Guidelines for genetic studies in single patients: lessons from primary immunodeficiencies

Abstract

Can genetic and clinical findings made in a single patient be considered sufficient to establish a causal relationship between genotype and phenotype? We report that up to 49 of the 232 monogenic etiologies (21%) of human primary immunodeficiencies (PIDs) were initially reported in single patients. The ability to incriminate single-gene inborn errors in immunodeficient patients results from the relative ease in validating the disease-causing role of the genotype by in-depth mechanistic studies demonstrating the structural and functional consequences of the mutations using blood samples. The candidate genotype can be causally connected to a clinical phenotype using cellular (leukocytes) or molecular (plasma) substrates. The recent advent of next generation sequencing (NGS), with whole exome and whole genome sequencing, induced pluripotent stem cell (iPSC) technology, and gene editing technologies-including in particular the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology-offer new and exciting possibilities for the genetic exploration of single patients not only in hematology and immunology but also in other fields. We propose three criteria for deciding if the clinical and experimental data suffice to establish a causal relationship based on only one case. The patient's candidate genotype must not occur in individuals without the clinical phenotype. Experimental studies must indicate that the genetic variant impairs, destroys, or alters the expression or function of the gene product (or two genetic variants for compound heterozygosity). The causal relationship between the candidate genotype and the clinical phenotype must be confirmed via a relevant cellular phenotype, or by default via a relevant animal phenotype. When supported by satisfaction of rigorous criteria, the report of single patient-based discovery of Mendelian disorders should be encouraged, as it can provide the first step in the understanding of a group of human diseases, thereby revealing crucial pathways underlying physiological and pathological processes.

Figure 1.

Distribution of single-patient inborn errors of immunity reported per year. The red dots indicate conditions that have not yet been reported in a second patient. It is notable that the number of single-gene defects reported per year is increasing with time, with two peaks, one in the years 1995–1999 and another in 2010–2013. The first peak (13 patients) corresponds mostly to the discovery of genetic etiologies of classical PIDs that had been long clinically delineated, all discovered by newly developed genetic tools for linkage analysis and a candidate gene approach. The second peak (15 patients) benefited from the advent of NGS (PI3K p85α, CARD11, OX40, and PCKδ deficiencies in a total of 5 patients) but also reflected the growth of the field and the exploration of novel phenotypes (e.g., IRF8, STAT2, and Ikaros deficiencies).