Genetic Misdiagnoses and the Potential for Health Disparities

Abstract

Background: For more than a decade, risk stratification for hypertrophic cardiomyopathy has been enhanced by targeted genetic testing. Using sequencing results, clinicians routinely assess the risk of hypertrophic cardiomyopathy in a patient's relatives and diagnose the condition in patients who have ambiguous clinical presentations. However, the benefits of genetic testing come with the risk that variants may be misclassified.

Methods: Using publicly accessible exome data, we identified variants that have previously been considered causal in hypertrophic cardiomyopathy and that are overrepresented in the general population. We studied these variants in diverse populations and reevaluated their initial ascertainments in the medical literature. We reviewed patient records at a leading genetic-testing laboratory for occurrences of these variants during the near-decade-long history of the laboratory.

Results: Multiple patients, all of whom were of African or unspecified ancestry, received positive reports, with variants misclassified as pathogenic on the basis of the understanding at the time of testing. Subsequently, all reported variants were recategorized as benign. The mutations that were most common in the general population were significantly more common among black Americans than among white Americans (P<0.001). Simulations showed that the inclusion of even small numbers of black Americans in control cohorts probably would have prevented these misclassifications. We identified methodologic shortcomings that contributed to these errors in the medical literature.

Conclusions: The misclassification of benign variants as pathogenic that we found in our study shows the need for sequencing the genomes of diverse populations, both in asymptomatic controls and the tested patient population. These results expand on current guidelines, which recommend the use of ancestry-matched controls to interpret variants. As additional populations of different ancestry backgrounds are sequenced, we expect variant reclassifications to increase, particularly for ancestry groups that have historically been less well studied. (Funded by the National Institutes of Health.).

Figure 1. Genetic Variants Associated with Hypertrophic Cardiomyopathy

Panel A shows variants associated with hypertrophic cardiomyopathy that are overrepresented in the general population. The five highest-frequency variants account for 74% of the misclassified variation in the general population. Panel B shows the minor-allele genotype frequencies for high-frequency variants associated with hypertrophic cardiomyopathy; all variants are significantly more common among black Americans than among white Americans (P<0.001 by the chi-square test for all five variants).

Figure 2. Prevention of Misclassification of Variants with the Use of Data from Diverse Populations

Panels A and B show frequencies of the nonreference allele (i.e., the allele that is not present in the reference sequence of the human genome) for the 1000 Genome Project populations ASW (African Ancestry in Southwest USA) (61 persons) and CEU (Utah Residents [CEPH] with Northern and Western European ancestry) (85 persons) for the genes MYBPC3 (Panel A) and TNNI3 (Panel B). Each point represents a distinct variant. There are significantly more private sites (sites for which the nonreference-allele frequency is nonzero in one population but zero in the other population) among black Americans (nonreference-allele frequency, 0% in CEU and >0% in ASW, with ASW private sites shown in orange) than among white Americans (nonreference-allele frequency, 0% in ASW and >0% in CEU). Panel C shows the chance of correctly ruling out pathogenicity for a truly benign variant that is found predominantly in one ancestry group; the probability generally increases with the fraction of the control cohort that is made up of that ancestry group and with the number of controls (numbers of control chromosomes are shown in the key). These simulations use the allele frequencies of the MYBPC3 G278E variant, which has a minor-allele frequency of 0.0157 among black Americans and 0.000122 among white Americans. Panel D shows a map of TNNT2 allele frequencies; the K247R variant of TNNT2 (rs3730238 in dbSNP) was genotyped in the Human Genome Diversity Project. Most populations around the world have a nonzero minor-allele frequency.