On March 8 2017, the US House of Representatives approved a Bill that would allow companies to require employees to undergo genetic testing and disclose the results to their employers [19]. As a response, the European Society of Human Genetics provided a statement that strongly argued against obligatory genetic testing as decisions on whether or not to undergo genetic testing must be a voluntary choice of the individual [20]. For both obligatory and voluntary testing of healthy individuals, it is, however, important to know the prevalence of medically actionable disease alleles in an unbiased population. In this study, we set out to determine this frequency by screening for secondary findings in a healthy population of European descent using existing (anonymized) WES data. From our data we conclude that 2.7% of healthy Dutch individuals has a (likely) pathogenic variant in a medically actionable dominant disease allele for which returning of secondary findings is indicated by the ACMG. These individuals are predisposed to develop for instance cancer or cardiomyopathy.

Given the wide range of reported secondary findings, we systematically compared our results to studies published previously from other populations [5,6,7,8,9,10,11,12,13] in order to explain the differences in frequencies observed, focussing on (i) the sequence technology used, (ii) the cohort tested, (iii) the certainty of pathogenicity of variants, as well as (iv) the genes for which pathogenic variants were assessed. This comparison yielded three distinct categories: those studies reporting lower [5, 7, 10, 11, 13], higher [6, 8, 9], or comparable [12] frequencies of secondary findings when compared to our observation of 2.7%.

In comparison to the first studies reporting incidental findings [5, 7, 10, 11], the frequency identified in our cohort is elevated up to twice as high. This could partially be explained by the presence of Dutch founder mutations. From the 33 unique dominant risk alleles detected, two have been reported as founder mutation for the Dutch population (BRCA1 (c.2685_2686del) and BRCA2 (c.9672dup)) [21]. However, both variants were observed in a single individual in our cohort, thus not accounting for the higher frequency observed in our study. We then examined whether the differences are explained by experimental design and data analysis, previous versions of databases for variant filtering and interpretation, absence of ethnicity specific variation information and a shorter list of ACMG medically actionable genes for disclosing secondary findings. However, all variants identified in our study were also present in databases at time of the initial studies, and also, the extension of the ACMG genes with 3 additional genes to 59 as analyzed here, is not sufficient to explain our observed higher frequency. It thus is more likely that the increased sequence coverage in our study allowed more sensitive detection of (likely) pathogenic variants. It is, however, noteworthy that, Thompson et al. [13] also identified a relatively low frequency (1.5%) of secondary findings when based on (likely) pathogenic variants in the 59 ACMG genes, despite using WES at an average sequence depth of 71×, covering 80% of bases at least 20-fold [13, 22]. Whether this coverage is also achieved for the coding sequencing of the 59 genes is, however, not reported [13], but any deviation from this, could potentially explain the differences observed. Overall, since also other recent publications report higher frequencies than the 1–1.5% previously reported, it seems reasonable to conclude that the frequencies initially reported are too low.

Higher prevalence of secondary findings compared to our 2.7% for the Dutch population have also been reported [6, 8, 9]. For instance, Dewey et al. (2016) reported 49 variants in the 59 ACMG genes in 1415 individuals (3.5%). Their cohort, however, consisted of patients of whom some were affected with conditions likely attributable to the disease alleles in the ACMG genes, thus creating bias towards higher frequency. When excluding this bias, their findings are more in line with our frequency. Interestingly, several papers report frequencies of over 5% [8, 9]. Since these studies were conducted at the same time as ours, the difference cannot be explained by the previously mentioned issues like sequence coverage and availability of newer releases of databases for variant filtering. As was also noted by Tang et al. [12], the high frequency reported in these studies is mainly due to improper classification of variants as pathogenic. For instance, the NM_198056.2:c.3575G > A variant in SCN5A reported by Lawrence et al. [9] is present in 6% of the Asian population (including homozygotes) and truncating variants in the RYR1 (NM_000540.2) gene are not causative for malignant hyperthermia susceptibility, as proposed by Jang et al. [8].

Importantly, the frequency of secondary findings observed in our cohort is almost identical to the prevalence of 2.5% published by Tang et al. [12], who tested a cohort of 954 East-Asian individuals using WGS. Interestingly, however, the distribution of pathogenic variants over the genes differs markedly despite the overall the frequency of secondary findings in the cardiogenetic genes and oncogenes being similar; that is, Tang et al. [12] reported 36% of their pathogenic variants in seven of the 59 ACMG genes in which no pathogenic variants were detected in our cohort. Conversely, in our Dutch cohort 48% of the detected pathogenic variants were in nine of the 59 ACMG genes in which no pathogenic variants were detected by Tang et al. Hence, this may indicate that, although the frequency of secondary findings is similar between different ethnicities, different genes contribute to their prevalence.

We also identified 2.2% of the population to be a carrier of a recessive pathogenic disease allele in one of the 59 ACMG genes. Whereas the identification of carriers of recessive disease alleles in the population is not unexpected given our study set up, our unbiased analysis of these alleles in the healthy population elicits discussion on their return. The ACMG recommends to only return bi-allelic pathogenic variants, but one may wonder whether it is not relevant to return carrier status (e.g., for reproductive decisions). Using the carrier frequency determined in our cohort, we can now determine that ~1 in 3000 and ~1 in 100,000 couples are both carrier of a heterozygous disease allele in MUTYH or ATP7B, respectively. For comparison, in March 2017 the Committee on Genetics of the American College of Obstetricians and Gynecologists stated that cystic fibrosis screening, with a carrier frequency of 1 in 30 in the Caucasian population, should be offered to all pregnant women, or ideally before pregnancy [23]. Our data do not only contribute to the discussion on genes that could be selected for preconception carrier screening based on absolute carrier frequency, such as here presented for MUTYH (~1:50), but also reopens the discussion whether or not more prevalent diseases, such as cystic fibrosis (~1:30), should be included in secondary screening programs.

Routine screening of healthy individuals for secondary findings in the 59 ACMG medically actionable dominant disease genes will impact at least 1 in 38 individuals. These individuals have an increased risk for life-threatening disease, and could profit from early monitoring and possible preventive treatment. On the other hand, some of the individuals in whom an incidental findings is identified may spend their lives worrying about a disease that may never manifest itself. This is mostly due to a highly variable disease penetrance for these conditions, ranging from 20 to 100%. Our study design did not allow to link the secondary findings to individuals and their families, but it can be expected that the penetrance is even lower in the absence of a positive family history. In terms of policy decisions about reporting and counseling of individuals in whom an incidental and/or secondary finding is observed, this may lead to a redefinition of what is perceived as a “medically actionable disease allele”. Also, individuals at risk may face difficulties—or may even be unable to—acquire job positions, obtain mortgages, and/or health and/or life insurances. These implications not only affect the individuals in whom the incidental or secondary finding was uncovered, but will also directly impact their blood relatives and extended families. Apart from practical implications, such as the impact on the health care system to screen healthy individuals, it is presently unclear whether the potential benefits of early monitoring and possible preventive treatment outweigh the risks of the emotional impact of the test result and possible stigmatization.

Taken together, we believe that our conclusion that 2.7% of healthy Dutch individuals has a dominant acting disease allele, is expected to be representative for the European population given the current guidelines on variant interpretation and the limited number of genes studied. Yet, with genetic knowledge still advancing, the number of genes and medically actionable variants for which disclosure could be considered will likely continue to expand. In addition, improvements in sequencing technology will likely allow detection of more variants, and simultaneously, increasing clinical interpretation of the noncoding parts of the genome will allow for the detection of more pathogenic variation. Hence, it may be expected that our estimate that 1 in 38 healthy individuals is genetically affected with a dominant high-risk disease is an underrepresentation for the true prevalence of dominant medically actionable disease alleles in the population.