed, access to extensive data storage and high-performance computing resources may be required. Many of these tools are open source and only run on Linux. Combining these tools into robust pipelines can be complicated and may require the assistance of a bioinformatician. Consult the bioinformatician section to get help.
Bioinformaticians are available through DIPLOMICS to assist you with your project.
The earlier you contact them, the more assistance they will be able to offer. Omics research is costly, choosing the most appropriate technology for your experiment, and budget is, therefore, crucial. In particular, it is essential to discuss the experimental design with a statistician to ensure your experiment has sufficient statistical power.
It is advisable to run a pilot study and have an expert check the quality of the results before continuing with the bulk of the analysis. The pilot project will familiarise you with the sample processing, data generated, and data processing, before embarking on the main project. Issues identified at this point can improve the quality of the data generated thereby making better use of the funds spent.
Omics technologies produce masses of data and require expertise for processing. Fortunately, Bioinformatics tools and resources are available to store and process omics data. Contact our team of expert bioinformaticians for assistance on all levels of your project. The earlier, the better.
