Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists

Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.

Recommendations for Specimen and Therapy Selection in Colorectal Cancer

INTRODUCTION

Next-generation sequencing has emerged as a clinical tool for the identification of actionable mutations to triage advanced colorectal cancer patients for targeted therapies. The literature is conflicted as to whether primaries or their metastases should be selected for sequencing. Some authors suggest that either site may be sequenced, whereas others recommend sequencing the primary, the metastasis, or even both tumors. Here, we address this issue head on with a meta-analysis and provide for the first time a set of sensible recommendations to make this determination.

METHODS

From our own series, we include 43 tumors from 13 patients including 14 primaries, 10 regional lymph node metastases, 17 distant metastases, and two anastomotic recurrences sequenced using the 50 gene Ion AmpliSeq cancer NGS panel v2.

RESULTS

Based on our new cohort and a meta-analysis, we found that ~ 77% of patient-matched primary-metastatic pairs have identical alterations in these 50 cancer-associated genes.

CONCLUSIONS

Low tumor cellularity, tumor heterogeneity, clonal evolution, treatment status, sample quality, and/or size of the sequencing panel accounted for a proportion of the differential detection of mutations at primary and metastatic sites. The therapeutic implications of the most frequently discordant alterations (TP53, APC, PIK3CA, and SMAD4) are discussed. Our meta-analysis indicates that a subset of patients who fail initial therapy may benefit from sequencing of additional sites to identify new actionable genomic abnormalities not present in the initial analysis. Evidence-based recommendations are proposed.

"Indeterminate" UroVysion Fluorescence In Situ Hybridization Results

OBJECTIVES

UroVysion cases with one to three abnormal cells that do not meet the threshold for positivity may be better classified as "indeterminate." The aim of this study is to determine the incidence and clinical significance of these indeterminate UroVysion results.

METHODS

The UroVysion fluorescence in situ hybridization (FISH) results over a 4-year period in our institution were retrospectively analyzed. Follow-up of the initial UroVysion cases, including urine cytology or bladder biopsy performed within 12 months of the initial diagnosis of the result, was obtained from pathology reports.

RESULTS

A significant fraction (178 of 1,907, 9.3%) of the UroVysion cases had indeterminate results. Overall, the subsequent malignancy rate of the group with indeterminate UroVysion results (14 of 59, 23.7%) was higher than the group with normal results (48 of 319, 15.0%), although the difference was not significant (P = .124). For patients without a history of urinary tract neoplasm, the subsequent malignancy rate in the group with indeterminate results (7 of 18, 38.9%) was significantly higher than the group with normal results (16 of 103, 15.5%) (P = .044).

CONCLUSIONS

Our results support that indeterminate UroVysion FISH result may warrant closer clinical follow-up in patients without a history of urinary tract neoplasm. We suggest reporting these cases as "aneusomy of undetermined significance."

Abstract 447: Circulating TP53 tumor DNA as a potential biomarker for pre-operative identification of uterine leiomyosarcoma

Uterine leiomyosarcoma (LMS) is a highly aggressive but rare malignancy with a dismal prognosis. In nearly all cases, LMS is unsuspected prior to resection for a presumed leiomyoma. The risk of occult uterine LMS is reported to be 0.2% (1 in 500) in the largest cohort study of women undergoing surgery for presumed fibroid disease. The major problem is that there is no reliable preoperative method to distinguish LMS from a leiomyoma (LM) or STUMP (smooth muscle tumor of uncertain malignant potential), and the patient's prognosis for LMS is even poorer if the tumor is transected, which occurs in procedures performed for LM. Effective therapy for LMS is lacking and most patients eventually succumb to the disease. Thus, there is a considerable need for a reliable preoperative test to triage patients into the proper surgical procedure for LMS. TP53 alterations are reportedly associated with uterine LMS in about 40% of cases. We screened plasma for TP53 variants in patients with pathologically confirmed LMS. We evaluated TP53 circulating tumor DNA (ctDNA) by deep next-generation sequencing in a cohort of 7 patients with LMS, 1 patient with STUMP, and 3 patients with LM. Clinical data were reviewed to assess disease burden. LMS patients' tumor burden ranged from no evidence to extensive metastatic disease. DNA extraction was performed using the QIAamp DNA Micro Kit, QIAamp DNA FFPE Tissue Kit, or QIAamp MinElute ccfDNA Mini Kit. DNA quality was assessed using the TapeStation Genomic DNA kit. NGS libraries targeting the entire exonic region of the p53 gene were prepared using the QIASeq Targeted DNA Custom Panel. Sequencing was performed on the MiSeq system using 150bp paired end sequencing with a minimum read depth of 2x0.5M reads for plasma and 2x1M reads for formalin-fixed paraffin embedded and fresh-frozen tissue samples. Raw sequencing data were demultiplexed by bcl2fastq to generate the FASTQ files. Then raw sequencing reads were aligned to the human reference genome GRCh38 by BWA-MEM 0.7.9a-r786. SmCounter2 was used for p53 variants calling and variants quality control. We discovered TP53 ctDNA variants in 5 of 7 (71.4%) LMS cases including p.E258V, p.R248Q, P.R337C, p.E221*, p.R174_R175delinsWC, but not in the control cases of LM or STUMP. In the 5 plasma samples with TP53 mutated LMS, the patients had extensive metastatic disease and in the 2 TP53 wild-type LMS and STUMP cases, the patients had no evidence of disease. To our knowledge, this is the first pilot study to demonstrate the comparative use of TP53 ctDNA in patients with LMS, LM, and STUMP. Further study of these rare LMS is needed to determine the preoperative utility of NGS TP53 ctDNA mutational status as a useful molecular biomarker to help guide surgery and avoid unwarranted manipulation and pelvic contamination of undetected LMS. Supported by the Gottlieb, Buss and Snyder Endowments in Surgical Oncology

Citation Format: Jean R. Lopategui, Bonnie Balzer, Yizhou Wang, Chintda Santiskulvong, Carissa A. Hyunh, Chun Yat Ong, Manuel Arana, Matthew Gayhart, Farin Amersi, Allan W. Silberman. Circulating TP53 tumor DNA as a potential biomarker for pre-operative identification of uterine leiomyosarcoma [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 447.

The State of the Art in Colorectal Cancer Molecular Biomarker Testing

The number of molecular biomarkers to inform treatment decisions in patients with metastatic colorectal cancer (mCRC) continues to expand and with it the methodologies that can be employed to evaluate these biomarkers. Beyond standard diagnostic and prognostic biomarkers, such as those used for Lynch syndrome, mutations in KRAS exon 2 are well established as predictive for lack of response to the antiepidermal growth factor receptor therapies panitumumab and cetuximab. Recent studies have extended these findings by demonstrating that mutations in KRAS exons 3 and 4 and in NRAS exons 2, 3, and 4 (with all KRAS and NRAS mutations collectively referred to as RAS) are also predictive for treatment outcomes among patients with mCRC receiving panitumumab and cetuximab in combination with chemotherapy or as monotherapy. Consequently, evaluation of these additional loci has been incorporated into current clinical guidelines, and pathologists will need to develop testing procedures and algorithms to reliably and rapidly evaluate RAS status. With the increased number of mutations that must be examined to evaluate the status of RAS and other emerging biomarkers, next-generation sequencing technologies are likely to become increasingly important in mCRC testing. This review describes new considerations for pathologists that have arisen as a consequence of the incorporation of additional biomarker testing into clinical practice for mCRC.

A novel method for the detection, quantitation, and breakpoint cluster region determination of t(15;17) fusion transcripts using a one-step real-time multiplex RT-PCR

Individuals with acute promyelocytic leukemia (APL) usually express 1 of 3 primary hybrid transcripts associated with a t(15;17). The 3 fusion transcripts are the result of heterogeneous breakpoint cluster regions (bcr) within the promyelocytic leukemia (PML) gene and are denoted bcr1 (long), bcr2 (variant), and bcr3 (short) forms. Many researchers have shown that real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) of the involved transcript is a valuable tool for monitoring APL and its treatment. In addition, some research suggests that identification of a specific breakpoint region may be used to predict an individual's likelihood of relapse and possibly their response to all-trans retinoic acid treatment. We describe the first reported 1-step multiplex RT-PCR assay capable of t(15;17) fusion transcript real-time relative quantitation and simultaneous transcript form identification in 2 reactions. This assay uses a novel dual-probe technique to achieve what has required a laborious procedure of 2 or more reactions followed by postamplification analysis. We found a correlation of 100% in detection and breakpoint determination of the long, short, and variant forms with a breakpoint 5' to nucleotide 1709 compared with results from traditional methods.

Absence of the t(2;5) in Hodgkin's disease

The cytogenetics of Hodgkin's disease (HD) is poorly understood. However, a t(2;5) is a common finding in CD30+ anaplastic large cell lymphoma (ALCL), a neoplasm thought by some to be closely related to HD. Recently, the t(2;5) has been cloned and found to represent fusion of the NPM gene with the ALK gene. Using Southern blot hybridization, one group has reported finding rearrangements of NPM in a proportion of cases of both ALCL and HD. In the current study, we used a highly sensitive reverse transcriptase-polymerase chain reaction methodology to analyze 34 cases of HD for the t(2;5). We were unable to find polymerase chain reaction evidence for the t(2;5) in any of the cases of HD, a result significantly different from our previous study of CD30+ non-Hodgkin's lymphomas (P < .02) including ALCL (P < .04), using identical methods. Our results do not support the hypothesis that the t(2;5) represents a common chromosomal abnormality for both HD and ALCL.

Low frequency association of the t(2;5)(p23;q35) chromosomal translocation with CD30+ lymphomas from American and Asian patients. A reverse transcriptase-polymerase chain reaction study

Although cytogenetic data suggest that the t(2;5)-(p23;q35) translocation occurs in many cases of CD30+ lymphomas, the exact frequency of this event is still unknown. To clarify this issue and its epidemiological characteristics, we examined 37 formalin-fixed, paraffin-embedded specimens of CD30+ lymphomas from the United States and Hong Kong by reverse transcriptase-polymerase chain reaction (RT-PCR) for the status of the NPM and ALK genes, which are typically juxtaposed by the t(2;5) translocation. Thirty-four cases were classified as anaplastic large cell lymphomas (ALCL), 2 cases as non-anaplastic large cell lymphomas (LCL), and 1 case as the small cell variant of CD30+ lymphoma. The t(2;5) translocation was detected in 6 cases (16%), including 3 of 18 American patients and 3 of 19 cases from Hong Kong. All cases had a 185-bp NPM RT-PCR product as detected by Southern blot analysis, indicating adequate preservation of mRNA. The 6 positive cases were among 4 of 34 adult lymphomas, as compared with 2 of 3 childhood cases. Five of 17 T-lineage cases were t(2;5)-positive, compared with 1 of 15 B-lineage cases and none of the 5 null-cell or mixed lineage cases. Our results therefore show that t(2;5) occurs at a low frequency among CD30+ lymphomas, at least in our adult-dominated series.

Infrequent association of Epstein-Barr virus with CD30-positive anaplastic large cell lymphomas from American and Asian patients

CD30 (Ki-1)-positive anaplastic large cell lymphoma (CD30+ ALCL) is a morphologically and immunophenotypically distinct subset of non-Hodgkin's lymphoma. Although the presence of Epstein-Barr virus (EBV) has been well documented in a significant proportion of cases of Hodgkin's disease, another CD30+ malignancy, few studies have examined the association of EBV with CD30+ ALCL. These latter studies have produced conflicting findings. To further investigate the existence of a putative association of EBV with CD30+ ALCL, and whether this association, if present, shows geographic variation, we examined 34 formalin-fixed, paraffin-embedded specimens from cases of CD30+ ALCL from the United States and Hong Kong. Immunophenotypically, 15 cases were of B lineage, 15 cases were of T lineage, one case expressed both B- and T-cell markers, and three were of null lineage. A highly sensitive in situ hybridization method was performed with use of an antisense oligonucleotide probe to the EBV-encoded RNA (EBER-1). EBV-RNA was identified in 3 of 14 CD30+ ALCL specimens from Hong Kong patients and in 1 of 20 from the American patients. The EBER-1 signal was present in all or virtually all of the tumor cell nuclei in the three EBV-RNA-positive CD30+ ALCL Hong Kong cases, but was only focally present in the single EBV-positive American case. The latent membrane protein-1 (LMP1) of EBV was identified in only one of the four positive cases, a Hong Kong case. Our results suggest that in contrast to Hodgkin's disease, EBV has no significant association with CD30+ ALCL.

Detection of Epstein-Barr viral RNA in sinonasal undifferentiated carcinoma from Western and Asian patients

Undifferentiated carcinoma of the nasopharynx has a well-known association with Epstein-Barr virus (EBV), but only an inconsistent relationship has been identified in undifferentiated carcinomas occurring at other sites. We investigated 22 formalin-fixed, paraffin-embedded cases of sinonasal undifferentiated carcinomas (SNUCs) occurring in Western and Asian patients. A highly sensitive in situ hybridization method was performed using an antisense oligonucleotide probe to the EBER1 gene of EBV. We identified EBV RNA in seven of 11 SNUCs from Asian patients, but in none of the Western SNUC patients (0/11). The EBER1 signal was present in all or virtually all of the tumor cell nuclei in the seven EBV-RNA-positive Asian SNUCs. The latent membrane protein-1 (LMP1) of EBV was not identified in any of the five positive cases tested. Our results suggest that genetic predisposition or environmental/geographical cofactors play an important role in determining the strength of the association of SNUC with EBV.