A genotype-first approach to defining the subtypes of a complex disease

Abstract

Medical genetics typically entails the detailed characterization of a patient's phenotypes followed by genotyping to discover the responsible gene or mutation. Here, we propose that the systematic discovery of genetic variants associated with complex diseases such as autism are progressing to a point where a reverse strategy may be fruitful in assigning the pathogenic effects of many different genes and in determining whether particular genotypes manifest as clinically recognizable phenotypes. This "genotype-first" approach for complex disease necessitates the development of large, highly integrated networks of researchers, clinicians, and patient families, with the promise of improved therapies for subsets of patients.

Figure 1. Schematic of Genotype-First Approach for ASD

(A–C) Following complex neurodevelopmental disease diagnosis in the clinic, step one is to apply next-generation sequencing (exome or whole-genome) to identify high-impact rare or de novo variants that exist(s) in an individual. Through screening of many individuals, recurrent mutations in a gene or locus are identified with a general diagnosis of ASD or DD. These candidates are selected for targeted resequencing using high-throughput, cost-effective technologies. Molecular inversion probe (MIP) technology, for example, applied to thousands of individuals with ASD or DD identifies genes with an excess mutational burden in probands when compared to controls. Such genes are most likely to contribute to disease etiology and represent future targets for therapeutic intervention. Families with these gene mutations are recontacted and brought back to the clinic for more comprehensive phenotyping (step two). There will be those genes that have a common, strong, single clinical phenotype (A); however, these will likely be rare. There may be those individual genotypes that all affect the same functional pathway (molecular subtypes) and result in similar or potentially opposing phenotypes (e.g., macrocephaly versus microcephaly) (B). Some mutations even within the same gene, however, may have multiple associated clinical phenotypes (C), suggesting high variability in the type of mutation relative to its gene function and/or incomplete penetrance. The latter especially will require more in-depth study for genetic background effects (step three). This approach will group patients foremost based on genotypes or sets of mutated genes. Larger groups of patients with the same presumptive genetic etiology are re-examined to identify specific clinical phenotypes, with the goal of improving diagnosis, patient care, and management.

Figure 2. The Autism Spectrum/Intellectual Disability Network

The Autism Spectrum/Intellectual Disability network (ASID), composed of 21 basic research and clinical laboratories from around the world, has assembled >15,000 patients for gene resequencing. The network is broader than the Autism Sequencing Consortium (ASC) in that it considers patients with ASD, ID, epilepsy, or DD due to their comorbidity. It emphasizes collections where parental DNA is available and where patient recontact is possible to accurately resolve phenotype-genotype correlations. The network includes 10 clinical research labs across the world (blue squares) and 11 labs in the USA (red dots) that recruited families as part of the SSC, where patient recontact has now been made possible after extensive IRB review. Subsets of patients with mutations in a common gene are being reassessed to determine whether the mutation defines a clinical subtype.

Figure 3. Potential Genetic Definition of Autism Subtypes

Individuals with autism have been described as having an increased head circumference size (HCZ) distribution (Courchesne et al., 2003). This is observed among ASD probands of the SSC where HCZ is positively skewed (blue arrow) when compared to a normal distribution (left). Subselecting patients (red) with de novo mutations in the β-catenin/Wnt-signaling network (Iossifov et al., 2012; Neale et al., 2012; O’Roak et al., 2012b; Sanders et al., 2012)—defined as those de novo proband events that cluster around the central CTNNB1 node using either STRING or Ingenuity Pathway Analysis enrichment (n = 26 individuals)—further transforms this into a bimodal distribution (right), suggesting reciprocal macrocephaly and microcephaly associated with de novo mutations in this pathway.