The genotype-first approach is a type of strategy used in genetic epidemiological studies to associate specific genotypes to apparent clinical phenotypes of a complex disease or trait. As opposed to “phenotype-first”, the traditional strategy that has been guiding genome-wide association studies (GWAS) so far, this approach characterizes individuals first by a statistically common genotype based on molecular tests prior to clinical phenotypic classification. This method of grouping leads to patient evaluations based on a shared genetic etiology for the observed phenotypes, regardless of their suspected diagnosis. Thus, this approach can prevent initial phenotypic bias and allow for identification of genes that pose a significant contribution to the disease etiology.

This approach is unaffected by phenotypic heterogeneity, incomplete penetrance and levels of expressivity. Therefore, it is useful in complex diseases that also overlap, such as autism spectrum disorder and intellectual disability, enabling the diseases to be distinguished, and specific subtypes of the disease based on the genomic content to be determined.

Currently, the genotype-first approach is used primarily for research objectives. However, the implications from these studies can have valuable clinical applications, including improved diagnosis, counselling, and support groups for individuals with the same genetic etiology.

Initially the idea of identifying the genotype of individuals and subsequently their associated phenotype(s) was first used in early cytogenetic studies. Around 1960 the discovery of Trisomy 21 led to the realization that genetics could be used to predict phenotype(s). From the 1960s to 1990s cytogenetic techniques such as chromosome banding and fluorescence in situ hybridization (FISH) were used to identify and phenotypically characterize patients with chromosomal abnormalities.

Complex diseases and traits pose many difficulties for epidemiological studies due to their nature as multifactorial diseases. More than one gene can underlie a complex disease and generally contributes a smaller effect than what is observed in monogenic diseases (Mendelian diseases). In addition, many of these complex diseases exhibit diverse phenotypes as well as a wide range of expressivity and penetrance. Genes can also be pleiotropic, accounting for many seemingly distinct clinical phenotypes. These features limit the ability of both research and clinical studies to designate causal genes or variants to the observed phenotypes and to classify disorders.

Clinicians are starting to recognize the need to classify genomic diseases by a common genotype rather than a common phenotype and how genotype-first approach can benefit this purpose.

Several methods can be used with a genotype-first approach, however, the following steps are usually included:

The genotyping is generated using next-generation sequencing technologies (including whole-genome sequencing and exome sequencing) and microarray analyses. The raw data is then statistically analyzed for population-based frequency of the variants. Common variants are filtered out, and pathogenicity is determined though predicted genetic implications. These steps allow for the identification of presumed highly penetrant variants and their specific locus. The selected variants are usually resequenced for validation (by targeted Sanger sequencing). Validated genomic variants can then be analyzed for recurrences among affected individuals within the cohort. Pathogenicity of a genomic variant is statistically based on its significantly abundant presence in the affected compared to the unaffected individuals, not exclusively on the deleteriousness of the variant. A candidate variant can then be associated with a shared phenotype with the aspiration that as more patients baring the same variant with the same phenotype will be identified, a stronger association can be made. Finally, delineation is made between a specific variant to associated clinical phenotypes [Figure 1].