Molecular Variants and Their Risks for Malignancy in Cytologically Indeterminate Thyroid Nodules

Abstract

Background: Gene panels are routinely used to assess predisposition to hereditary cancers by simultaneously testing multiple susceptibility genes and/or variants. More recently, genetic panels have been implemented as part of solid tumor malignancy testing assessing somatic alterations. One example is targeted variant panels for thyroid nodules that are not conclusively malignant or benign upon fine-needle aspiration (FNA). We systematically reviewed published studies from 2009 to 2018 that contained genetic data from preoperative FNA specimens on cytologically indeterminate thyroid nodules (ITNs) that subsequently underwent surgical resection. Pooled prevalence estimates per gene and variant, along with their respective positive predictive values (PPVs) for malignancy, were calculated. Summary: Our systematic search identified 540 studies that were supplemented by 18 studies from bibliographies or personal files. Sixty-one studies met all inclusion criteria and included >4600 ITNs. Overall, 26% of nodules contained at least 1 variant or fusion. However, half of them did not include details on the specific gene, variant, and/or complete fusion pair reported for inclusion toward PPV calculations. The PPVs of genomic alterations reported at least 10 times were limited to BRAF^V600E (98%, 95% confidence interval [CI 96-99%]), PAX8/PPARG (55% [CI 34-78%]), HRAS^Q61R (45% [CI 22-72%]), BRAF^K601E (42% [CI 19-68%]), and NRAS^Q61R (38% [CI 23-55%]). Excluding BRAF^V600E, the pooled PPV for all other specified variants and fusions was 47%. Multiple variants within the same nodule were identified in ∼1% of ITN and carried a cumulative PPV of 77%. Conclusions: The chance that a genomic alteration predicts malignancy depends on the individual variant or fusion detected. Only five alterations were reported at least 10 times; BRAF^V600E had a PPV of 98%, while the remaining four had individual PPVs ranging from 38% to 55%. The small sample size of most variants and fusion pairs found among ITNs, however, limits confidence in their individual PPV point estimates. Better specific reporting of genomic alterations with cytological category, histological subtype, and cancer staging would facilitate better understanding of cancer prediction, and the independent contribution of the genomic profile to prognosis.

Keywords: fine-needle aspiration; indeterminate cytology; molecular diagnostics; molecular testing; thyroid cancer; thyroid nodule.

FIG. 1.

Literature review flowchart. Breakdown of search results and study inclusion. See Supplementary Table S2 for details on exclusion. *One reflexed to RAS if BRAF was negative (no RAS positives in indeterminate nodules) (30), while another only assessed BRAF for variants and RET/PTC fusions (one RET/PTC1 was noted) (31). ^†One study (32) combined data for patients run on either 7-gene or 14-gene panel. ^‡Nodules from certain publications (33–36,38) were tested by 7- or 14-gene panels but only reported data on a subset of genes, variants, and/or fusions. ^§One publication (37) analyzed nodules and reported data on two different panels.

FIG. 2.

Specified breakdown of variants/fusions. Percentage of positive nodules identified with unspecified amino acid changes or incomplete fusions pairs versus those that had them specified. H-/K-/N-RAS data are significantly lower for specified variant designation than BRAF (p < 0.0001) when looking at these data for sequence variants alone.

FIG. 3.

RAS data breakdown. Ratios of specified versus unspecified amino acid changes separated by data for all RAS-positive nodules, data for RAS without the gene specified, and data for H-/K-/N-RAS along with the corresponding breakdown of true and false positives. This figure shows that specified data were very minimal for this gene category (66/607 RAS-positive nodules).