Concordance Study of CD30 Expression Detected By Multiple Immunohistochemistry Assays and Ventana CD30 Assay in Chinese Lymphoma Patients

Background: CD30 is emerging as an important biomarker guiding the clinical diagnosis, treatment, and evaluating the efficacy and prognosis of lymphoma. However, there is no standard procedure for specification and interpretation of the pathological detection of CD30 in China. This study intends to evaluate the staining and interpretation concordance of CD30 expression detected by the VENTANA CD30 assay and other multiple immunohistochemistry (IHC) assay in Chinese malignant lymphoma patients. Design: This is a multi-center, observational study enrolling 1,000 adult patients with a diagnosis of histologically confirmed malignant lymphoma in China. Patients, aged 18 years or older at diagnosis and who provided available formalin-fixed paraffin-embedded (FFPE) samples stored within 2 years, with diagnosis of classical Hodgkin's lymphoma, anaplastic large-cell lymphoma, large cell transformation of mycosis fungoides, diffuse large B-cell lymphoma, primary mediastinal B-cell lymphoma, extranodal NK/T-cell lymphoma, peripheral T cell lymphoma not otherwise specified, angioimmunoblastic T-cell lymphoma, and pcCD30+ T-cell lymphoproliferative disease were eligible to participate. Exclusion criteria included sample insufficiency for CD30 testing, incomplete sample information, lack of written informed consent. Methods: Each eligible patient provides an available r FFPE sample. Tissue slides obtained from each eligible FFPE sample will be stained by the VENTANA CD30 assay and at least one of the following IHC assays [umAB256 (zhongshanjinqiao) + Ventana BenchMark; Ber-H2 (Maixin) + Ventana BenchMark；Ber-H2 (Maixin) + DAKO; Ber-H2 (DAKO) + DAKO; Ber-H2 (DAKO) + Ventana BenchMark;umAB256 (Zhongshanjinqiao) + Leica; JCM182 (Leica) + Ventana BenchMark;JCM182 (Leica) + Leica; Ber-H2 (DAKO) + Leica]. CD30 expression of all immunostained slides will be independently interpreted as a percentage of CD30 positive cells by trained pathologists. The primary endpoint will be the staining concordance of percentages of positive cells for CD30 expression detected by each of the nine IHC assays and VENTANA CD30 assay (interpreted by expert panel) Secondary endpoints will be the interpretation concordance of pathologists at sites and the expert panel by assessing CD30 expression detected by various IHC assays. Both primary and secondary endpoint will be evaluated by intraclass correlation coefficient ICC, Bland-Altman, and Pearson correlation method. Discussion: This planned study will explore more equivalent testing methods to detect the expression of CD30 in Chinese patients with lymphoma. Disclosures Shi: Takeda Pharmaceuticals: Current Employment. Li: Takeda Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Other: Receiving lecture fees.

67 B-cell receptor heavy chain repertoire profiling using an augmented transcriptome

BackgroundComprehensive profiling of the tumor and tumor microenvironment (TME) is a critical tool for furthering our understanding of tumor progression and response to treatment, including immunotherapies. To address this challenge, we developed an augmented, immuno-oncology-optimized exome/transcriptome platform, ImmunoID NeXTTM, which provides a more comprehensive view of the tumor and TME from limited FFPE tumor biopsies. We have recently added the ability to profile the B-cell receptor (BCR) heavy chain. Here, we show that ImmunoID NeXT is now able to accurately and reproducibly profile abundant B-cell clones and provide information on the diversity of B-cells in tumor samples.MethodsWe analyzed multiple replicates of PBMCs to examine the reproducibility of BCR sequence identification using ImmunoID NeXT. Utilizing a standalone BCR sequencing approach, we further evaluated the concordance of top clones to those identified by ImmunoID NeXT. In addition, we analyzed the reproducibility of BCR sequences in patient-derived FFPE samples. Finally, we used ImmunoID NeXT to profile the B-cell clonal diversity across over 500 solid tumor samples.ResultsReproducibility in PBMC samples was very high, with abundances of clones shared between replicates being very concordant (R2>0.92, R2>0.86, and R2>0.97 for IgG, IgM, and IgA, respectively). When comparing to a standalone BCR sequencing method that profiles IgM and IgG, we observed highly concordant abundances (R2>0.72 and R2>0.82 in IgM and IgG, respectively), as well as strong overlaps of top clones. When comparing subsequent curls of a tumor FFPE sample, we also achieved a high concordance of clonal abundances (R2>0.92, R2>0.93, and R2>0.76 for IgG, IgM, and IgA, respectively). Finally, we observed differences in clonal diversity of B-cell repertoires across over 500 solid tumor samples.ConclusionsWe demonstrate that ImmunoID NeXT can be used to reproducibly, sensitively, and accurately profile high-abundance BCR heavy chain clones, including coverage of all major isotypes. In addition, we show how ImmunoID NeXT can profile the diversity of the BCR repertoire across a variety of tumor samples. Combined with the platform’s TCR profiling capabilities, ImmunoID NeXT can provide insight into the diversity of the immune repertoire, contributing to its ability to provide comprehensive analysis of both the tumor and TME from a single FFPE sample.

Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples

Background. Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same tumor. Results. We first compared the calls between an FF and an FFPE sample from a metastatic prostate tumor, showing that on average 50% of the calls in the FF are recovered in the FFPE sample, with notable differences between variant callers. Combining the variants of the different callers using a simple heuristic, increases both the precision and the sensitivity of the variant calling. Validating the heuristic on nine additional matched FF-FFPE samples, resulted in an average F1-score of 0.58 and an outperformance of any of the individual callers. In addition, we could show that part of the discrepancy between the FF and the FFPE samples can be attributed to intra-tumor heterogeneity (ITH). Conclusion. This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.

Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples

Background. Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same tumor. Results. We first compared the calls between an FF and an FFPE from a metastatic prostate tumor, showing that on average 50% of the calls in the FF are recovered in the FFPE sample, with notable differences between variant callers. Combining the variants of the different callers using a simple heuristic increases both the precision and the sensitivity of the variant calling. Validating the heuristic on nine additional matched FF-FFPE samples, resulted in an average F1-score of 0.58 and an outperformance of any of the individual callers. In addition, we could show that part of the discrepancy between the FF and the FFPE samples can be attributed to intra-tumor heterogeneity (ITH). Conclusion. This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.

Comparative analysis of somatic variant calling on matched FF and FFPE WGS from a metastatic prostate sample

Background. Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, do collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artifacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same prostate metastatic tumor. Results. We first compared the calls between FF and FFPE, showing that on average 50% of the calls in FF are recovered in FFPE, with notable differences between variant callers. Remarkably, this overlap was better than the overlap between different variant callers on the same sample. Inspecting the Variant Allele Frequency (VAF), we observed that many of the calls common to FF and FFPE belonged to the same clonal subpopulation but were detected at a lower VAF in FFPE. We also demonstrated that these calls receive higher significance scores and are often identified by more than one variant caller. Based on this observation, we propose a simple heuristic to perform reliable variant calling in FFPE samples. Our heuristic identified 3684 common calls at a F1-score of 0.83. Conclusion. This study illustrates that when using the correct variant calling strategy, the overlap between the FF and FFPE sample in somatic SNVs increases to such an extent that a large fraction of the calls detected in the FFPE sample are contained in the FF sample and the number of variants unique to each sample remains restricted. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.