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In the field of genetic sequencing, genotyping by sequencing, also called GBS, is a method to discover single nucleotide polymorphisms (SNP) in order to perform genotyping studies, such as genome-wide association studies . [1] GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples. [2]
Personal genomics or consumer genetics is the branch of genomics concerned with the sequencing, analysis and interpretation of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips (typically 0.02% of the genome), or partial or full genome sequencing. Once ...
Due to current technological limitations, almost all genotyping is partial. That is, only a small fraction of an individual's genotype is determined, such as with (epi)GBS (Genotyping by sequencing) or RADseq. New [2] mass-sequencing technologies promise to provide whole-genome genotyping (or whole genome sequencing) in the future.
Computational genomics refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, [1] including both DNA and RNA sequence as well as other "post-genomic" data (i.e., experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays).
Next-generation sequencing technologies such as pyrosequencing sequence less than 250 bases in a read which limits their ability to sequence whole genomes. However, their ability to generate results in real-time and their potential to be massively scaled up makes them a viable option for sequencing small regions to perform SNP genotyping.
The end of the 20th century saw the emergence of the first projects to sequence complete genomes. Among these projects, the Human Genome Project was the most ambitious at the time, aiming to sequence for the first time a genome of several gigabases. This required the sequencing centres to carry out major methodological development in order to ...
The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects.
An important part of the design of variant calling methods using NGS data is the DNA sequence used as a reference to which the NGS reads are aligned. In human genetics studies, high quality references are available, from sources such as the HapMap project , [ 10 ] which can substantially improve the accuracy of the variant calls made by variant ...