Prospective Study of Cancer Genetic Variants

Variation in Rate of Reclassification by Ancestry

Thomas P. Slavin; Lily R. Van Tongeren; Carolyn E. Behrendt; Ilana Solomon; Christina Rybak; Bita Nehoray; Lili Kuzmich; Mariana Niell-Swiller; Kathleen R. Blazer; Shu Tao; Kai Yang; Julie O. Culver; Sharon Sand; Danielle Castillo; Josef Herzog; Stacy W. Gray; Jeffrey N. Weitzel;

Disclosures

J Natl Cancer Inst. 2018;110(10):1059-1066. 

In This Article

Results

Not counting within-family duplicate variants, the study enrolled 1816 nonbenign variants. Those represented 96.6% of all eligible, nonbenign variants (n = 1880) identified at the participating hereditary cancer risk assessment sites during the study recruitment period. Further eliminating nonfamily duplicate variants yielded the study sample (n = 1483), comprised of 1282 unique variants in 42 actionable genes (Supplementary Table 1, available online) and another 201 variants that differed in ancestry, laboratory, or initial classification from otherwise similar variants. Discordant classification of variants between laboratories was rare, occurring in four (0.3%) variants (one each within BRCA1, BRCA2, CHEK2, and CDKN2A).

Observation time per study variant ranged from 63 days to 20.2 years (median = 3.55 years). During follow-up, reclassification was observed for 268 (18.1%) variants, of which 40/268 (14.9%) were reclassified more than once (Supplementary Figure 1, available online).

Supplementary Figure 1.

Sequence of Reclassification of 268 Variants.
LB=Likely Benign, LP=Likely Pathogenic, P=Pathogenic, VUS=Variant of Uncertain Significance, B= Benign

Overall, 693 (46.7%) variants involved BRCA1/2 (Figure 1). Nearly all BRCA1/2 variants (87.6%) were tested by Lab A, except in the final two years of the study, when Other Labs tested most (79.6%) BRCA1/2 variants. Overall, Other Labs also tested most (89.7%) variants of PTEN and all variants of another 18 genes; variants in the remaining 21 genes were tested approximately equally by Lab A and Other Labs (Supplementary Table 1, available online).

Figure 1.

Nonbenign variants (n = 1483) accrued per year, by class of gene. The volume of BRCA1/2 variants (hatched bars) fluctuated moderately from year to year. In contrast, the volume of non-BRCA1/2 variants (solid bars) went from negligible to very large in the final years of the study. We interpret the latter finding as consistent with the recent increase in use of multigene panel testing (1,11).

Table 1 presents additional characteristics of BRCA1/2 and non-BRCA1/2 variants. In both groups, reclassification was more common among variants tested by Lab A and rare among pathogenic variants (Table 1). As illustrated in Figure 2, variants initially classified as pathogenic were almost never reclassified, but other classes of nonbenign variants were commonly reclassified and had similar times to first reclassification.

Figure 2.

Time to first reclassification of the variant, by initial classification. For ease of interpretation, this Kaplan-Meier plot illustrates follow-up of the 1483 variants through their first reclassification only. Variants are distinguished by their initial classification: likely benign (dotted line), likely pathogenic (dash-dot line), pathogenic (dashed line), variant of uncertain significance (solid line). Numbers of unreclassified variants remaining in follow-up are shown below the plot. As the plot indicates, variants initially classified as pathogenic were almost never reclassified. In contrast, the other three classes of variants were often reclassified, with a shared pattern of time to first reclassification that suggests that almost all nonpathogenic, nonbenign variants will be reclassified eventually. LB = likely benign; LP = likely pathogenic; P = pathogenic; VUS = variant of uncertain significance.

Multivariable analyses of reclassification rate were conducted separately for BRCA1/2 and non-BRCA1/2 variants (Table 2). At the start of observation, BRCA1/2 variants from three ancestries (African, Ashkenazi, and Chinese) had reduced rates of reclassification; those from non-Chinese Asian, Hispanic, and Native American ancestries had rates no different than the non-Hispanic European referent category; and those from Middle Eastern ancestry had a higher rate. Over time, rate of reclassification increased in all ancestral categories of BRCA1/2, but it did so faster in each of the three ancestries initially associated with reduced rates (Table 2, Figure 3A). After a period of increase, each ancestry's rate of BRCA1/2 reclassification began to decline toward its initial rate (Figure 3A), a pattern indicated by the quadratic term in the model (Table 2). For simplicity, Figure 3A ignores initial variation in reclassification rate among ancestries. Figure 3B, on the other hand, applies each ancestry's initial rate to its rate over time, plotting relative rates of reclassification by year for each ancestry. In this way, it can be seen that, for variants from all minority ancestries except non-Chinese Asian and Hispanic, the annual rate of reclassification eventually equaled or surpassed the non-Hispanic European rate (Figure 3B).

Figure 3.

Model-derived estimates of annual growth in rate of reclassification of BRCA1 variants, by ancestry. These panels illustrate two ways of plotting the ancestry-specific variation in reclassification of BRCA1/2 variants as reported in Table 2. For clarity, these plots use estimates for that model's referent category, specifically nonpathogenic BRCA1 variants from females tested by Lab A. Estimates for BRCA2 or pathogenic variants, or those from males or Other Labs, can be obtained by applying the corresponding relative rates in Table 2 to these plots. In both, the x-axis corresponds to the calendar year when the variant was initially classified. A) In this plot, the reclassification rate in 1997 was set to 1.00 for all ancestries, ignoring the substantial initial variation among ancestries in favor of illustrating ancestry-specific patterns of change in reclassification rate over time. B) In contrast, here each ancestry's estimated annual growth in reclassification rate was applied to its own baseline rate from 1997, relative to the reference category of non-Hispanic European (NHE). From this second plot, we conclude that, for variants from all minority ancestries except non-Chinese Asian and Hispanic, the rate of reclassification eventually equaled or surpassed the NHE rate.

In contrast to BRCA1/2 variants, reclassification rates of non-BRCA1/2 variants did not vary over time (Table 2), a finding consistent with the fact that, unlike BRCA1/2 variants, non-BRCA1/2 variants were mostly accrued during a brief period near the end of the study (Figure 1). Moreover, overall reclassification rates were elevated for non-BRCA1/2 variants from most minority ancestries (African, Ashkenazi, Hispanic, and to lesser degree Middle Eastern and Chinese). The exceptions were non-BRCA1/2 variants from non-Chinese Asian and Native American ancestries, which had reclassification rates similar to variants from non-Hispanic European ancestry (Table 2).

Among reclassified variants, few (26/268, 9.7%) underwent a net upgrade in pathogenicity. Excluding variant classifications (pathogenic, likely benign) never observed to be upgraded left 241 reclassified variants that could have undergone net upgrade. Per multivariable logistic regression (Table 3), reclassified variants were more likely to have been a net upgrade if they had been classified originally as likely pathogenic, belonged to a male participant, or had undergone initial testing earlier during the study period. Specifically, the chances that a reclassified variant represented a net upgrade decreased nonlinearly over time: following a sigmoid curve, that decrease in risk was initially minor (ie, approximately −8% at four years into the study) but accelerated over time (reaching −40% at 10 years, −70% at 15.5 years, and −90% at 18 years). Neither ancestry, type of mutation, nor BRCA1/2 status was associated with reclassification being a net upgrade.

Incidentally, 17.1% of variants overall were obtained from persons who reported mixed ancestry. However, the proportion of mixed ancestry varied by group: It was absent by definition among participants with non-Hispanic European ancestry but common among persons with Ashkenazi (42.7% of whose variants were associated with mixed ancestry, chiefly non-Hispanic European), African (53.0% mixed ancestry, chiefly non-Hispanic European or Native American), or non-African Native American background (87.0% mixed ancestry, chiefly Hispanic or non-Hispanic European). Finally, 10.0% of Chinese, 12.4% of non-Chinese Asian, 15.6% of Middle Eastern, and 17.6% of Hispanic variants came from participants with mixed ancestry.

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