Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer

PURPOSE

The progression of ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) in humans is highly variable. To better understand the relationship between them, we performed a multi-omic characterization of co-occurring DCIS and IBC lesions in a cohort of individuals.

METHODS

Formalin-fixed paraffin-embedded tissue samples from 50 patients with co-occurring DCIS and IBC lesions were subjected to DNA-seq and whole transcriptome RNA-seq. Paired DCIS and IBC multi-omics profiles were then interrogated for DNA mutations, gene expression profiles and pathway analysis.

RESULTS

Most small variants and copy number variations were shared between co-occurring DCIS and IBC lesions, with IBC exhibiting on average a higher degree of additional mutations. However, 36% of co-occurring lesions shared no common mutations and 49% shared no common copy number variations. The most frequent genomic variants in both DCIS and IBC were PIK3CA, TP53, KMT2C, MAP3K1, GATA3 and SF3B1, with KMT2C being more frequent in DCIS and TP53 and MAP3K1 more frequent in IBC, though the numbers are too small for definitive conclusions. The most frequent copy number variations were seen in MCL1, CKSB1 and ERBB2. ERBB2 changes were not seen in IBC unless present in the corresponding DCIS. Transcriptional profiles were highly distinct between DCIS and IBC, with DCIS exhibiting upregulation of immune-related signatures, while IBC showed significant overexpression in genes and pathways associated with cell division and proliferation. Interestingly, DCIS and IBC exhibited significant differential expression of different components of extracellular matrix (ECM) formation and regulation, with DCIS showing overexpression of ECM-membrane interaction components while IBC showed upregulation of genes associated with fibronectin and invadopodia.

CONCLUSION

While most co-occurring DCIS and IBC were mutationally similar and suggestive of a common clonal progenitor, transcriptionally the lesions are highly distinct, with IBC expressing key pathways that facilitate invasion and proliferation. These results are suggestive of additional levels of regulation, epigenetic or other, that facilitate the acquisition of invasive properties during tumor evolution.

Real-World Impact of Comprehensive Genomic Profiling on Biomarker Detection, Receipt of Therapy, and Clinical Outcomes in Advanced Non-Small Cell Lung Cancer

PURPOSE

Therapeutic decision making for patients with advanced non-small cell lung cancer (aNSCLC) includes a growing number of options for genomic, biomarker-guided, targeted therapies. We compared actionable biomarker detection, targeted therapy receipt, and real-world overall survival (rwOS) in patients with aNSCLC tested with comprehensive genomic profiling (CGP) versus small panel testing (SP) in real-world community health systems.

METHODS

Patients older than 18 years diagnosed with aNSCLC between January 1, 2015, and December 31, 2020, who received biomarker testing were followed until death or study end (September 30, 2021), and categorized by most comprehensive testing during follow-up: SP (≤52 genes) or CGP (>52 genes).

RESULTS

Among 3,884 patients (median age, 68 years; 50% female; 73% non-Hispanic White), 20% received CGP and 80% SP. The proportion of patients with ≥one actionable biomarker (actionability) was significantly higher in CGP than in SP (32% v 14%; P < .001). Of patients with actionability, 43% (CGP) and 38% (SP) received matched therapies (P = .20). Among treated patients, CGP before first-line treatment was associated with higher likelihood of matched therapy in any line (odds ratio, 3.2 [95% CI, 1.84 to 5.53]). CGP testing (hazard ratio [HR], 0.80 [95% CI, 0.72 to 0.89]) and actionability (HR, 0.84 [95% CI, 0.77 to 0.91]) were associated with reduced risk of mortality. Among treated patients with actionability, matched therapy receipt showed improved median rwOS in months in CGP (34 [95% CI, 21 to 49] matched v 14 [95% CI, 10 to 18] unmatched) and SP (27 [95% CI, 21 to 43] matched v 10 [95% CI, 8 to 14] unmatched).

CONCLUSION

Patients who received CGP had improved detection of actionable biomarkers and greater use of matched therapies, both of which were associated with significant increases in survival.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.

Race-Associated Genomic Correlates of Therapeutic Response in African American Patients With Non-Small-Cell Lung Cancer

PURPOSE

African American individuals are disproportionately affected by lung cancer in terms of incidence and mortality. In oncogene-driven non-small-cell lung cancer (NSCLC), emerging evidence indicates that underlying molecular heterogeneity, which can be affected by ancestry, contributes to variable drug sensitivity and therapeutic responses. The purpose of this study was to evaluate race-associated differences in reported treatment decisions, therapeutic outcomes, and molecular features in KRAS- and EGFR-mutant NSCLC.

MATERIALS AND METHODS

This is a retrospective study using real-world clinical-genomic data from health systems in the United States to evaluate race-associated outcomes in advanced-stage KRAS- or EGFR-driven NSCLC. Our overall objectives were to evaluate race-associated therapeutic outcomes and to describe molecular features in non-Hispanic Black (NHB) and non-Hispanic White (NHW) patients with NSCLC.

RESULTS

A total of 723 NSCLC patients with KRAS and 315 patients with EGFR oncogenic mutations were evaluated. In KRAS-mutant patients, variable outcomes were observed in NHB and NHW patients on the basis of receiving chemotherapy alone or in combination with immune checkpoint inhibitors. NHB patients received treatment at significantly lower rates compared with NHW patients. In the EGFR-mutant cohort, NHB and NHW patients received EGFR-targeted agents at similar rates, and overall survival was not significantly different. Race-associated differences in molecular features included a higher frequency of TP53 comutation in KRAS-mutant NHB patients and higher prevalence of EGFR G719S subtype in NHB patients.

CONCLUSION

In a real-world cohort of patients with NSCLC, we identified race-associated differences in therapeutic outcomes and described molecular characteristics in NHB and NHW patients with NSCLC. To proactively identify patients most likely to respond to systemic therapies, a more comprehensive approach is needed to help guide therapy selection in individualized patient populations.

Inferring Negative Molecular Biomarker Data at Scale

PURPOSE

Patients who represent the negative biomarker population, those tested for a biomarker but found to be negative, are a critical component of the growing molecular data repository. Many next-generation sequencing (NGS)-based tumor sequencing panels test hundreds of genes, but most laboratories do not provide explicit negative results on test reports nor in their structured data. However, the need for a complete picture of the testing landscape is significant. Syapse has created an internal ingestion and data transformation pipeline that uses the power of natural language processing (NLP), terminology management, and internal rulesets to semantically align data and infer negative results not explicitly stated.

PATIENTS AND METHODS

Patients within the learning health network with a cancer diagnosis and at least one NGS-based molecular report were included. To obtain this critical negative result data, laboratory gene panel information was extracted and transformed using NLP techniques into a semistructured format for analysis. A normalization ontology was created in tandem. With this approach, we were able to successfully leverage positive biomarker data to derive negative data and create a comprehensive data set for molecular testing paradigms.

RESULTS

The application of this process resulted in a drastic improvement in data completeness and clarity, especially when compared with other similar data sets.

CONCLUSION

The ability to accurately determine positivity and testing rates among patient populations is imperative. With only positive results, it is impossible to draw conclusions about the entire tested population or the characteristics of the subgroup who are negative for the biomarker in question. We leverage these values to perform quality checks on ingested data, and end users can easily monitor their adherence to testing recommendations.

Race-specific genomic determinants of therapeutic response in African American NSCLC patients

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Background: African American (AA) individuals are disproportionately affected by lung cancer in terms of incidence and mortality, despite lower tobacco exposure compared to Caucasian Americans (CA). Since molecular profiling is critically important to guide therapy selection in non-small cell lung cancer (NSCLC), we compared treatment-relevant molecular data in a cohort of AA and CA patients with EGFR or KRAS-driven NSCLC. Methods: This is a retrospective study using a clinicogenomic electronic medical record database from health systems in the United States designed to evaluate outcomes in advanced stage NSCLC. Eligibility criteria for analysis included a diagnosis of NSCLC between 2010 and 2020, stage III or IV, available race/ethnicity data, and identification of common KRAS or EGFR activating variant within 60 days of diagnosis. The primary objective was to define the type of EGFR or KRAS activating variant and determine the frequency of co-occurring alterations in NSCLC-associated genes by cohort (AA and CA). Secondary objectives included examining the timing of genetic testing and use of targeted therapy in these cohorts. Results: A total of 642 NSCLC patients with KRAS (15.0% AA; 81.6% CA) and 348 patients with EGFR oncogenic mutations (13.8% AA; 70.1% CA) met inclusion criteria. Mean time from diagnosis to first molecular test result was 20.9 days for AA vs. 19.9 days for CA (p = 0.5). The EGFR G719S variant was more prevalent in the AA cohort (6.3% AA v 0.4%) with no significant differences observed in the most common KRAS or EGFR variants tested (Table). A total of 100 KRAS-mutant patients (16 AA, 86 CA) had a reported result in at least one co-mutation of interest. The most frequent co-mutations were TP53 (81.3% AA v 65% CA, p = 0.92); KEAP1 (18.8% AA v 8.3% CA, p = 0.52); ATM (18.8% AA v 9.5% CA, p = 0.54); and PTEN (0% AA v 8.3% CA, p = 0.5). A total of 35 EGFR-mutant patients (4 AA, 31 CA) had a co-mutation reported in TP53 (75% AA v 65% CA, p = 0.77). EGFR targeted therapy was reported in 47.9% of AA and 52.9% of CA (p = 0.639). In the KRAS-mutant cohort, delivery of immune checkpoint inhibitors (ICIs) was reported in 29.2% of AA and 39.3% of CA (p = 0.08); chemotherapy was reported in 36.5% AA and 45.2% of CA (p = 0.14). Delivery of both ICI and chemotherapy was reported in 13.5% of AA and 21.9% of CA (p = 0.08). Conclusions: In a real-world cohort of NSCLC patients, we found similar frequencies of common KRAS and EGFR variants in AA and CA, but higher rates of EGFR G719S variant in AA patients. A more comprehensive analysis is needed to further evaluate the trends in co-mutations observed in our analysis, to determine the race-specific impact of these alterations in EGFR and KRAS-driven NSCLC.[Table: see text]

Actionability of comprehensive genomic profiling (CGP) compared to single-gene and small panels in patients with advanced/metastatic non-small cell lung cancer (aNSCLC): A real-world study

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Background: Biomarker testing for patients with aNSCLC includes testing for specific alterations in single genes, hotspot multigene panels, or CGP. Historically, CGP has been used following progression on early lines of systemic therapy to identify genomic alterations not captured by single-gene/hotspot testing, or to determine clinical trial(CT) eligibility. We compared the proportion of patients with genomic alterations for which FDA has approved targeted therapies(TT) (actionable alterations) identified through CGP vs. single-gene/small panel(“small panel”) testing in the real-world setting. Methods: In a retrospective study, patients initially diagnosed-with/progressed-to aNSCLC between 1/1/2015-12/31/2020, treated in the US community health setting, were categorized based on small panel or CGP testing. Patients were followed until the earliest of last contact/death/study-end on 9/30/2021. Testing between 30 days prior to initial NSCLC diagnosis and end of follow-up was used to determine actionability based on OncoKB levels, and eligibility for two basket-CTs(ASCO-TAPUR, NCI-MATCH). Results: Of 7,242 aNSCLC patients in this study, 5,154 (72%) received molecular testing (50% only small panel; 14% CGP; and 7% with an unknown size panel), 22% of patients remained untested and 7% were tested for only PD-L1. Among CGP-tested patients evaluated for tumor mutational burden (TMB), 18% were classified as TMB-High. > 75% of patients presented with advanced cancer at initial diagnosis, 51% were female, 50% were White, and median age was 68 years. Molecular testing rate increased from 9% to 20%(CGP) and 42% to 51%(small panel) between 2015–2020. The proportion of patients with ≥1 actionable biomarker was significantly higher with CGP than small panels (34%vs.15%; p < 0.001). Of tested patients. the proportion of CT eligible patients was also significantly greater for CGP than small panels (56%vs.4%; p < 0.001). The proportion of tested patients that received an FDA-approved TT or immunotherapy(IO) within 30 days of testing was higher in CGP cohort compared to small panel (9%vs.3%; p < 0.001). Conclusions: Although rates of CGP and small panel testing are increasing over time, overall molecular testing remains underutilized, and the proportion of patients who received TT/IO post-testing is low. Use of CGP is associated with higher identification of actionable biomarkers and patients receiving TT/IO, and CT eligibility.

Rapid adoption of immunotherapy in community health systems, associated with changing treatment guidelines

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Background: In the quickly evolving landscape of developmental therapeutics, uptake of new standards of care is a critical issue. Community health systems (CHS) provide > 50% of cancer care in the US. Rapidly changing immunotherapy (IO) guidelines provide a window into changing practice patterns. This analysis describes how IO use has evolved within CHS. Methods: Patients (pts) selected were ≥ 18 years, diagnosed with advanced or metastatic NSCLC 2015-2020, with 2+ EHR encounters before 4/1/2021. Two sub cohorts were analyzed. Cohort 1: pts receiving IO in any line of therapy (L); first use of IO by L was assessed over time. Cohort 2: pts receiving any first L (1L) therapy; 1L use of IO, alone or with chemotherapy (IO combo), was assessed over time. Results: In cohort 1, IO use in 1L grew from 24% of all IO pts in 2016 to 93% in 2020, increasing from 33% in Q4 2016 to 62% in Q1 2017. In cohort 2, 1L therapy shifted from 4% of all pts receiving IO in 1L in 2016 to 59% in 2020, increasing from 6% in Q4 2016 to 24% in Q1 2017. Within IO 1L pts, IO combo use grew from 29% to 68% in 2020, increasing from 35% in Q1 2018 to 53% in Q2 2018. Conclusions: We observed two rapid shifts in care patterns. First, 1L IO use grew rapidly from Q4 2016 to Q1 2017, following 1L IO approval (10/2016). Second, 1L IO use shifted rapidly toward IO combo use from Q1 2018 to Q2 2018, coinciding with pivotal trial results and FDA priority review (4/2018), but preceding label expansion (8/2018). Two RWD analyses from independent oncology practices observed less substantial shifts during similar periods of time. These results demonstrate that CHS can rapidly adjust to evolving clinical evidence and associated changes in standards of care.[Table: see text]

Biomarker testing patterns among patients with early and late-onset metastatic colon cancer

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Background: Molecular testing is essential in considering targeted therapies, particularly for the increasing number of metastatic colon cancer (mCC) patients (pts) diagnosed at younger ages who may present with more aggressive disease. This analysis compares demographic and clinical characteristics, and biomarker testing and positivity rates of mCC pts diagnosed at younger versus older ages. Methods: We analyzed 1029 pts with mCC (stage IV at diagnosis) between 01/01/2016 - 12/31/2020 who received care in community health systems in the United States. Pts 18-49 years at mCC diagnosis were considered early onset (EO), and those 50 or older were considered late onset (LO). We compared the distributions of year at diagnosis, gender, race/ethnicity, smoking status, histology, stage at diagnosis, tumor sidedness, KRAS, NRAS, and BRAF testing, and positivity rates between EO and LO mCC pts. Differences in distributions were assessed using chi-square tests. Results: EO pts (n = 148) were more likely to have left-sided tumors than LO pts (n = 881, 55% vs. 36%; p-value < 0.001), and were less likely to be ever smokers (24% vs. 40%; p-value < 0.001); the remaining demographic and clinical characteristics were similar between the two groups. Testing was significantly more common among EO than LO pts for KRAS (71% vs 48%), NRAS (39% vs 29%), and BRAF (41% vs 31%) (Table). Annual NRAS and BRAF testing rates increased between 2016 - 2020 for both groups: NRAS rates increased from 13% to 41%, and 5% to 37%, for EO and LO pts, respectively; BRAF rates increased from 13% to 41%, and 5% to 40%, for EO and LO pts, respectively. KRAS testing rates held at a consistent rate over time for EO pts, and increased over time among LO mCC pts (35% - 52%). The positivity rates for KRAS, NRAS and BRAF mutations were similar among tested pts in both groups. Conclusions: In this real world analysis, pts with EO mCC were more likely to have left sided primary cancers, and less likely to have a smoking history. Of note, BRAF testing showed a marked increase over time among all mCC pts. EO pts were more likely to receive KRAS, NRAS and BRAF testing. Further understanding of the correlates of EO mCC, biomarker testing practices, and subsequent treatment decisions is critical to improving pt outcomes.[Table: see text]

Abstract P3-08-05: Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer

Background: Simultaneous ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC) is very common. However, it is not clear how often these histologies are clonally related or the mechanism by which DCIS evolves into IBC. In this study we evaluated tissue samples of DCIS and IBC by DNA and RNA sequencing from 39 patients with concurrent disease.Methods: Patients were identified from the Swedish Cancer Institute Breast Cancer Database starting sequentially with 2018 backwards to identify candidates with simultaneous DCIS and IBC. Individual pathologic review was performed from the cohort of patients who had had modified radical mastectomy to select 50 cases for analysis of normal breast, DCIS, and invasive disease. Sequencing was performed using the Tempus xT solid tumor assay (DNA-seq of 648 genes at 500x coverage, full transcriptome RNA-seq). The mutations identified by this assay include germline and/or somatic single nucleotide variants, insertions/deletions, and copy number variations. Results: Thirty-nine cases had adequate tissue for both DCIS and IBC for DNA and 31 for RNA analysis. DCIS and IBC were in the same quadrant of the breast for all cases. All IBC cases were ductal carcinoma. 38/39 IBC were estrogen receptor (ER) positive, 33/39 were progesterone receptor (PR) positive. 5 were HER2/neu amplified (three ER+/PR-, 1 ER+/PR+, 1 ER/PR-). 32/39 had Ki67 of 20% or less (IQR 14(9,19.5)). 35/39 were T1 or T2. Three were T3 and one T4. 21/39 were N0, 4/39 N1mic, 9/39 N1a, 3/33 N2a 2/39 N3a.For DCIS 24/39 had both genomic variants and copy number changes (V+C+), 7/39 were V+C-, 5/39 were V-C+ and 3/39 V-C-. For IBC 25/39 were V+C+, 7/39 were V+C-, 6/39 were V-C+, and 1/39 V-C-. In total, there were 36 unique genomic variants seen in DCIS but not the corresponding invasive sample. In contrast, there were 32 total unique variants seen in invasive but not the corresponding DCIS and 38 variants were seen in both samples. The one BRCA variant seen in both samples of a single patient was BRCA1 p.Q284, a known pathogenic variant but gBRCA normal. There were 86 copy number changes seen in DCIS but not IBC, 75 copy number changes seen in IBC but not DCIS and 47 copy number changes seen in both DCIS and IBC. 24/39 patients shared at least one common variant and 22/39 shared at least one copy number change. 4/39 had no copy changes in either sample but all of these had genomic variants. 5/39 had no variants in either sample but all of these had copy number changes. PIK3CA was seen in 2/39 IBC, 2/39 DCIS and 2/39 in both. TMB IQR was 1.6(1.1, 3.4) for IBC and 2.1 (1.1,3.2) for DCIS. All samples tested for MSI were stable. Only one patient had identical genomic variants and copy changes in both DCIS and IBC. The most frequent changes were:

RNA sequencing revealed 1178 genes with significant gene expression differences between paired DCIS and IBC (q&lt;0.001). RNA-seq data was quantified using Kallisto and differential gene expression was assessed using DESeq2. Pathway enrichment was performed using rank GSEA against the MSigDB C2 collection (filtered to KEGG, Reactome and Biocarta pathways only). Upregulated pathways in DCIS involved more immunogenic pathways while IBC upregulated pathways involved proliferation and cell cycling. Conclusions: The transition from DCIS to IBC is a dynamic process. How much of these differences are the result of tumor heterogeneity and temporal factors as opposed to truly separate clones will require more study. This could have significant implications for the treatment of DCIS.

VariantGain/Loss of FunctionIBC onlyDCIS onlySame in BothTotalTP53Loss53614MAP3K1Loss51511GATA3Gain3249KM2TCLoss0538PTENLoss2237Copy ChangeMCL1 (1q21.2)Gain68822CKS1B (1q21.3)Gain95619ERRB2 (17q12)Gain0459JAK1 (1p31.3)Loss2428IKZF1 (7p12.1)Loss2327

Citation Format: Henry G Kaplan, Anna B Berry, Alexa Dowdell, Brian Piening. Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-08-05.

A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee

Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which we define as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.

Abstract 2618: Staged analysis of standard of care tumor molecular testing among patients with metastatic colorectal cancer in the community health system setting

Background: National Comprehensive Cancer Network guidelines have recommended metastatic colorectal cancer patients (mCRC pts) undergo BRAF, KRAS, NRAS, and microsatellite instability/mismatch repair deficiency (MSI/MMR) testing since 2015. Previous studies have reported molecular testing rates from academic and community cancer centers, but there is a lack of information on testing rates in community health systems (HS) which account for approximately half of US cancer care.

Methods: Tumor molecular testing rates were assessed in a first stage analysis for pts with mCRC in HS, in order to inform a second stage analysis focused on treatment decisions and pt outcomes. For the first stage analysis, we randomly selected 200 pts (50 pts from each of 4 HS sites) diagnosed with mCRC between 1/1/2015 and 9/1/2020. The 200 pts were identified through technology-enabled curation, followed by retrospective review performed by certified tumor registrars. An anticipated cohort of 1000 evaluable pts is planned for the second stage analysis.

Results: 53% of pts were tested for all four biomarkers at some point during their care (Table). Pts more likely to have been tested include those: from HS Site 1 (P = 4.2x10-5); age &lt;65 years old at mCRC diagnosis (P = 0.014); and with commercial insurance (P = 0.015). Among pts tested, the median times from metastatic diagnosis to BRAF, KRAS, and NRAS testing results were 35, 33, and 34 days, respectively.

Conclusion: This first stage analysis of molecular testing in mCRC pts revealed variation in testing rates by site, biomarker, and patient characteristics, which may in part be explained by the implementation of a precision medicine testing program at HS Site 1. A second stage analysis assessing the impact of biomarker testing on treatment decisions and pt outcomes will be guided by this initial characterization of testing rates and possible confounders.

Biomarker testing rates among metastatic colorectal patients across four health system sitesSite 1 (n=50)Site 2 (n=50)Site 3 (n=50)Site 4 (n=50)BRAF tested43 (86%)25 (50%)24 (48%)26 (52%)Count (%)KRAS tested44 (88%)35 (70%)32 (64%)35 (70%)Count (%)NRAS tested42 (84%)23 (46%)26 (52%)30 (60%)Count (%)MSI/MMR tested49 (98%)37 (74%)44 (88%)44 (88%)Count (%)All biomarkers tested40 (80%)19 (38%)20 (40%)26 (52%)Count (%)

Citation Format: Chenan Zhang, Mahder Teka, Francesca F. Coutinho, Joseph R. Burkhart, Louise E. Widmer, Ronda G. Broome, Mary T. Tran, Michael A. Thompson, Antony M. Ruggeri, Jennifer J. Godden, James L. Weese, Douglas J. Reding, Anna B. Berry, Yanina Natanzon, Thomas D. Brown. Staged analysis of standard of care tumor molecular testing among patients with metastatic colorectal cancer in the community health system setting [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 2618.

The Cancer Immunotherapy Biomarker Testing Landscape

CONTEXT.—

Cancer immunotherapy provides unprecedented rates of durable clinical benefit to late-stage cancer patients across many tumor types, but there remains a critical need for biomarkers to accurately predict clinical response. Although some cancer immunotherapy tests are associated with approved therapies and considered validated, other biomarkers are still emerging and at various states of clinical and translational exploration.

OBJECTIVE.—

To provide pathologists with a current and practical update on the evolving field of cancer immunotherapy testing. The scientific background, clinical data, and testing methodology for the following cancer immunotherapy biomarkers are reviewed: programmed death ligand-1 (PD-L1), mismatch repair, microsatellite instability, tumor mutational burden, polymerase δ and ε mutations, cancer neoantigens, tumor-infiltrating lymphocytes, transcriptional signatures of immune responsiveness, cancer immunotherapy resistance biomarkers, and the microbiome.

DATA SOURCES.—

Selected scientific publications and clinical trial data representing the current field of cancer immunotherapy.

CONCLUSIONS.—

The cancer immunotherapy field, including the use of biomarker testing to predict patient response, is still in evolution. PD-L1, mismatch repair, and microsatellite instability testing are helping to guide the use of US Food and Drug Administration-approved therapies, but there remains a need for better predictors of response and resistance. Several categories of tumor and patient characteristics underlying immune responsiveness are emerging and may represent the next generation of cancer immunotherapy predictive biomarkers. Pathologists have important roles and responsibilities as the field of cancer immunotherapy continues to develop, including leadership of translational studies, exploration of novel biomarkers, and the accurate and timely implementation of newly approved and validated companion diagnostics.

Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine

Biospecimens acquired during routine medical practice are the primary sources of molecular information about patients and their diseases that underlies precision medicine and translational research. In cancer care, molecular analysis of biospecimens is especially common because it often determines treatment choices and may be used to monitor therapy in real time. However, patient specimens are collected, handled, and processed according to routine clinical procedures during which they are subjected to factors that may alter their molecular quality and composition. Such artefactual alteration may skew data from molecular analyses, render analysis data uninterpretable, or even preclude analysis altogether if the integrity of a specimen is severely compromised. As a result, patient care and safety may be affected, and medical research dependent on patient samples may be compromised. Despite these issues, there is currently no requirement to control or record preanalytical variables in clinical practice with the single exception of breast cancer tissue handled according to the guideline jointly developed by the American Society of Clinical Oncology and College of American Pathologists (CAP) and enforced through the CAP Laboratory Accreditation Program. Recognizing the importance of molecular data derived from patient specimens, the CAP Personalized Healthcare Committee established the Preanalytics for Precision Medicine Project Team to develop a basic set of evidence-based recommendations for key preanalytics for tissue and blood specimens. If used for biospecimens from patients, these preanalytical recommendations would ensure the fitness of those specimens for molecular analysis and help to assure the quality and reliability of the analysis data.

Abstract 997: Impact of a personalized medicine research program (PMRP), using targeted tumor profiling and a cloud based clinical trials matching platform, on clinical decision-making

Background: Cancer care is evolving to a model of precision medicine where genomic changes in a patient's tumor are used to inform individualized management (mgmt). The optimal approach and impact of tumor profiling on cancer care remain important research questions. We report the impact on clinical decision-making by results from a PMRP in a research practice.

Methods: A custom designed next generation sequencing (NGS) 68 gene alteration (GA) panel, covering clinically relevant genes and regions was developed in 2014. The NGS results were used to: 1) prioritize standard therapies; 2) match patients (pts) with clinical trials (CT); and 3) serve as a data mining resource. NGS testing was offered early in the course of mgmt. An Institutional Review Board approved prospective registration protocol (PMRP) was activated in 2014, with the objective of establishing a centralized longitudinal, molecular phenotypic, and research data repository. Primary endpoints include proportion of pts where NGS impacted mgmt, to include enrollment onto CT. A cloud-based informatics platform was developed to: manage PMRP; facilitate CT matching; perform quality assurance/quality improvement; pursue research initiatives.

Results: As of 11/15/2016, 869 pts gave informed consent, with 844 pts enrolled. The top primary sites included: breast (115); colorectal (111); central nervous system (103); lung (91); ovary (49); hematologic malignancies (46); pancreas (37); uterus (28); esophagus (25); skin (21). Of solid tumor pts with documented clinical stage, 130 (40%) pts had early stage cancer (I, II and III), and 193 (60%) pts had advanced stage (IV) cancer. NGS results: 739 (88%) pts with GA found; 27 (3%) pts without GA. Of pts with GA, 178 (24%) pts had actionable (on-label drugs) GA and 476 (64%) pts had applicable (off-label or CT) GA, for a total of 546 (74%) pts with actionable and/or applicable GA. The top actionable GA were: KRAS (125); PIK3CA (17); BRAF (13); EGFR (12); NRAS (11); AKT1 (3); TET2 (2); ERBB2 (2); HRAS (2). The top applicable GA, included: TP53 (225); TPMT (78); TYMS (78); PIK3CA (77); APC (56); PTEN (52); IDH1 (34); CDNK2A (22); CTNNB1 (18); TET2 (16). Care mgmt impact was reported by physicians for 508 pts with actionable/applicable GA. Physicians reported mgmt impact, at time of reporting, for 105 (21%) pts, to include: new treatment (Tx) in 30 (6%) pts; no Tx given in 18 (4%) pts; Tx changed in 12 (2%) pts; Tx stopped in 1 (&lt;1%) pt; 6 (1%) pts enrolled onto CT. In 403 (79%) pts, physicians reported no mgmt impact, to include: insufficient evidence in 294 (58%) pts; drugs/CT access in 91 (18%) pts; refused Tx in 17 (3%) pts.

Conclusions: NGS profiling of tumors with this 68 GA panel has an impact on clinical decision- making in a minority, though substantial number, of pts. Impact on CT participation remains modest. Access to drugs and CT remains an important barrier.

Citation Format: Thomas D. Brown, Paul D. Tittel, Philip J. Gold, Charles W. Drescher, John M. Pagel, J D. Beatty, Patra Grevstad, Desiree Iriarte, Shlece Alexander, Madeleine Brindle, Xiaoyu Liu, Donielle O'connor, Mariko Tameishi, Danbin Xu, Anna B. Berry. Impact of a personalized medicine research program (PMRP), using targeted tumor profiling and a cloud based clinical trials matching platform, on clinical decision-making [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 997. doi:10.1158/1538-7445.AM2017-997

Nodular Fasciitis: Definitive Diagnosis by Fine Needle Aspiration

OBJECTIVES

Nodular fasciitis (NF) is a self-limited, mass-forming, fibrous proliferation that can occur in the head and neck and may mimic malignancy. Fine-needle aspiration biopsy (FNAB) is a minimally invasive, rapid, accurate method of obtaining diagnostic material from head and neck masses. In this study, we verify the usefulness of FNAB in obtaining a definitive diagnosis of NF.

METHODS

Cases were identified from our laboratory information system. Cytology slides were reviewed to note morphologic features and confirm diagnoses. Clinical history was obtained to document the case presentations and outcomes.

RESULTS

All 9 cases were found to have clinical presentations and common distinguishing morphologic features consistent with NF. Two cases were excised surgically, and the remainder regressed spontaneously. There were no recurrences.

CONCLUSIONS

FNAB can produce a definitive diagnosis of NF, providing an opportunity to avoid surgical excision in patients with a typical clinical presentation.

Reflex ImmunoCyt testing for the diagnosis of bladder cancer in patients with atypical urine cytology

BACKGROUND

ImmunoCyt/uCyt (Scimedx, Denville, NJ, USA) is a well-established urinary marker assay with high sensitivity for the diagnosis of urothelial carcinoma (UC) and can function as a second-level test to arbitrate atypical reads of urine cytology.

OBJECTIVE

To determine the utility of uCyt as a reflex test for atypical cytology in patients undergoing a hematuria evaluation or surveillance with a history of UC.

DESIGN, SETTING, AND PARTICIPANTS

The uCyt assay was performed as a second-level reflex test on all voided urine cytology tests read as atypical between January 2007 and June 2010 in an academic medical center. Records were retrospectively reviewed. Three hundred twenty-four patients underwent a total of 506 uCyt assays.

INTERVENTION

Reflex uCyt assay on atypical urine cytology.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The uCyt test characteristics include sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV).

RESULTS AND LIMITATIONS

Reflex uCyt was performed on 506 atypical voided urine samples that were followed by cystoscopy within 90 d. Reflex uCyt with a history of UC showed a sensitivity of 73%, a specificity of 49%, and an NPV of 80%. In those with a history of low-grade UC, reflex uCyt had a sensitivity of 75%, a specificity of 50%, and an NPV of 82%, while in those with a history of high-grade UC, it had a sensitivity of 74%, a specificity of 44%, and an NPV of 79%. Without prior history of UC, reflex uCyt had a sensitivity of 85%, a specificity of 59%, and an NPV of 94%. This study's limitations include its retrospective design and interobserver variability inherent to cystoscopy, which was used as the reference test.

CONCLUSIONS

When used as a reflex test on atypical urine cytology, negative uCyt may predict a negative cystoscopy in select patients and modulate the urgency and further work-up in those with no prior history or low-grade disease.

Mexican American women's expressions of the meaning of culturally congruent prenatal care

The purpose of this study was to describe, explicate, and systematically analyze the meanings, expressions, and experiences of generic and professional care during pregnancy of Mexican American women in their home and prenatal clinic contexts. The ethnonursing method was used to describe cultural care among 16 key and 34 general informants. Generic culture care was valued and considered essential by informants for healthy childbearing. Six major themes were synthesized from 30 cultural patterns: (a) generic culture care included the protection of the mother and fetus by older Mexican American women and was greatly influenced by religion and family beliefs and practices; (b) generic culture care was family obligation for provision of filial (family) succorance, sharing of self, and being with the childbearing mother; (c) culture care was respect for familial caring roles in relation to age and gender; (d) childbearing Mexican American women viewed culture care by professional nurses as concern for, professional knowledge, protection, being attentive to, and explaining; (e) culture care was use of the Spanish language in caring interactions in diverse environmental contexts; and (f) professional prenatal care was valued by Mexican American women and was influenced by legal, economic, and technological factors in the social structure.

Variability of Doppler flow velocity and cerebral perfusion pressure is reduced in the neonate by sedation and neuromuscular blockade

Doppler flow velocity (DFV) in the anterior cerebral artery was recorded every 12 h and cerebral perfusion pressure (CPP) continuously in 21 sick, ventilated preterm neonates for 48 h from shortly after birth. Ten received a neuromuscular blocker, seven were sedated with morphine infusions and five received neither of these treatments. Variability of DFV and CPP was assessed by the coefficient of variation (CV) and the autocorrelation function (ACF). Variability of both signals was lowest in the group treated by neuromuscular blockade (DFV CV 3, s.d. = 0.8; CPP CV 9, s.d. = 2.2; CPP ACF 37, s.d. = 19.2), intermediate in the group receiving sedation by morphine infusion (DFV CV 3.4, s.d. = 0.7; CPP CV 11, s.d. = 2.2; CPP ACF 31, s.d. = 21.6) and highest in the group receiving neither treatment (DFV CV 5, s.d. = 1.8; CPP CV 14, s.d. = 2.3; CPP ACF 27, s.d. = 16.7). Variability also increased with decreasing gestational age, suggesting that immature cerebrovascular regulatory mechanisms were present in the least mature neonates.

Fontanelle pressure and cerebral perfusion pressure: continuous measurement in neonates

Fontanelle pressure (FP) and cerebral perfusion pressure (CPP) were measured continuously for the first 5 postnatal days in 21 preterm neonates. A new application device for use with the sensor of an intracranial pressure monitor allows accurate, continuous FP measurement. Accuracy of the technique was established by comparing results using the new device with 14-h continuous intraventricular pressure recordings from four infants before ventricular shunting. Agreement between the two techniques was satisfactory with the mean difference being 0.4 mm Hg. FP rose on each of the first 5 days after birth. CPP also rose over the 5 days but there were periods during suctioning of the endotracheal tube, crying, and vigorous activity when CPP was very low.

Oesophageal atresia in father and daughter

We report oesophageal atresia without tracheo-oesophageal fistula in a father and daughter, the first case of recurrence of oesophageal atresia without fistula to be reported in a parent and offspring.