College Of American Pathologists Research Articles

Abstract 2288: Identification of gene fusions in soft tissue sarcoma improved by integrative DNA and RNA sequencing

Abstract Background: More than 50 different histologic subtypes of soft tissue sarcoma (STS) with mesenchymal origin have been recognized, and their overlapping morphology and histology make clinical diagnosis challenging. Gene fusion has been described as an important molecular biological feature of STS, which can assist in its diagnosis and treatment. Conventional DNAseq methods have limitations for gene fusion detection, while the RNAseq method might circumvent them. In this study, we evaluated the clinical value of integrated DNA and RNA sequencing in the detection of STS gene fusions. Methods: Formalin-fixed and paraffin embedded (FFPE) tumor samples and matched blood of 142 Chinese STS patients were collected and tested by the next-generation sequencing (NGS)-based 825-gene DNA panel and 395-gene RNA panel at Genetronhealth, a laboratory accredited by College of American Pathologists and Clinical Laboratory Improvement Amendments. Results: The genetic landscape of 75 male and 67 female Chinese patients with STS was analyzed. The median age of enrolled patients was 39 years (range, 1-82 years). Multiple histological subtypes were collected, including rhabdomyosarcoma (n = 15), liposarcoma (n = 15), myofibroblastic sarcoma (n = 11) and other types which were all less than 10 cases. Overall, 83 different fusions were detected in 60 patients. Of these, 25 fusions could be detected both by DNA and RNA panels in 18 patients, five fusions were detected only by the DNA panel in four patients, and 53 fusions only by the RNA panel in 39 patients. Compared to DNA-NGS individual testing, integrative panels increased the detection rate of fusion in patients with STS by 177% (53/30). The five gene fusions detected only by the DNA panel, including FOSL1-RELA, intergenic-RUNX2, ADAMTS16-TERT, NCR3LG1-KMT2A and YAP1-MAMLD1, remain clinical significance uncertain in STS. Fusion genes, such as PAX3-FOXO1, ASPSCR1-TFE3, COL1A1-PDGFB, EWSR1-ERG, were detected separately by the RNA panel, which could assist the diagnosis or targeted therapy. Additionally, unreported DIP2B-EWSR1 and AMLD1-SSX1 gene fusions were detected in a patient with clear cell sarcoma and a patient with synovial sarcoma respectively, which might be helpful in clinical diagnosis. Conclusions: Our results showed that the integrated DNA and RNA sequencing can effectively improve the detection rate of STS gene fusions, which might benefit more STS patients. Citation Format: Jiayong Liu, Shu Li, Tian Gao, Chunyang Wang, Qifan He, Xiaojuan Wang, Tonghui Ma. Identification of gene fusions in soft tissue sarcoma improved by integrative DNA and RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2288.

Assessment of serum total 25-hydroxyvitamin D assay commutability of Standard Reference Materials and College of American Pathologists Accuracy-Based Vitamin D (ABVD) Scheme and Vitamin D External Quality Assessment Scheme (DEQAS) materials: Vitamin D Standardization Program (VDSP) Commutability Study 2.

An interlaboratory study was conducted through the Vitamin D Standardization Program (VDSP) to assess commutability of Standard Reference Materials® (SRMs) and proficiency testing/external quality assessment (PT/EQA) samples for determination of serum total 25-hydroxyvitamin D [25(OH)D] using ligand binding assays and liquid chromatography-tandem mass spectrometry (LC-MS/MS). A set of 50 single-donor serum samples were assigned target values for 25-hydroxyvitamin D2 [25(OH)D2] and 25-hydroxyvitamin D3 [25(OH)D3] using reference measurement procedures (RMPs). SRM and PT/EQA samples evaluated included SRM 972a (four levels), SRM 2973, six College of American Pathologists (CAP) Accuracy-Based Vitamin D (ABVD) samples, and nine Vitamin D External Quality Assessment Scheme (DEQAS) samples. Results were received from 28 different laboratories using 20 ligand binding assays and 14 LC-MS/MS methods. Using the test assay results for total serum 25(OH)D (i.e., the sum of 25(OH)D2 and 25(OH)D3) determined for the single-donor samples and the RMP target values, the linear regression and 95% prediction intervals (PIs) were calculated. Using a subset of 42 samples that had concentrations of 25(OH)D2 below 30nmol/L, one or more of the SRM and PT/EQA samples with high concentrations of 25(OH)D2 were deemed non-commutable using 5 of 11 unique ligand binding assays. SRM 972a (level 4), which has high exogenous concentration of 3-epi-25(OH)D3, was deemed non-commutable for 50% of the LC-MS/MS assays.

Lack of Inter-Laboratory Agreement in the Monitoring of Unfractionated Heparin Using the Anti-Factor Xa Activity and the Anti-Factor Xa-Correlated Activated Partial Thromboplastin Time

Background: Unfractionated heparin (UFH) has been in clinical use for more than half a century. Due to the risk of hemorrhage in case of over dosage and the risk of thrombosis in case of under dosage, monitoring UFH treatments is mandatory. The activated partial thromboplastin time (aPTT) is the most widely used method as it is simple, cheap, and readily available. However, it is also poorly standardized and affected by many parameters, both analytic and pre-analytic, that are unrelated to the heparin effect. Particularly, the UFH-induced prolongation of aPTT is highly dependent on the reagent and analyzer used. In an effort to improve inter-laboratory agreement in the monitoring of UFH, the College of American Pathologists (CAP) recommends that the aPTT therapeutic range must be defined in each laboratory through correlation with a direct measure of heparin activity such as the factor Xa (FXa) inhibition assay. Such a strategy was endorsed years ago by the American College of Chest Physicians (ACCP) and the 9thACCP Consensus guideline recommends monitoring UFH treatments by using either the anti-FXa activity, with the therapeutic range between 0.30 and 0.70 IU/mL, or the anti-FXa-correlated aPTT. However, whether and to what extent this approach enhances the inter-laboratory agreement of UFH monitoring has been weakly evaluated, so far.Objectives: To compare the inter-laboratory agreement of the anti-FXa activity and the anti-FXa-correlated aPTT for monitoring therapeutic UFH treatment, we conducted a cross-validation study among 3 accredited coagulation laboratories that used different technical conditions.Patients and Methods: 125 inpatients treated with UFH were sampled in one of the centers. Blood was collected into evacuated polymer tubes containing 3.2% tri-Na citrate. Tubes were centrifuged twice within 2 h after collection, and plasma was stored frozen in aliquots at -70°C that were shipped in dry ice to the 2 other centers to be locally evaluated. Anti-FXa activity (in IU/mL) was evaluated using 4 chromogenic assays i.e. Biophen Heparin LRT (Hyphen BioMed), HemosIL Liquid Anti-Xa (Instrumentation Laboratory, IL), Innovance Heparin (Siemens), and STA-Liquid Anti-Xa (Stago). APTT (expressed as the patient-to-control ratio) was evaluated using 4 reagents i.e. HemosIL SynthASil and HemosIL APTT SP (IL), Pathromtin SL (Siemens), and STA-PTT Automate 5 (Stago). With some exceptions, participating centers used combinations of reagents and analyzers from the same manufacturer i.e. ACL TOP 700 (IL), CS-5100 (Siemens) and STAR (Stago).Results: In the studied population, anti-FXa test results were found to be highly variable depending of the assay used, with the median activity ranging from 0.57 IU/mL with one reagent to 0.37 IU/mL with another, the two other reagents giving intermediate results (Table). Test results obtained using the different reagents were well correlated (r>0.91 in all cases) even though some comparisons performed according to Bland-Altman demonstrated unacceptable bias. If 0.30 to 0.70 IU/mL was used as the therapeutic range of anti-FXa activity, such a discrepancy in test results led to a lack of agreement as to whether a sample was subtherapeutic, therapeutic or supratherapeutic in more than 25% of the patients.The median aPTT test result (ratio) ranged from 2.22 with the less sensitive to 2.93 with the most sensitive reagent. Using the anti-FXa-correlation method, aPTT therapeutic ranges were found to be highly different from one combination of reagent/analyzer to another (Table), and the same applied when correlations were made between one single aPTT reagent and different anti-FXa assays performed on the same analyzer. Consequently, agreement among all aPTT reagents was found in in less than 40% of the patient samples.Conclusions: The reported discrepancy between test results evaluated using commercially available anti-FXa assays are consistent with the results of various national and international EQA programs, and clearly suggests a lack of standardization of that assay. As the consequence, the anti-FXa-correlated aPTT therapeutic range could be significantly impacted. In addition, the anti-FXa-correlation method did not appear to enhance interlaboratory agreement in UFH monitoring as it produces considerable disparity in UFH dosing decisions among different centers, although the clinical impact of this disparity is not known. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Reappraisal of HER2 Amplification in High-Grade Urothelial Carcinoma Based on 2018 ASCO/CAP Clinical Practice Guidelines.

To examine and compare human epidermal growth factor receptor 2 (HER2) amplification status in high-grade urothelial carcinoma (HGUCa), using both 2013 and 2018 HER2 reporting guidelines for breast carcinoma from the American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP). HER2 status by fluorescence in situ hybridization (FISH) assay in 78 cases of HGUCa was compared using 2013 and 2018 HER2 reporting guidelines. HER2 amplification was observed in 22 (28.2%) of 78 tumors, of which 17 were in group 1, 1 in group 2, and 2 each in groups 3 and 4 (FISH assay, 2018). The remaining 14 HER2-amplified tumors (FISH assay, 2013) became negative, falling into group 2 (FISH assay, 2018) and were either negative or equivocal on immunohistochemistry (IHC, 2018). All FISH-negative tumors (n = 37) using 2013 criteria remained negative (group 5, 2018). FISH-equivocal tumors (2013) were further categorized into HER2 amplified (n = 1) and HER2 negative (n = 4) (2018). Overall, 20 (25.6%) tumors had discordant HER2 FISH results (2018 vs 2013). Implementing 2018 guidelines, HER2 amplification decreased from 36 to 22 cases. The group with a HER2/CEP17 ratio of 2 or more and average HER2 copy number less than 4 (group 2) were predominantly negative by IHC, suggesting a biologically distinct group of HGUCa that is different from HER2-amplified tumors, which may not respond to HER2-targeted therapy.

Digital PCR detection of EGFR somatic mutations in non-small-cell lung cancer formalin fixed paraffin embedded samples

BackgroundDigital PCR (dPCR) is proposed to replace real time PCR and Sanger sequencing for detection and quantification of rare mutations, frequently unnoticed in the mass of tumoral cells. Screening of endothelial growth factor receptor (EGFR) mutations is mandatory before treatment with EGFR-targeted therapy with small-molecule tyrosine kinase inhibitors, which has been approved for the treatment of advanced non-small-cell lung cancer (NSCLC). ObjectiveIn order to establish a cost-effective method for detection of mutations, we optimized dPCR identification of EGFR mutations in exons 18–21, and determined dPCR sensitivity, limits of detection (LoD) and quantification (LoQ). MethodsFor clinical validation, we compared the performance of dPCR and castPCR in 57 NSCL formalin fixed paraffin embedded samples and 10 lung cancer-free formalin fixed paraffin embedded samples. ResultsEGFR mutations DEL19, p.L858R, p.G719X, p.L861Q and p.T790 M were detected by dPCR in 27 samples versus 11 detected by castPCR (p = 0.014). LoD was determined as 100 molecules of DNA/uL and LoQ as 1%. Most of the samples (87%) identified by competitive Allele-Specific TaqMan (castPCR) as wild-type and by dPCR as mutated, presented less than 10% mutated DNA molecules (mean 4.57%). Accuracy of dPCR was 94.44%, as measured with the assay recommended by the College of American Pathologists. ConclusionThese results indicated higher sensibility and specificity of dPCR for screening EGFR mutations in NSCLC biopsies, compared to castPCR.

Updated Review on Pathology of Endocervical Adenocarcinoma with Emphasis on Clinically Relevant Findings.

In the present review, we summarize and critically appraise recent advances in the pathology of endocervical adenocarcinoma. In recent years, the diagnosis of endocervical adenocarcinoma has shifted from morphologic criteria classification in 2014 World Health Organization (WHO) to etiology- based classification of International endocervical adenocarcinoma criteria and classification (IECC). IECC recommends classifying endocervical adenocarcinoma into Human Papillomavirus (HPV)- associated and non-HPV-associated. Ultimately, this approach may lead to different treatment options based on molecular pathways rather than purely based on the tumor's grade and stage. Recently, the College of American Pathologists (CAP) has incorporated stromal invasion patterns as an optional data set in the synoptic report. The pattern of invasion classification is a valuable prognostic tool in excision specimens. CONCLUSION: IECC is a simple classification system that recognizes and classifies endocervical tumors based on pathogenesis and association to HPV. The pathologists should also be familiar with the pattern-based classification of endocervical adenocarcinoma.

The \u201cReal R0\u201d: A Resection Margin Smaller Than 0.1 cm is Associated with a Poor Prognosis After Oncologic Esophagectomy

BackgroundAlthough resection margin (R) status is a widely used prognostic factor after esophagectomy, the definition of positive margins (R1) is not universal. The Royal College of Pathologists considers R1 resection to be a distance less than 0.1 cm, whereas the College of American Pathologists considers it to be a distance of 0.0 cm. This study assessed the predictive value of R status after oncologic esophagectomy, comparing survival and recurrence among patients with R0 resection (> 0.1-cm clearance), R0+ resection (≤ 0.1-cm clearance), and R1 resection (0.0-cm clearance).MethodsThe study enrolled all eligible patients undergoing curative oncologic esophagectomy between 2012 and 2018. Clinicopathologic features, survival, and recurrence were compared for R0, R0+, and R1 patients. Categorical variables were compared with the chi-square or Fisher’s test, and continuous variables were compared with the analysis of variance (ANOVA) test, whereas the Kaplan-Meier method and Cox regression were used for survival analysis.ResultsAmong the 160 patients included in this study, 113 resections (70.6%) were R0, 34 (21.3%) were R0+, and 13 (8.1%) were R1. The R0 patients had a better overall survival (OS) and disease-free survival (DFS) than the R0+ and R1 patients. The R0+ resection offered a lower long-term recurrence risk than the R1 resection, and the R status was independently associated with DFS, but not OS, in the multivariate analysis. Both the R0+ and R1 patients had significantly more adverse histologic features (lymphovascular and perineural invasion) than the R0 patients and experienced more distant and locoregional recurrence.ConclusionsAlthough R status is an independent predictor of DFS after oncologic esophagectomy, the < 0.1-cm definition for R1 resection seems more appropriate than the 0.0-cm definition as an indicator of poor tumor biology, long-term recurrence, and survival.

Impact of pathological response after neoadjuvant chemotherapy on adjuvant therapy decisions and patient outcomes in gastrointestinal cancers.

BackgroundNeoadjuvant chemotherapy (NAC) is frequently used in gastrointestinal cancers (GIC), and pathological, radiological, and tumor marker responses are assessed during and after NAC.AimTo evaluate the relationship between pathologic, radiologic, tumor marker responses and recurrence‐free survival (RFS), overall survival (OS), adjuvant chemotherapy (AC) decisions, and the impact of changing to a different AC regimen after poor response to NAC.Methods and resultsMedical records of GIC patients treated with NAC at Mount Sinai between 1/2012 and 12/2018 were reviewed. One hundred fifty‐six patients (58.3% male, mean age 63 years) were identified. Primary tumor sites were: 43 (27.7%) pancreas, 62 (39.7%) gastroesophageal, and 51 (32.7%) colorectal. After NAC, 31 (19.9%) patients had favorable pathologic response (FPR; defined as College of American Pathologists [CAP] score 0–1). Of 107 patients with radiological data, 59 (55.1%) had an objective response, and of 113 patients with tumor marker data, 61 (54.0%) had a ≥50% reduction post NAC. FPR, but not radiographic or serological responses, was associated with improved RFS (HR 0.28; 95% CI 0.11–0.72) and OS (HR 0.13; 95% CI 0.2–0.94). Changing to a different AC regimen from initial NAC, among all patients and specifically among those with unfavorable pathological response (UPR; defined as CAP score 2–3) after NAC, was not associated with improved RFS or OS.ConclusionsGIC patients with FPR after NAC experienced significant improvements in RFS and OS. Patients with UPR did not benefit from changing AC. Prospective studies to better understand the role of pathological response in AC decisions and outcomes in GIC patients are needed.

Impact of updated 2013 human epidermal growth factor receptor-2 testing guidelines on HER2 positive invasive breast cancer diagnosis: A three year retrospective study.

e12554 Background: Breast cancer is a frequently diagnosed malignancy in the United States accounting for approximately 266,000 cases and 40,000 deaths annually. Human epidermal growth factor receptor 2 (HER2) is a surface protein shown to affect cell proliferation, migration and survival - the hallmarks of neoplastic cells. HER2 is overexpressed in 20-35% of breast cancer cases and has a strong prognostic and therapeutic significance. This discovery led to development of therapeutic agents targeting HER 2 receptor. In 2013, College of American Pathologists (CAP) updated their recommendations for HER2 testing by incorporating an algorithm with immunohistochemistry (IHC) and In situ hybridization (ISH). The primary objective of our study was to assess for variance in HER2 interpretation by applying the updated 2013 criteria to all diagnosed cases in our hospital for the immediate previous three years. Methods: We retrospectively reviewed charts of patients diagnosed with invasive breast carcinoma from January 1, 2010 to December 31, 2012 at our hospital. The new American college of pathology criteria assessing FISH HER2 copy number and HER2/CEP ratio for each patient was compared to the old criteria to assess for variance in HER2 interpretation. Categorical variables are presented as percentages and kappa statistic was used to assess for variance. Results: We reviewed 526 charts with an invasive breast cancer diagnosis over a 3-year period. 10.83% of patients were HER2 amplified, 86.12% were non-amplified and 3.04% were equivocal. Applying the updated 2013 CAP criteria, we found that 11.21% were amplified, 74.33% were non amplified, and 14.44% remained equivocal. Kappa statistic indicated substantial agreement (0.804) between the old and new criteria. A review of our cohort revealed an overall lower level of HER2 positive cases at 10.83% (old criteria) and 11.21% (updated criteria) when compared to historical studies. The increase in equivocal cases from 3.04% to 14.44% with the new criteria suggests under diagnosis of HER2 positive cases. Due to the lack of IHC performed (as per old standards), further classification of equivocal cases (based on new criteria) was not possible. While we saw some movement in our data from non-amplified to equivocal, our analysis indicated substantial statistical agreement between the old and the new diagnostic criteria Conclusions: Our study did not show a variance in HER2 interpretation between the 2007 and 2013 CAP criteria which is reassuring. An increase of 11.4% cases in the equivocal category was noted and may reveal a significant difference if further delineation is feasible. This variance could be important given the prognostic and therapeutic implications in HER2 positive breast cancer.[Table: see text]

Responsibility of immune microenvironment for poor response to immune checkpoint inhibitors in CRC patients with KRAS mutation.

e15588 Background: The clinical trial Keynote 177 is a breakthrough research in colon rectal cancer (CRC), however, the results of subgroups revealed that immunotherapy did not benefit more than chemotherapy in patients with KRAS mutation. Here we assessed characteristics of tumor immune microenvironment in patients with or without KRAS mutation, to find out the underlying mechanisms that prevent KRAS-mutated CRC patients from benefiting from immunotherapy. Methods: Tumor tissue samples of 77 CRC patients were collected from Janary 2019, several kinds of immune cells including CD8+ T cells, M1/M2 tumor associated macrophages (TAM), CD56bright NK cells and CD56dim NK cells in the tumor tissue were evaluated by multiple fluorescence immunohistochemistry (mIHC), and expression of PD-L1 were detected by using Dako PD-L1 IHC 22C3 pharmDx, Tumor Proportion Score (TPS) was used to determine expression of PD-L1. In addition, gene mutation was detected by means of next generation squesing (NGS). All these detections were performed in a College of American Pathologists (CAP)-certified and Clinical Laboratory Improvement Amendments (CLIA)-accredited lab for gene mutation analysis (3D Medicines Inc.,Shanghai, China). Statistical analysis was performed using GraphPad Prism (version 7.01) and SPSS version 21.0 (SPSS,Inc.). Results: According to whether KRAS is mutated, these 77 patients were divided into two groups, KRAS wild type (WT) (n = 49) and KRAS mutation group (n = 28). There was no significant difference in the CD8+T cells infiltrated in tumor tissue of KRAS WT and KRAS mutation samples, however, less CD8+ T cells were found in stroma of tumor tissue of KRAS WT samples than in KRAS mutation. What’s more, both the ratio of M1:M2 and CD56dim NK: CD56bright NK cells in the tumor tissues of KRAS WT were significantly higher than in KRAS mutation samples(p &lt; 0.05). No significant difference was found between two groups, while higher MSI-H proportion was found in KRAS mutation group than in KRAS WT (33.4% and 12.5%, respectively). The proportion of positive PD-L1expression (TPS≥1) in both groups is very low, especially, proportion of strong positive (TPS≥50). Conclusions: The different response to immune checkpoint inhibitors therapy for CRC patient with or without KRAS mutation mainly associated with factors of TIME, not only CD8+T cells, but tumor associated macrophages and different sub-population of NK cells should be put into consideration.

Distribution of BRCA1/2 germline and somatic alterations across cancer type.

10590 Background: PARP inhibitors (e.g. Olaparib or niraparib) have been approved by FDA as a targeted therapy for many tumors harboring germline or somatic BRCA1/2 (g or sBRCA1/2), including ovarian cancer, prostate cancer, breast cancer and pancreases cancer. It is imperative to study the distribution of BRCA1/2 across cancer type. In this study, we aim to assess the landscape of BRCA1/2 alterations in solid tumors and evaluate the feasibility of circulating tumor DNA (ctDNA) tested by next-generation sequence (NGS) as a tool to detect BRCA1/2 alterations. Methods: For tissue specimen, genomic DNA from formalin fixed paraffin-embedded (FFPE) tumor specimens or fresh tumor tissues was used for sequence analysis. Genomic DNA (gDNA) from white blood cells was extracted using the QIAamp DNA Mini Kit (Qiagen). For ctDNA, cell-free DNA libraries were prepared using the KAPA Hyper Prep Kit following the manufacturer’s protocol. The captured libraries were loaded onto a NovaSeq 6000 platform (Illumina) for 100bp paired-end sequencing. The testing was performed in the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA) -certified 3D Medicines Library. Results: A total of 27, 835 patients were tested using tumor tissue during Jan. 1th 2017 to June 1th 2020, including 43% (N = 12089) of non-small cell lung cancer, 19% (N = 5357) of colorectal cancer, 8% (N = 2181) of liver cancer, 6% (N = 1621) of gastric cancer, 5% (N = 1479) of biliary tract cancer, 4% (N = 1084) of kidney cancer, 4% (N = 1045) of pancreas cancer, 3% (N = 689) of breast cancer and 2% (N = 599) of ovarian cancer. Across all tumor types, the known or likely deleterious BRCA1/2 alterations were identified in 2147 (7.7%) patients. Ovarian cancer had the highest frequency of BRCA1/2 alteration (23.4%), followed by endometrial cancer (12.7%) and breast cancer (10.6%). BRCA1/2 alteration was found in 8.8% prostate cancer and 4.2% pancreas cancer respectively. Across all tumor types, the known or likely deleterious gBRCA1/2 alterations were identified in 369 (1.3%) patients. Notably, ovarian cancer had the highest frequency of gBRCA1/2 alteration (13.9%), followed by breast cancer (7%), prostate cancer (4.4%) and endometrial cancer (4.1%). No clear hotspot mutations and mutated codons were spread throughout g or sBRCA1/2 mutations. Additionally, among 15699 patients who suffered ctDNA sequencing, any known or likely deleterious sBRCA1/2 alterations were identified in 358 (2%) patients. Similar to the results of tissue sequencing, ovarian cancer had the highest frequency of sBRCA1/2 alteration (16.67%), followed by endometrial cancer (9.68%), prostate cancer (7.18%) and breast cancer (5.58%) in the blood cohort. Conclusions: BRCA1/2 alterations existed across tumor types and the landscape of g or sBRCA1/2 alterations varied according to cancer type. Furthermore, ctDNA can be used as a potential tool to detect BRCA1/2 alterations.

Comprehensive understanding of genomic profile of bone cancer by the combination of DNA and RNA detection.

e23513 Background: The diagnosis of bone tumors is mainly based on clinical manifestations, imaging examination, tissue biopsy and laboratory examination. However, most of the bone tumors have no specific clinical manifestations, which makes the diagnosis and differential diagnosis difficult. The genomic profile of bone tumor is helpful to provide molecular basis for its molecular diagnosis. Methods: A total of 357 Chinese bone cancer patients were enrolled in this study. The NGS-based YuanSu S panel which includes both DNA and RNA detection was performed by OrigiMed, a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory, Shanghai, China, for genomic alteration identification. Results: The 357 Chinese bone cancer patients were enrolled, including 206 adult patients and 151 juvenile patients, with a median age of 20 years old (ranged from 1 to 88 years). Among them, there were 214 males and 143 females. The most commonly mutated genes with a mutation frequency more than 10% were TP53 (31.65%), NCOR1 (15.69%), VEGFA (13.73%), RB1 (12.61%), CCND3 (11.76%), CDKN2A, GID4, and CCNE1 (11.48%, for each), TERT (10.64%), and MAP2K4 (10.08%). Germline mutations were detected in 28 patients, including 13 patients with HRD related mutations, such as ATM, FANCA, BRCA2, RAD50, RAD51D and FANCD2. A total of 179 gene fusions were detected in 130 bone cancer patients. Notably, 19 gene fusions such as SH2D2A-NTRK1, EMILIN1-ALK, and SZRD1-SPEN, were detected in 16 patients with the assistance of RNA detection. Statistical analysis showed that the mutations of NCOR1 (P = 1.1X10-4), VEGFA (P = 3.4X10-6), CCND3 (P = 1.0X10-5), GID4 (P = 1.1X10-6), CCNE1 (P = 3.0X10-7), RB1 (P = 0.03), and MAP2K4 (P = 1.5X10-4)were significantly associated with juvenile patient group, as well as the mutation of H3F3A (P = 7.5X10-5) was significantly associated with adult patient group. Conclusions: Here we identified the mutational characteristics of Chinese bone tumor patients. In addition, the inclusion of RNA detection effectively increased the detection of gene fusions. Our results provided the evidence for the precise treatment of bone tumors in the future.

Molecular characteristic of proximal and distal esophagogastric junction adenocarcinomas.

e16077 Background: Esophagogastric junction adenocarcinomas (EGJA) are devastating diseases with increasing incidence. The 8th Edition TNM staging of American Joint Committeeon Cancer and Union for International Cancer Control defined that the epicenter of EGJA within 2 cm of the cardia (hereinafter referred to proximal EGJA) is staged according to the staging standard of esophageal cancer, while that more than 2 cm distal from the EGJA (hereinafter referred to distal EGJA) is staged according to the staging standard of stomach cancer. However, the rationality of the new definition in clinical practice is still controversial. Methods: A randomized retrospective study was conducted. Targeted next-generation sequencing of 450 cancer-related genes was performed, by OrigiMed, a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory, Shanghai, China, for genomic alteration identification. Results: A total of 198 EGJ patients were included in this study with a median age of 63 years (ranged from 39 to 88 years). Among them, 140 were distal EGJA and 58 were proximal EGJA. Genomic alterations with a high mutation frequency in EGJ include There is no significant difference in the frequencies of these genes between proximal EGJA and distal EGJA. Mutation frequencies of FGFR2 and ZEN217 in distal EGJ were significantly higher than those in proximal EGJA (15.8% vs 5.0%, P = 0.02 and 7.0% vs 0.7%, P = 0.03, respectively). Multivariate regression analysis showed that tumor stage and lymph nodes number were the main factors positively associated with the poor prognosis. However, we found that there was no significant difference in OS between proximal and distal (P = 0.139). Furthermore, our results showed that LRP2 and SPTA1 mutations were significantly associated with better OS of the EGJA patients. Conclusions: In conclusion, with the identification of the mutation landscape of EGJA, the FRFR2 and ZNF127 genes mutations were potential biomarkers to distinguish distal EGJA from proximal EGJA, whereas the LRP2 and SPTA1 gene mutations were potential biomarkers for prognosis prediction in EGJA.

Exploring the applicability of immunotherapy in different EGFR mutation subgroups based on data analysis of 9,659 Chinese patients with NSCLC.

e21020 Background: Here we assessed TMB level, PD-L1 expression, and their correlation in 9649 Chinese NSCLC patients with or without EGFR mutation, and different subtypes of EGFR mutations, to find out the underlying mechanisms that different outcomes of ICI for EGFR wild type and EGFR mutation NSCLC patients, and the possibility of ICI therapy for NSCLC patients of different EGFR mutation subtypes. Methods: Tumor tissue samples of 9649 NSCLC patients were collected from Janary 2018, expression of PD-L1 were detected by using Dako PD-L1 IHC 22C3 pharmDx, Tumor Proportion Score (TPS) was used to determine expression of PD-L1. Gene mutation was detected by means of next generation sequencing (NGS). Performed Whole-Exome Sequencing (WES) on 70 tissue samples and corresponding White Blood Cells (WBCs) as matched control. Other samples were detected with panel covering whole exon regions of 733 cancer related genes. All these detections were performed in a College of American Pathologists (CAP)-certified and Clinical Laboratory Improvement Amendments (CLIA)-accredited lab for gene mutation analysis (3D Medicines Inc.,Shanghai, China). Statistical analysis was performed using GraphPad Prism (version 7.01) and SPSS version 21.0 (SPSS,Inc.). Results: Results showed that the proportion of EGFR mutation in Chinese patients with NSCLC was 51.3%, and the proportion of EGFR mutation subtypes were 42.6% L858R, 39.5% exon 19del, 2.3% exon 20in, 4.3% T790M. These samples were divided into different groups according to EGFR mutation, both WES based and panel-based results showed that EGFR wild type group displayed higher TMB level than EGFR mutation group (P &lt; 0.05). However, except for exon 19del, L858R, exon 20in, no significant differences were found between wild type and other EGFR mutation subtypes. Furthermore, results of IHC revealed that, higher proportion of strong positive PD-L1 expression (TPS≥50) were found in EGFR wild type than exon 19del, L858R and exon 20in, no significant correlation was found between TMB level and PD-L1 expression. Conclusions: EGFR mutations account for half of Chinese NSCLC patients. The biomarkers of immune checkpoint inhibitors (such as TMB and PD-L1) are different in various EGFR mutation subtypes, which may indicate that for some NSCLC patients with EGFR mutation subtypes, they may also respond to ICI treatment as wild-type.

HER‐2/neu‐positive breast cancer neoadjuvant chemotherapy response after implementation of 2018 ASCO/CAP focused update

Human Epidermal Growth Factor Receptor 2 (HER2), a routinely tested breast cancer marker, is associated with worse prognosis yet increased sensitivity to targeted neoadjuvant therapy (NAT) in breast cancer patients. The presence of HER2 in breast carcinoma can be detected with either immunohistochemistry (IHC) or in situ hybridization (ISH). In this study, we examine the relationship between clinicopathological features, HER2 detection method (IHC vs ISH), and prognostic outcomes in NAT-treated HER2-positive breast cancer patients. We included 99 HER2-positive patients from three academic institutions following 2018 HER2 testing updates and conducted a retrospective correlational study. Seventy-one (72%) were HER2-positive by IHC and 28 (28%) were positive following reflexive ISH. Multivariate analysis showed biomarker status to be significantly associated with pathologic complete response (pCR) (p=0.003), Residual Cancer Burden (RCB) (p=0.007), and tumor size downstaging (p = 0.002) and HER2 detection method of IHC to be significantly associated with pCR (p=0.05), RCB (p=0.004), and nodal downstaging (p= 0.03). In conclusion, HER2 detection method and biomarker subtype allow for further prognostic stratification of HER2-positive patients when 2018 American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guideline updates are applied.

A Holistic Approach to Pathology Education During the Coronavirus Disease 2019 (COVID-19) Pandemic

A Holistic Approach to Pathology Education During the Coronavirus Disease 2019 (COVID-19) Pandemic

An Evaluation of Clinicopathological Correlation and Outcome of Human Epidermal Growth Factor Receptor 2 Subgroups Reclassified According to the Latest ASCO/CAP Guideline

BackgroundThe latest American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guideline has updated the interpretation of uncommon human epidermal growth factor receptor 2 (HER2) in situ hybridization (ISH) patterns (groups 2-4) with concomitant HER2 immunohistochemistry, leading to changes in the diagnosis of these subgroups. We sought to assess the clinicopathological features and outcomes in these subgroups in detail with our local cohort. Patients and MethodsClinicopathologic features of groups 2 to 4 were compared to the typical amplified group (group 1: HER2/CEP17 ≥ 2, HER2 ≥ 4) and non-amplified group (group 5: HER2/CEP17 < 2, HER2 < 4). ResultsGroup 2 (HER2/CEP17 ≥ 2, HER2 < 4) cases showed lower Ki67 expression and grade (P ≤ .002) than group 1 but no differences compared with group 5. Group 4 (HER2/CEP17 < 2, HER2 = 4-6) cases were associated with less necrosis, more estrogen receptor positivity, lower grade, more nodal metastases, and more special histotypes (P ≤ .037) than group 1, but higher grade and more nodal metastases (P ≤ .021) than group 5. Except for presenting as a larger tumor and of special histotypes, group 3 (HER2/CEP17 < 2, HER2 ≥ 6) cases showed no other significant differences from group 1, but were of higher grade and Ki67 level than groups 2, 4, and 5. Group 4, similar to group 5, showed worse survival than group 1 (disease-free survival: log-rank = 5.547, P = .019; overall survival: log-rank = 4.678, P = .031). The rate of relapse was similar in group 4 with and without anti-HER2 therapy, albeit with limited cases. ConclusionOur findings indicate more similarities among groups 2, 4, and 5 than between groups 1 and 3, supporting the HER2 categorization in the latest guideline. Additional studies may be warranted to assess the outcomes of these patients with different management approaches.

Detailed Reanalysis of 500 Breast Cancers With Equivocal HER2 Immunohistochemistry and Borderline ERBB2 Fluorescence In Situ Hybridization Results.

We investigated the impact of our laboratory's reflex testing process for resolving ERBB2 (HER2) status on breast cancer samples that require additional workup after fluorescence in situ hybridization (FISH), per guideline recommendations published in 2018 by the American Society of Clinical Oncology (ASCO) and the College of American Pathologists (CAP). In total, 500 breast cancer specimens with ERBB2 FISH results in groups 2 through 4 (all reported as immunohistochemistry [IHC] equivocal [2+] at external laboratories) were resubmitted for IHC testing in our laboratory. Per the ASCO/CAP guideline, FISH was rescored when internal IHC was also equivocal (2+), targeted to tumor areas demonstrating more intense IHC staining, if observed. Reflex IHC/FISH testing changed the final reported ERBB2 status in 185 of 500 (37.0%) samples. Result changes included discordant IHC (n = 4 score 0, n = 132 score 1+, and n = 16 score 3+) and discordant FISH (n = 33). Numerical differences in FISH scores were comparable for targeted vs nontargeted FISH rescoring (P = .086 for ERBB2 copy number; P = .49 for ERBB2 ratio). Two cases showed larger differences in FISH scores, suggesting heterogeneity. Retesting of breast cancer samples with equivocal IHC frequently changes IHC results, but targeted reanalysis of borderline FISH results rarely identifies significant differences in ERBB2 copy number or ratio.

Improving the Diagnosis, Treatment, and Prevention of Endocrine Diseases Through Accurate and Reliable Laboratory Measurements With CDC Clinical Standardization Programs

Laboratory measurements are critical for correct diagnosis and treatment of patients with chronic diseases such as hypogonadism, PCOS, and thyroid diseases. Inaccurate measurements of disease biomarkers can lead to misclassification of patients/incorrect treatment and prevent the effective use of research findings in patient care. The CDC Clinical Standardization Programs (CDC CSP) improve the accuracy and reliability of clinical biomarker measurements by assessing and improving the analytical performance of assays. The CDC CSP assist with assay calibration, the certification of analytical performance, and the monitoring of routine patient and research testing. The CDC CSP work with clinical/research laboratories and assay manufacturers to improve laboratory measurements. Its current programs include the following analytes: total testosterone (TT), estradiol (E2), vitamin D (VD), free thyroxine (FT4), total cholesterol (TC), total glycerides (TG), HDL-cholesterol (HDL-C), and LDL-cholesterol (LDL-C). The work is being conducted through certification/monitoring programs and technical assistance. Most assays participating in the certification programs have seen performance improvements and maintain performance over time by continuous participation. Most major commercial laboratories and assays manufactures are enrolled in the certification programs. Currently certified and non-certified assays are available. Assays certified by CDC CSP are listed on the website at https://www.cdc.gov/labstandards/hs.html. The CDC Lipid Standardization Programs and CDC Accuracy-based Monitoring Programs allow for weekly monitoring of analytical performance of routine tests for analytes including TT, VD, TC, TG, HDL-C, apolipoprotein A1 and B. These monitoring programs assist researchers with assessing measurement accuracy of research studies over time and across laboratories. The CDC CSP also support accuracy-based external quality assurance surveys such as those offered by the College of American Pathologists (CAP). The CDC CSP assist researchers and stakeholders with developing and establishing reference intervals and conducting studies to better assess and diagnose patients. Based on the needs and requests from clinical community, programs for new biomarkers such as Lp(a), PTH and glucose are being developed. The CDC CSP work with stakeholders, such as the Endocrine Society and the Partnership for the Accurate Testing of Hormones, to educate the clinical and laboratory communities about the importance of using standardized assays in patient care, research, and public health.

Does the law require reinterpretation and return of revised genomic results?

Does the law require reinterpretation and return of revised genomic results?