Genotyping: From QPCR To Microarrays And NGS Sequencing

Genotyping or genotyping is understood as the process of specific genetic characterization of a biological organism, this by determining the genotype or genetic variants present.

The most common form of genetic variation is single nucleotide polymorphisms or SNPs, in addition to variations in copy number – CNV, and / or structural changes in DNA such as insertions and deletions (indels).

In general, there are 3 techniques that allow to determine the genotype of an organism: quantitative PCR or qPCR, microarrays and next generation sequencing . The scope and challenges of these experimental techniques are presented below:

  Scopes Challenges
qPCR Workflow already known

Necessary equipment already available in many laboratories

Cost-efficient in a short number of variants to interrogate

Limited number of genetic variants that allows questioning

Under the power to discover new variants

Low scalability

Next generation sequencing ( targeted sequencing ) High power of discovery of new variants

High scalability to a greater number of samples and genetic variants

Impact on cost-efficiency if a small number of variants is chosen

Impact on test time if a small number of variants is chosen

 

  Scopes Challenges
Genetic expression microarrays Efficient in detecting the expression of known genes and transcripts in a certain period of time

Efficient in identifying point mutations, structural variants and / or specific methylation assays

Scalable to a high number of monthly and annual samples to be characterized

Requires specific hybridization probes for each target sequence

Under the power to discover new variants

Lower dynamic range in the measurement of genetic expression (10 3 ) due to signal saturation and background interference

Lower sensitivity to low expression and / or low abundance transcripts

Next generation sequencing (transcriptomic – RNA-seq ) Greater resolving power when describing complete expression profiles

High discovery power of new transcripts, gene fusions, single nucleotide variants, indels and unknown structural changes

Greater dynamic range in the measurement of genetic expression (> 10 5 )

Greater specificity and sensitivity to expressed genes, transcribed with low expression and / or low abundance

 

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