The estimation of tumor cell percentage for molecular testing by pathologists is not accurate

Abstract

Molecular pathology is becoming more and more important in present day pathology. A major challenge for any molecular test is its ability to reliably detect mutations in samples consisting of mixtures of tumor cells and normal cells, especially when the tumor content is low. The minimum percentage of tumor cells required to detect genetic abnormalities is a major variable. Information on tumor cell percentage is essential for a correct interpretation of the result. In daily practice, the percentage of tumor cells is estimated by pathologists on hematoxylin and eosin (H&E)-stained slides, the reliability of which has been questioned. This study aimed to determine the reliability of estimated tumor cell percentages in tissue samples by pathologists. On 47 H&E-stained slides of lung tumors a tumor area was marked. The percentage of tumor cells within this area was estimated independently by nine pathologists, using categories of 0-5%, 6-10%, 11-20%, 21-30%, and so on, until 91-100%. As gold standard, the percentage of tumor cells was counted manually. On average, the range between the lowest and the highest estimate per sample was 6.3 categories. In 33% of estimates, the deviation from the gold standard was at least three categories. The mean absolute deviation was 2.0 categories (range between observers 1.5-3.1 categories). There was a significant difference between the observers (Po0.001). If 20% of tumor cells were considered the lower limit to detect a mutation, samples with an insufficient tumor cell percentage (o20%) would have been estimated to contain enough tumor cells in 27/72 (38%) observations, possibly causing false negative results. In conclusion, estimates of tumor cell percentages on H&E-stained slides are not accurate, which could result in misinterpretation of test results. Reliability could possibly be improved by using a training set with feedback.

Assessing Copy Number Alterations in Targeted, Amplicon-Based Next-Generation Sequencing Data

“…In one recent study comparing nine pathologists, 38% of samples containing <20% tumor content were inappropriately judged to be sufficient for testing (>20% tumor). 21 Given the relative uncertainty surrounding H&E-based estimates of tumor content, there remains a risk for false-negative CNA calls, particularly in the setting of low tumor fraction and borderline alterations (close to 1.5 or 0.5 for copy number ratio). Such calls need to be interpreted carefully.…”

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

“…and L.Z.). 26 We selected a 10% tumor nuclei adequacy requirement, in part because this was standard practice in our laboratory for the pyrosequencing assay, but also to mitigate potential biochemical and analytic artifacts intrinsic to low-level variants. 27,28 Tumor fraction estimation values were also helpful to distinguish true variants from artifacts; expected VAFs for diploid heterozygous mutations could be inferred, whereas discrepant VAFs were scrutinized.…”

Techniques for maximizing the performance of molecular pathology testing: responsibilities of all pathologists

“…The most variable samples usually occur in specimens containing dense lymphocytic infiltrates or a mucinous stroma. In a study where the tumor cell ratio was below 20%, this difference was shown to be greater (108). Macrodissection had a reducing effect on the differences between tumor percentage estimations.…”

“…Although the effects of over or undercount in most pathology laboratories are unknown, it is appropriate to set up previously known sets of tumor cell numbers and practice on them (108).…”