Preparing pathology for precision medicine: challenges and opportunities

Precision Medicine Is Changing the Roles of Healthcare Professionals, Scientists, and Research Staff: Learnings from a Childhood Cancer Precision Medicine Trial

Precision medicine programs aim to utilize novel technologies to identify personalized treatments for children with cancer. Delivering these programs requires interdisciplinary efforts, yet the many groups involved are understudied. This study explored the experiences of a broad range of professionals delivering Australia's first precision medicine trial for children with poor-prognosis cancer: the PRecISion Medicine for Children with Cancer (PRISM) national clinical trial of the Zero Childhood Cancer Program. We conducted semi-structured interviews with 85 PRISM professionals from eight professional groups, including oncologists, surgeons, clinical research associates, scientists, genetic professionals, pathologists, animal care technicians, and nurses. We analyzed interviews thematically. Professionals shared that precision medicine can add complexity to their role and result in less certain outcomes for families. Although many participants described experiencing a greater emotional impact from their work, most expressed very positive views about the impact of precision medicine on their profession and its future potential. Most reported navigating precision medicine without formal training. Each group described unique challenges involved in adapting to precision medicine in their profession. Addressing training gaps and meeting the specific needs of many professional groups involved in precision medicine will be essential to ensure the successful implementation of standard care.

Application of a treatment planning system-assisted large-aperture computed tomography simulator to percutaneous biopsy: initial experience of a radiation therapist

Objective

To evaluate the application of treatment planning system (TPS)-assisted large-aperture computed tomography (CT) simulator to percutaneous biopsy.

Methods

This retrospective study enrolled patients that underwent TPS-assisted large-aperture CT simulator-guided percutaneous biopsy from November 2018 to December 2019. Retrospective analyses of puncture accuracy were compared using paired t-test and a Wilcoxon rank sum test. The risk factors for puncture accuracy and complications were identified.

Results

A total of 38 patients were included in this study. There were no significant differences between the planned and actual puncture depth and angle. Pulmonary puncture was significantly associated with the accuracy of the puncture angle. The diagnostic rate of malignancy was 76% (29 of 38), of which 20 of 25 patients were in the group initially diagnosed with unconfirmed lesions and nine of 13 patients were in the group of treated patients that needed additional pathological analyses. For patients that underwent a pulmonary biopsy, 12 had minor pneumothorax and three suffered needle track bleeding. No other complications were observed. Regression analyses indicated a significant correlation between puncture angle and the incidence of pneumothorax.

Conclusion

TPS-assisted large-aperture CT simulator may improve the percutaneous biopsy procedure by combining the advantages of radiotherapy specialties with computer targeting.

The implementation of a commercially available multi-gene profile test for breast cancer characterization in a department of pathology: what have we learned from the first 100 cases?

Analysis of breast cancer prognostic and predictive factors is still nowadays poorly accurate and standardized. The advent of multi-gene expression profiles (MGEPs) has improved the prediction of breast cancer outcome, particularly regarding early luminal breast cancers (LBCs). The availability in our Institute of EndoPredict® (EP), a last-generation prognostic gene signature assay, has prompted us to study a series of LBCs, firstly verifying its reproducibility on six routine representative cases, either presenting non-optimal preanalytical conditions or different tumor samples from the same patient; secondly, correlating EP results on 8 retrospectively recruited samples with patients' follow-up; thirdly, applying prospectively EP on 100 routinely diagnosed cases, assessing the oncologists' and pathologists' attitude toward it. The complete reproducibility of EP on all the samples investigated in the first phase allowed to state that EP overcomes the detrimental effects of an inaccurate pre-analytic phase, determining the most appropriate prognostic and predictive parameters of breast cancer. The second phase confirmed EP as a fundamental tool in guiding therapeutic decision, improving the classical bio-pathological characterization and recovering 38% patients' inadequately managed. Finally, the study disclosed how oncologists sometimes inadequately requested EP, but also how it allows a better stratification of breast cancer otherwise considered poorly aggressive and not requiring an EP test, such as G1 neoplasms or tubular histotype. In conclusion, the introduction of EP test in an Anatomic Pathology Department emerges as a useful tool in routine breast cancer diagnosis, both for the characterization of individual cases and, as a result, for more appropriate therapeutic choices.

Clinicopathological characteristics of lung adenocarcinoma with compound EGFR mutations

The extensive clinical applications of next-generation sequence analyzers have made uncommon and compound EGFR mutations more prevalent than previously described. However, clinicopathological impacts of compound EGFR mutations in lung adenocarcinoma remain unclear. We earlier examined the presence of compound EGFR mutations primarily in the cis allele by EGFR exon sequencing and droplet digital polymerase chain reaction in 462 completely resected EGFR-mutated adenocarcinomas of the lung and identified 64 tumors with compound mutations. We evaluated clinicopathological characteristics of lung adenocarcinomas with compound EGFR mutations in comparison with cases with common or uncommon single mutations. Among 64 compound EGFR mutations, L858R/E709G (9%) was the most frequent mutation type, followed by L858R/S768I (8%), L858R/T790M (8%), and L858R/L833V (6%). We observed both single and compound mutations frequently in women, never or light smokers; their adenocarcinomas showed thyroid transcription factor-1 immunoreactivity. In contrast, compound mutations were significantly associated with lymph node metastases (p = 0.0242; single vs. compound cases) and the presence of tumor cells with clear cytoplasm (p = 0.0014; single vs. compound cases). Furthermore, patients with compound mutations had significantly poorer prognoses than cases with single EGFR mutations (p = 0.043). Overall, clinicopathological features of common, uncommon, and compound EGFR mutations are similar; however, tumors with compound mutations may be characterized by aggressive behavior and histological findings of clear cell features.

Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients

Next-generation sequencing (NGS) has become a promising approach for tumor somatic mutation detection. However, stringent validation is required for its application on clinical specimens, especially for low-quality formalin-fixed paraffin-embedded (FFPE) tissues. Here, we validated the performance of an amplicon-based targeted NGS assay, OncoAim™ DNA panel, on both commercial reference FFPE samples and clinical FFPE samples of Chinese colorectal cancer (CRC) patients. Then we profiled the mutation spectrum of 648 Chinese CRC patients in a multicenter study to explore its clinical utility. This NGS assay achieved 100% test specificity and 95-100% test sensitivity for variants with mutant allele frequency (MAF) ≥ 5% when median read depth ≥ 500×. The orthogonal methods including amplification refractory mutation system (ARMS)-PCR and Sanger sequencing validated that NGS generated three false negatives (FNs) but no false positives (FPs) among 516 clinical samples for KRAS aberration detection. Genomic profiling of Chinese CRC patients with this assay revealed that 63.3% of the tumors harbored clinically actionable alterations. Besides the commonly mutated genes including TP53 (52.82%), KRAS (46.68%), APC (24.09%), PIK3CA (18.94%), SMAD4 (9.47%), BRAF (6.15%), FBXW7 (5.32%), and NRAS (4.15%), other less frequently mutated genes were also identified. Statistically significant association of specific mutated genes with certain clinicopathological features was detected, e.g., both BRAF and PIK3CA were more prevalent in right-side CRC (p < 0.001 and p = 0.002, respectively). We concluded this targeted NGS assay is qualified for clinical practice, and our findings could help the diagnosis and prognosis of Chinese CRC patients.