Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation

Abstract

Background: Whole-exome sequencing can provide insight into the relationship between observed clinical phenotypes and underlying genotypes.

Methods: We conducted a retrospective analysis of data from a series of 7374 consecutive unrelated patients who had been referred to a clinical diagnostic laboratory for whole-exome sequencing; our goal was to determine the frequency and clinical characteristics of patients for whom more than one molecular diagnosis was reported. The phenotypic similarity between molecularly diagnosed pairs of diseases was calculated with the use of terms from the Human Phenotype Ontology.

Results: A molecular diagnosis was rendered for 2076 of 7374 patients (28.2%); among these patients, 101 (4.9%) had diagnoses that involved two or more disease loci. We also analyzed parental samples, when available, and found that de novo variants accounted for 67.8% (61 of 90) of pathogenic variants in autosomal dominant disease genes and 51.7% (15 of 29) of pathogenic variants in X-linked disease genes; both variants were de novo in 44.7% (17 of 38) of patients with two monoallelic variants. Causal copy-number variants were found in 12 patients (11.9%) with multiple diagnoses. Phenotypic similarity scores were significantly lower among patients in whom the phenotype resulted from two distinct mendelian disorders that affected different organ systems (50 patients) than among patients with disorders that had overlapping phenotypic features (30 patients) (median score, 0.21 vs. 0.36; P=1.77×10^-7).

Conclusions: In our study, we found multiple molecular diagnoses in 4.9% of cases in which whole-exome sequencing was informative. Our results show that structured clinical ontologies can be used to determine the degree of overlap between two mendelian diseases in the same patient; the diseases can be distinct or overlapping. Distinct disease phenotypes affect different organ systems, whereas overlapping disease phenotypes are more likely to be caused by two genes encoding proteins that interact within the same pathway. (Funded by the National Institutes of Health and the Ting Tsung and Wei Fong Chao Foundation.).

Figure 1. Models of Nonmendelian Inheritance

Panel A shows digenic inheritance of pathogenic alleles at different loci from each parent, resulting in an affected offspring. Panel B shows dual molecular diagnoses — in this case, one homozygous pathogenic variant in a recessive disease gene inherited from each carrier parent and one de novo variant that resulted in a second, independent autosomal dominant disorder. Many combinations are possible: autosomal dominant plus autosomal dominant, autosomal dominant plus autosomal recessive, autosomal dominant plus X-linked, autosomal recessive plus autosomal recessive, autosomal recessive plus X-linked, and X-linked plus X-linked.

Figure 2. Frequencies and Modes of Inheritance in Multiple Molecular Diagnoses

Panel A shows the percentage of all patients with two or more molecular diagnoses. Panel B shows the percentage of all diagnoses in patients with two or more molecular diagnoses, according to mode of inheritance and de novo status. AD denotes autosomal dominant, AR autosomal recessive, and XL X-linked. Panel C shows the percentage of patients with two molecular diagnoses represented by each combination of modes of inheritance. The contribution of de novo versus inherited variants is represented within each bar as percentages of diagnoses (not patients). Panel D shows the percentage of patients with two molecular diagnoses represented by each combination of modes of inheritance. The percentage of patients with one or two de novo variants contributing to diagnoses is indicated within each bar.

Figure 3. Blended Phenotypes among Patients with Dual Diagnoses

Dual molecular diagnoses may result from variants at two loci (Gene A and Gene B) and can result in distinct clinical features (Panel A) or similar phenotypic features (Panel B).

Figure 4. Phenotypic Similarity of 80 Disease Pairs with Blended Phenotypes Categorized as Overlapping or Distinct

Panel A shows the distribution of cases plotted across the range of phenotypic similarity scores. Panel B shows the relative disease-pair similarity scores calculated by the symmetric Resnik method with the use of Human Phenotype Ontology (HPO) terms assigned to disease identification numbers in the Online Mendelian Inheritance in Man database. Each disease pair is represented by a single diamond; cases classified by two physician scientists as distinct or overlapping are indicated. Increasing phenotypic similarity (determined bioinformatically) corresponds to higher similarity scores. Eight pairs of diseases associated with proteins that have physical or pathway interactions with one another are indicated by yellow diamonds (secondary interaction) or orange diamonds (tertiary interaction); the ninth patient (Patient 12) is not shown here, because neither disease in the pair was mapped to the HPO. Horizontal bars indicate means, and I bars indicate standard errors. Panel C shows box plots of the degree of phenotypic similarity for dual diagnoses that were clinically assigned to distinct or overlapping phenotype categories. The lower and upper limits of the box indicate the first and third quartiles, the bar inside the box the median, and the T bars the minimum and maximum or 1.5 times the interquartile range (whichever value was smaller).