Analytical Performance of a Gene Expression Classifier for Medullary Thyroid Carcinoma.
The aim of this study was to demonstrate the analytical validity of an RNA classifier for medullary thyroid carcinoma (MTC).



Fresh-frozen tissue specimens were obtained from commercial sources, and MTC diagnoses were confirmed by histopathology review. De-identified patient fine-needle aspiration biopsies (FNABs) and whole blood from normal donors were obtained. Total RNA was extracted, amplified, and hybridized to custom microarrays for gene expression analysis. Gene expression data were normalized and classified via a machine learning algorithm. Positive control materials were produced from MTC tissues and tested across multiple experiments and laboratories. Twenty-seven MTC tissue specimens were used to evaluate the sensitivity of the MTC classifier. Gene expression data from tissues and FNABs were used to model classifier response to mixtures of MTC samples with normal thyroid tissue, a benign thyroid nodule, a Hürthle cell adenoma, and whole blood. Select mixture conditions were confirmed in vitro. Assay tolerance to RNA input variation (5-25 ng) and genomic DNA contamination (30% by mass) was evaluated. The intra- and inter-run reproducibility and inter-laboratory accuracy of MTC classifier results were characterized.



The MTC classifier sensitivity of 96.3% [confidence interval 81.0-99.9%] was determined retrospectively using 27 MTC confirmed tissue specimens. One false-negative result in a necrotic tissue implicated sample necrosis in reduced classifier sensitivity. Dilution modeling of MTC samples with normal or benign tissues showed consistent detection of MTC down to 20% sample proportions, with in vitro confirmation of 20% analytical sensitivity. Classifier tolerance to RNA input variation (5-25 ng), genomic DNA contamination (30% by mass), and an interfering substance (blood) was demonstrated with 100% accurate classifier results under all tested conditions. The maximum observed run-to-run score difference for a single FNAB sample was ∼1 unit compared with the average score difference between 38 MTC and non-MTC FNABs of ∼32 units. MTC classifier results for 20 tissues processed from total RNA in two different laboratories showed 100% concordance.



The MTC classifier, offered as part of the routine molecular testing of cytology-indeterminate thyroid nodules, demonstrates robust analytical sensitivity, specificity, accuracy, and reproducibility.
1 Veracyte, Inc. , South San Francisco, California.
Daniel G
DG
Pankratz
1 Veracyte, Inc. , South San Francisco, California.
Zhanzhi
Z
Hu
1 Veracyte, Inc. , South San Francisco, California.
Su Yeon
SY
Kim
1 Veracyte, Inc. , South San Francisco, California.
Robert J
RJ
Monroe
1 Veracyte, Inc. , South San Francisco, California.
Mei G
MG
Wong
2 Thyroid Cytopathology Partners , Austin, Texas.
S Thomas
ST
Traweek
1 Veracyte, Inc. , South San Francisco, California.
Richard T
RT
Kloos
1 Veracyte, Inc. , South San Francisco, California.
P Sean
PS
Walsh
1 Veracyte, Inc. , South San Francisco, California.
Giulia C
GC
Kennedy
D000328:Adult; D000368:Aged; D044963:Biopsy, Fine-Needle; D018276:Carcinoma, Medullary / Q000097:blood / Q000175:diagnosis / Q000378:metabolism* / Q000473:pathology; D018278:Carcinoma, Neuroendocrine / Q000097:blood / Q000175:diagnosis / Q000378:metabolism* / Q000473:pathology; D019295:Computational Biology; D005103:Expert Systems; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D057230:Limit of Detection; D000069550:Machine Learning; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism*; D012334:RNA, Neoplasm / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013961:Thyroid Gland / Q000378:metabolism* / Q000473:pathology; D013964:Thyroid Neoplasms / Q000097:blood / Q000175:diagnosis / Q000378:metabolism* / Q000473:pathology; D014015:Tissue Banks; D055815:Young Adult
D009363:Neoplasm Proteins; D012334:RNA, Neoplasm
analytical verification; fine-needle aspiration biopsy; gene expression classifier; medullary thyroid carcinoma; molecular diagnostic