Limited-Variant Screening vs Comprehensive Genetic Testing for Familial Hypercholesterolemia Diagnosis

Abstract

Importance: Familial hypercholesterolemia (FH) is the most common inherited cardiovascular disease and carries significant morbidity and mortality risks. Genetic testing can identify affected individuals, but some array-based assays screen only a small subset of known pathogenic variants.

Objective: To identify the number of clinically significant variants associated with FH that would be missed by an array-based, limited-variant screen when compared with next-generation sequencing (NGS)-based comprehensive testing.

Design, setting, and participants: This cross-sectional study compared comprehensive genetic test results for clinically significant variants associated with FH with results for a subset of 24 variants screened by a limited-variant array. Data were deidentified next-generation sequencing results from indication-based or proactive gene panels. Individuals receiving next-generation sequencing-based genetic testing, either for an FH indication between November 2015 and June 2020 or as proactive health screening between February 2016 and June 2020 were included. Ancestry was reported by clinicians who could select from preset options or enter free text on the test requisition form.

Main outcomes and measures: Number of pathogenic or likely pathogenic (P/LP) variants identified.

Results: This study included 4563 individuals who were referred for FH diagnostic testing and 6482 individuals who received next-generation sequencing of FH-associated genes as part of a proactive genetic test. Among individuals in the indication cohort, the median (interquartile range) age at testing was 49 (32-61) years, 55.4% (2528 of 4563) were female, and 63.6% (2902 of 4563) were self-reported White/Caucasian. In the indication cohort, the positive detection rate would have been 8.4% (382 of 4563) for a limited-variant screen compared with the 27.0% (1230 of 4563) observed with the next-generation sequencing-based comprehensive test. As a result, 68.9% (848 of 1230) of individuals with a P/LP finding in an FH-associated gene would have been missed by the limited screen. The potential for missed findings in the indication cohort varied by ancestry; among individuals with a P/LP finding, 93.7% (59 of 63) of self-reported Black/African American individuals and 84.7% (122 of 144) of Hispanic individuals would have been missed by the limited-variant screen, compared with 33.3% (4 of 12) of Ashkenazi Jewish individuals. In the proactive cohort, the prevalence of clinically significant FH variants was approximately 1:191 per the comprehensive test, and 61.8% (21 of 34) of individuals with an FH-associated P/LP finding would have been missed by a limited-variant screen.

Conclusions and relevance: Limited-variant screens may falsely reassure the majority of individuals at risk for FH that they do not carry a disease-causing variant, especially individuals of self-reported Black/African American and Hispanic ancestry.

Figure 1.. Percentage of Individuals With Clinically Significant Familial Hypercholesterolemia Variants as Detected by a Comprehensive Test and a Limited-Variant Screen

Positive detection rate (%) in the familial hypercholesterolemia indication cohort (n = 4563) and the proactive cohort (n = 6482) as detected by comprehensive gene sequencing (comprehensive test) and projected for 24 familial hypercholesterolemia variants included in a limited-variant screen (limited screen). Heterozygous familial hypercholesterolemia included findings of a single pathogenic or likely pathogenic (P/LP) variant in LDLR, APOB, or PCSK9. Homozygous familial hypercholesterolemia included 2 (homozygous or compound-heterozygous) P/LP variants in LDLR, APOB, or PCSK9. Autosomal recessive hypercholesterolemia included findings of 2 P/LP variants in LDLRAP1. Autosomal recessive hypercholesterolemia carrier included a single P/LP variant in LDLRAP1. Analyses included only gain-of-function variants in APOB and assumed that the limited-variant screen does not report zygosity.

Figure 2.. Self-reported Ancestry of Familial Hypercholesterolemia–Positive Individuals Who Would Be Missed by a Limited-Variant Screen

Among all individuals in the indication cohort positive for a clinically significant familial hypercholesterolemia variant, some would have been identified by both the comprehensive genetic test and a limited-variant screen (dark blue), while others would have been identified only by the comprehensive genetic test (light blue). The multiple category includes 1 or more combinations of the ancestry groups listed in the Figure or included in Other, which includes French Canadian, Mediterranean, Native American, Pacific Islander, and Sephardic Jewish.