OpenFlexTyper features (Kesako)

[kounkou]

Hi there,

FlexTyper features :

Genotyping known alleles

• SNP genotyping (used in ancestry, population genetics, GWAS)
• SV genotyping (used to search directly for the presence of SV breakpoints)

Identification of specific large sequences

• Foreign pathogens

Genotyping known alleles	results	dataset
Ancestry	✔️	Polaris African, European, Asian
population genetics	❌
GWAS	❓

Structural variant genotyping	results	dataset
SV BP	not tested

Specific large sequence identification
Foreign pathogens	✔️	EBV, HIV, U21941, FR751039

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Genotyping
Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence.

GWAS
A genome-wide association study (GWAS) is an approach used in genetics research to associate specific genetic variations with particular diseases. The method involves scanning the genomes from many different people and looking for genetic markers that can be used to predict the presence of a disease.

SV
Structural variation (also genomic structural variation) is the variation in the structure of an ... The definition of structural variation does not imply anything about frequency or ... diseases, using methods that are used for quantitative SNP genotyping. .... each being based on patterns that are diagnostic of different classes of SV.

Population genetics
Population genetics is the study of genetic variation within populations, and involves the examination and modelling of changes in the frequencies of genes and alleles in populations over space and time. ... In natural populations, however, the genetic composition of a population's gene pool may change over time.

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References :
https://www.genome.gov/genetics-glossary/Genome-Wide-Association-Studies
https://en.wikipedia.org/wiki/Structural_variation
https://en.wikipedia.org/wiki/Genotyping
https://www2.le.ac.uk/projects/vgec/highereducation/topics/population-genetics
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1