Using arrays to identify mutations can be a very effective way of doing genetic testing. The collections are easy to use and provide results in a matter of hours. They are also less expensive than other methods. They are beneficial for detecting insertions and deletions in the sample. They are also suitable for identifying mutated variants in genes related to the disease.
GWAS
GWAS genotyping arrays are powerful tools for the genetic studies of complex diseases. However, they are limited in their ability to interrogate many SNPs. They must use indirect imputation to achieve the best possible representation of common variants. Imputation methods include using algorithms that leverage linkage disequilibrium between sequenced and GWAS variants.
Another approach is to use custom SNP arrays that allow dense genotyping of loci in large populations. This may be useful in filtering out nonfunctional SNPs at novel loci. However, it may also introduce bias into the estimation.
GWAS studies have uncovered hundreds of loci associated with the disease. But only a small number of these loci are causal variants. In the post-GWAS era, common variant-focused approaches have reemerged. These strategies have allowed for further loci studies, including identifying functional variants.
A similar approach is being undertaken to identify causal variants in new loci for plasma lipids. However, this work requires further validation of the causal genes. It also entails elucidation of the biological mechanisms underlying the genes. In addition, it requires a large sample size. This can be prohibitively expensive. Integrative analysis is a more robust method for accelerating the search for disease-causing mutations. This method effectively compares common SNPs’ effect sizes and rare variants’ effects.
Pharmacogenetics
Array genotyping has long been used in genome-wide association studies (GWAS) and is now widely used for the imputation of polygenic scores. But what are the best genotyping arrays for pharmacogenetics? Identifying the best collection depends on several factors.
The GWAS method has been proven to be a successful method of discovering genetic factors for complex diseases. The density of SNVs on arrays can be used to measure specificity for structural variant analysis. The ACMG list also significantly influences the design of displays, as it contains medically actionable variants that could lead to severe outcomes. The latest genotyping arrays were designed with imputation quality in mind. Unlike GWAS, arrays can tag untyped SNVs through linkage disequilibrium. This enables them to call otherwise unidentified variants.
Detection of insertions and deletions in the samples
Detection of insertions and deletions in the samples is one of the more challenging tasks in the genomics arena. These structural variants provide novel structural elements and contribute to protein-protein interactions. They also offer a valuable source of structural variation within protein superfamilies. The first step in detecting hidden insertions and deletions is to design the proper primers. The next step is to perform a quantitative “copy number” PCR to confirm the presence of any potential insertions.
The most successful approach is to use a combination of PCR fragment size analysis and a broader fragment library. This approach increases the probability that deletion will be identified but also poses significant pitfalls. PCR fragment size analysis can detect single nucleotide insertions, while a more extensive library can provide an improved chance of detecting larger deletions.
Many tools are available to detect and quantify small insertions and deletions, but using a robust probabilistic algorithm is the best approach. This approach was tested on several modern layer chicken lines. In addition to testing individual genes, we also analyzed several chicken lines for overall indel detection.
Genotyping-by-sequencing
Molecular markers are used to detect genetic variation. Genetic diversity is then quantified by comparing loci from various samples. This can be used in association studies, genetic selection, genomic selection, and linkage mapping.
Next-generation sequencing (NGS) has dramatically expanded genotyping. This technology is an economical, efficient method for genotyping large numbers of SNP markers. It provides ultra-throughput sequences with integrated SNP sets. The high density of SNP markers from NGS will be applied to genome-wide association studies (GWAS), metagenomic analysis of environmental samples, and marker-assisted selection (MAS) in plant breeding.
Genetic diversity-focused genotyping-by-sequencing (gd-GBS) is a relatively new approach that combines one step of marker discovery and genotyping. Most GBS protocols follow a similar sequence of core steps. However, some GBS protocols may include additional steps. The first step involves sequencing DNA from individuals of interest. The second step involves mapping reads to a reference genome. The third step requires haplotype identification. Depending on the NGS platform, the steps may vary.
The fourth step involves ligations of adaptors. These include bar-coding regions in the adapter. Finally, the fifth step consists of amplifying small fragments by PCR. In addition to being a cost-effective and rapid genotyping method, GBS applies to many different types of genetics. It has been used in large crop genomes for genome-wide association studies. It can also be applied to germplasm sets and non-model species.
