Statistical analysis of high-dimensional biomedical data: a gentle introduction to analytical goals, common approaches and challenges

BACKGROUND

In high-dimensional data (HDD) settings, the number of variables associated with each observation is very large. Prominent examples of HDD in biomedical research include omics data with a large number of variables such as many measurements across the genome, proteome, or metabolome, as well as electronic health records data that have large numbers of variables recorded for each patient. The statistical analysis of such data requires knowledge and experience, sometimes of complex methods adapted to the respective research questions.

METHODS

Advances in statistical methodology and machine learning methods offer new opportunities for innovative analyses of HDD, but at the same time require a deeper understanding of some fundamental statistical concepts. Topic group TG9 "High-dimensional data" of the STRATOS (STRengthening Analytical Thinking for Observational Studies) initiative provides guidance for the analysis of observational studies, addressing particular statistical challenges and opportunities for the analysis of studies involving HDD. In this overview, we discuss key aspects of HDD analysis to provide a gentle introduction for non-statisticians and for classically trained statisticians with little experience specific to HDD.

RESULTS

The paper is organized with respect to subtopics that are most relevant for the analysis of HDD, in particular initial data analysis, exploratory data analysis, multiple testing, and prediction. For each subtopic, main analytical goals in HDD settings are outlined. For each of these goals, basic explanations for some commonly used analysis methods are provided. Situations are identified where traditional statistical methods cannot, or should not, be used in the HDD setting, or where adequate analytic tools are still lacking. Many key references are provided.

CONCLUSIONS

This review aims to provide a solid statistical foundation for researchers, including statisticians and non-statisticians, who are new to research with HDD or simply want to better evaluate and understand the results of HDD analyses.

Comparison of AYA versus non-AYA ovarian cancer genomic landscape in NCI-MATCH trial

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Background: NCI-MATCH, a signal-finding precision medicine trial, centrally screened tumors from ̃6000 patients age > 18 with refractory/relapsed cancer using Oncomine Comprehensive Assay (OCA) targeted gene panel. Screened cohort included a subset of patients with ovarian cancer age 18-39 yrs, overlapping adolescent and young adult (AYA) range (NCI consensus definition: 15-39 yrs). Objective of this study was to compare tumor genomic features of AYA to non-AYA ovarian cancers. Methods: Patient clinicopathologic, demographic, and tumor mutation (SNVs, Indels, CNVs by central OCA) data from NCI-MATCH were available. Analyses were restricted to mutation profiles generated by OCA version 2 (OCA v2), which assessed 143 genes and was used for most samples. Proportions of cases with mutations in each gene were compared for AYA and non-AYA groups by 2-sided Fisher’s exact tests. For each gene, association between age (continuous independent variable) and presence of mutation (binary dependent variable) was assessed using logistic regression. Benjamini-Hochberg adjusted p-values were computed; false discovery rate (FDR) was controlled at 10%. Results: Data from 455 ovarian cancers (437 epithelial, 18 stromal), including 21 AYA and 434 non-AYA cases, were included in this analysis. Among the 28 genes most frequently (in > 6 patient tumors) mutated and altered, CTNNB1 was mutated in 9.5% of AYA patients compared to 0.9% in non-AYA (unadj. p=0.027) but failed to meet 10% FDR criterion (FDR-adj. p=0.7). KRAS mutation was more frequent in AYA than non-AYA but not significantly after adjustment (FDR-adj. p=0.7). Logistic regression results showed TP53 mutation was significantly associated with older age (FDR-adj. p<0.0001), and ATM mutation was borderline associated with younger age (FDR-adj. p=0.052). No other differences, including in clinically actionable mutations ( BRCA1/2, MSH2), were observed. Table displays selected results. Conclusions: This preliminary study shows that no genes were mutated in significantly different proportion between AYA and non-AYA groups, but modeling age as a continuous variable highlighted known association of TP53 mutation with older age and a trend towards association of ATM mutation with younger age. More comprehensive tumor mutation profiling and analyses of additional tumor types may reveal further insights into rare AYA cancers. [Table: see text]

Blood-based detection of actionable alterations from NCI-MATCH patients with no tissue results

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Background: The National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) multi-arm phase II clinical trial tested tumor tissue from 5,954 patients with advanced refractory cancer to assign treatment based on the molecular profile. Molecular profiling was successful for 93% of patients. For 267 of the patients who were not enrolled because molecular profiling was not successful, plasma cfDNA was evaluated to provide insight into the potential utility of blood-based testing in a broad spectrum of histologies when tissue is not evaluable. Methods: Cell-free DNA was extracted from plasma collected from Streck blood tubes and quantitated. Libraries were constructed using ³ 15 ng cfDNA into the Illumina TruSight Oncology 500 ctDNA RUO Assay, including unique molecular identifiers and duplex barcodes for error correction. Libraries were sequenced on the NovaSeq 6000 with S4 XP flow cells. Results: Of the 267 samples, 250 samples (94%) were evaluable, representing 72 histologies, including colorectal cancer (N = 36), lung adenocarcinoma (N = 15), pancreatic adenocarcinoma (N = 14), and invasive breast carcinoma (N = 12). Of these, 231 (92%) had ³ 1 OncoKB annotated mutation, with 208 patients (83%) having putative somatic mutations detected in genes not commonly associated with clonal hematopoiesis. The most common somatic mutations were in TP53, KRAS, APC, and PIK3CA, reported in 51%, 20%, 12%, and 12% of patients respectively. A total of 109 patients (44%) had ³ 1 actionable mutation of interest (aMOI) reported that could have been used for treatment assignment in the NCI-MATCH clinical trial. After applying histology and molecular exclusions, 75 patients (30%) had ³ 1 aMOI. The most common assignable treatment arms were Z1B/Z1BX1 (palbociclib with CCND1/2/3, N = 13), Z1F (copanlisib with PIK3CA Mutations, N = 13), S1/S1X1 (trametinib with NF1 mutation, N = 12), and Z1C/Z1CX1 (palbociclib with CDK4/CDK6 Amplification and Rb Expression by IHC, N = 10). Mutations in genes commonly associated with clonal hematopoiesis (CH) were prevalent in this population. Along with the expected high frequency of DNMT3A (21% of patients) and TET2 (11%) mutations, PPM1D mutations were the highest amongst CH genes, with 61 patients (24%) having ³ 1 PPM1D mutation, likely due to the heavily pre-treated nature of these patients. Conclusions: Variants observed in the blood are consistent with what is reported in the tissue. Using liquid biopsy when tissue is not evaluable can expand the ability of patients to obtain mutation information that can inform treatment compared to using tumor tissue only. Cell-free DNA provided valuable mutation information for these patients and could have resulted in up to an additional 75 patients being eligible for treatment selection based on their mutation profile. These results indicate that blood-based screening could be a tool for future NCI-sponsored clinical studies.

Phase II study of vismodegib in patients with SMO or PTCH1 mutated tumors: Results from NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol T

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Background: NCI-MATCH (EAY131) is a platform trial enrolling patients (pts) with solid tumors, lymphomas, or multiple myeloma to targeted therapies based on matching genomic alterations (NCT02465060). Subprotocol Arm T evaluated vismodegib (GDC0449), a hedgehog signaling pathway inhibitor with anti-tumor activity in pts with tumors harboring PTCH1 and SMO mutations. Methods: Pts whose tumors had SMO or PTCH1 mutations were eligible; results were confirmed by NCI-MATCH central labs if possible. Pts received oral vismodegib (150 mg daily) for 4-week cycles until progression/toxicity. Tumor response was assessed every 2 cycles. Primary endpoint was ORR; secondary endpoints included PFS, 6-month PFS, OS, and predictive biomarkers. Cutaneous basal cell carcinomas were excluded. Results: Of 34 pts enrolled (6/20/16 – 9/22/20); 2 were ineligible and 1 did not start therapy. The 31 analyzable pts’ demographics were primary tumor sites/histology [gastrointestinal (n = 9), skin/soft tissue (n = 7), gynecologic (n = 5), lung (n = 4), unknown primary (n = 4), ductal breast (n = 1), meningioma (n = 1)]; median age 64 (range 19-81); 48.4% women; 61.3% (19/31) > 3 lines of prior therapy; 74% (23/31) > 1 co-occurring mutation [median 2 co-alterations (range 1-20)]. 8/31 > 4 co-occurring alterations. 9 pts had SMO mutant tumors (all SNVs); 5/9 had > 1 co-occurring gene alterations. 22 pts had PTCH1 alterations (7 SNVs and 15 indels); 18/22 pts had > 1 additional gene alteration. Of 31 analyzable pts, 22 were MATCH-confirmed (i.e. had central confirmation of tumor PTCH1/SMO mutations). MATCH-confirmed pts had ORR 9.1% (2/22) while all analyzable pts had ORR 6.5% (2/31). 2 PRs were seen in pts with a skin/soft tissue sarcoma ( PTCH) and a meningioma ( SMO) with a median duration of response 14 months. The 6-month PFS rate was similar in MATCH-confirmed and analyzable pts (22.4% and 23.2% respectively) and median PFS was identical at 1.8 months. Median OS was 9.1 months in MATCH-confirmed and 7.3 months in analyzable pts. Within analyzable SMO variants: 1 PR, 3 SD, 4 PD, and 1 unevaluable responses were documented. Within analyzable PTCH1 variants: 1 PR, 7 SD, 10 PD, and 4 unevaluable responses were seen. 4 pts (12.9%) discontinued therapy due to AE. Among 33 pts starting therapy, 18 (54.5%) had grade 1-2 toxicity, while 2 (6.1%) had grade 3 treatment-related toxicity. Most common toxicities: grade 1-2 fatigue (n = 11), anorexia (n = 8), weight loss (n = 7), alopecia (n = 7), and dysgeusia (n = 6). There were 4 on-study deaths, but none were treatment related. Conclusions: Although the primary endpoint was not reached, vismodegib was well-tolerated with mostly grade 1-2 toxicities and substantial responses were seen in patients with SMOPro641Ala and PTCHGlu947Ter alterations. Further study of the impact of concomitant molecular alterations may yield additional insights into vismodegib mechanisms of response. Clinical trial information: NCT02465060.

Abstract 160: LASSO-based protein signatures for survival prediction in human cancer cohorts

Background: Large-scale multi-omics data characterizing human tumors are increasingly available and can be leveraged to develop a deeper understanding of biological processes and predict clinical outcomes. Reverse-phase protein array (RPPA) is a high-throughput, antibody-based method that provides a more direct assessment of cellular activity compared to DNA and RNA sequencing, which generate data that do not always correlate with protein expression. Multiple studies have demonstrated the prognostic value of RPPA data. Some of these studies have used pathway-driven approaches, relying on prior knowledge from the literature to group proteins into biological pathways, to develop prognostic signatures or predictors of treatment response.

Methods: We obtained normalized RPPA data for up to 258 total, cleaved, acetylated, or phosphorylated protein species from The Cancer Proteome Atlas (TCPA). Starting from a published RPPA-based seven-protein signature of receptor tyrosine kinase (RTK) pathway activity in the form of an unweighted sum of the seven protein measurements, shown to have prognostic value in a 445-patient renal clear cell carcinoma cohort (TCGA-KIRC), we demonstrated that strong stratification of patients into high and low risk groups can be achieved by using a statistical approach—LASSO regression—with no a priori biological knowledge, to select from the 233 proteins and optimally combine their RPPA measurements into a weighted risk score. Method performance was assessed using two unbiased approaches: 1) 10 iterations of 3-fold cross-validation for unbiased estimation of hazard ratio and difference in 5-year survival (by Kaplan-Meier method) between predictor-defined high and low risk groups; and 2) a permutation test to evaluate the statistical significance of the cross-validated log-rank statistic.

Results: For the first evaluation approach, the median hazard ratio between high and low risk groups across the held-out folds in the cross-validation based on the 7-protein RTK score was 2.4, compared to 3.3 when using the risk score derived by LASSO applied to the training data folds. Furthermore, the median difference in overall survival probability at 5 years based on the LASSO-derived risk score was 32.8%, compared to 25.2% when using the 7-protein RTK score. The permutation test p values were 5.0e-4 for both the RTK pathway-driven and the LASSO data-driven approaches. Finally, we demonstrated the applicability and performance of our approach for overall survival prediction in additional TCGA cohorts; namely, ovarian serous cystadenocarcinoma (TCGA-OVCA), sarcoma (TCGA-SARC), and cutaneous melanoma (TCGA-SKCM).

Conclusions: The data-driven nature of our LASSO-based approach makes it versatile and particularly well-suited for the discovery of unexplored protein/disease associations that could aid in therapeutic discovery.

Citation Format: Mariam M. Konaté, Ming-Chung Li, Lisa McShane, Yingdong Zhao. LASSO-based protein signatures for survival prediction in human cancer cohorts [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 160.

A phase 2 study of defactinib (VS-6063) in patients with NF2 altered tumors: Results from NCI-match (EAY131) subprotocol U

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Background: The NCI-MATCH trial assigns patients (pts) with solid tumors, lymphomas, or multiple myeloma to targeted therapies based on genetic alterations identified in tumor biopsies. Neurofibromatosis 2 (NF2)-inactivated tumors demonstrate increased sensitivity to FAK inhibition in preclinical models. Arm U evaluated the FAK inhibitor defactinib in pts with NF2 altered tumors. Methods: Patients found to harbor an inactivating NF2 mutation on NGS were assigned to the ARM U substudy MATCH. Defactinib 400 mg was given by mouth twice daily until progression or intolerable toxicity. The primary endpoint was objective response rate (ORR). Secondary endpoints included toxicity, progression-free survival (PFS), and 6-month PFS. Results: Of 5,548 cases with sufficient tissue for genomic analysis, 51 pts were found to have NF2 alterations (< 1% of the total analyzed). While NF2 alterations are known to occur more commonly in meningiomas and mesotheliomas, alterations were also detected in an array of other tumor types, including renal cell carcinomas and ovarian cancers. Thirty-five pts were ultimately enrolled; 33 patients were started on therapy, with 2 of those determined to be ineligible for outcome analysis. All pts had received at least one prior therapy, with 52% (16/31) having received 3 or more prior lines of therapy. Median follow-up was 35.9 months. ORR [90% CI] was 3% (1/31, [0.16, 14.86]), with the one partial response in a pt with choroid meningioma. Of the twelve pts whose best response was stable disease (39%, 12/31), 8 demonstrated some degree of tumor shrinkage (Table) with a disease control rate of 42% (13/31). Median PFS was 1.9 months for the 31 eligible pts who received study treatment, with median PFS of 9.3 months for the 9 patients who had a best response of stable disease or better. Six pts achieved a PFS of greater than 5.5 months. Among all treated pts (n=33), the most common treatment-related toxicities were fatigue (36%), nausea (33%), and hyperbilirubinemia (27%). There were no grade 4 or 5 toxicities; 27% of pts had grade 3 toxicities. No correlation could be made between clinical outcomes and tumor histology or specific NF2 genotype. Conclusions: Defactinib monotherapy had limited clinical activity in this cohort of previously treated patients with solid tumors exhibiting NF2 loss. Clinical trial information: NCT04439331. [Table: see text]

Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group

Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC's Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors' presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.

Abstract CT061: Binimetinib in patients with tumors with NRAS mutations: NCI-MATCH ECOG-ACRIN Cancer Research Group subprotocol EAY131-Z1A

Background: NRAS-mutations are established oncologic drivers in many malignancies with no effective targeted therapy options. Preclinical and clinical data have suggested that downstream inhibition with a MEK inhibitor, such as binimetinib, might be efficacious for NRAS-mutated cancers. Methods: Patients who enrolled in the multicenter NCI-MATCH trial master protocol underwent tumor biopsy and molecular profiling by targeted next generation sequencing with a custom Oncomine AmpliSeq™ panel. Patients with refractory solid tumors harboring codon 12, 13, or 61 NRAS-mutations were enrolled in subprotocol Z1A, a single arm study of binimetinib 45 mg twice daily. Patients with melanoma were excluded. The primary endpoint was objective response rate (ORR). Secondary endpoints included progression-free survival (PFS) and overall survival (OS). A post-hoc analysis examined association of NRAS-mutation allele with outcome and histology. Results: 47 eligible patients with refractory solid tumors harboring codon 12, 13, or 61 NRAS-mutations were treated on this trial. The most common cancer types enrolled on this subprotocol were colorectal adenocarcinoma (24/47, 51%), cholangiocarcinoma (7/47, 15%), low-grade papillary serous carcinoma of the ovary (3/47, 6%), and endometrioid endometrial adenocarcinoma patients (3/47, 6%). Observed toxicity was moderate, similar to previous reports, and 27.7% (13 of 47) of eligible patients discontinued binimetinib because of adverse events. The ORR was 2.1% (1 of 47 patients), and the median PFS was 3.5 months. The sole confirmed partial response (PR) was observed in a codon 61 NRAS-mutated indolent malignant ameloblastoma. One patient with a colorectal cancer harboring a NRAS codon 61 mutation had an unconfirmed PR, and two others with NRAS codon 61 mutated colorectal cancer had stable disease for at least 12 months. In a post-hoc analysis, patients with cancers bearing a codon 61 NRAS-mutation (n=22) had a significantly longer OS (p=0.04) and PFS (p=0.006) than those with tumors harboring codon 12 or 13 NRAS-mutations (n=25). Similarly, colorectal cancer patients with NRAS codon 61 mutations treated with binimetinib (n=8) had a significantly longer OS (p=0.03) and PFS (p=0.007) than those with NRAS codon 12 or 13 mutated (n=16) tumors. Conclusions: Single-agent binimetinib did not demonstrate promising efficacy in NRAS-mutated solid tumors. Further studies are needed to clarify whether the increased OS and PFS observed in codon 61 NRAS-mutated cancers reflects a more favorable prognosis for this subtype.

Citation Format: James M. Cleary, Victoria Wang, Rebecca Heist, Scott Kopetz, Edith P. Mitchell, James Zwiebel, Helen X. Chen, Shuli Li, Robert Gray, Lisa McShane, Larry Rubinstein, David Patton, Funda Meric-Bernstam, Melissa Dillmon, Mickey Williams, Stanley Hamilton, Barbara Conley, Peter O'Dwyer, Lyndsay Harris, Carlos Arteaga, Alice Chen, Keith Flaherty. Binimetinib in patients with tumors with NRAS mutations: NCI-MATCH ECOG-ACRIN Cancer Research Group subprotocol EAY131-Z1A [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT061.

Phase II study of copanlisib in patients with tumors with PIK3CA mutations (PTEN loss allowed): NCI MATCH EAY131-Z1F

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Background: The NCI-MATCH (EAY131) is a platform trial that enrolls patients (pts) with solid tumors, lymphomas, or multiple myeloma to targeted therapies based on matching genomic alterations of interest (NCT02465060). Arm Z1F evaluated copanlisib, a highly selective, pan-Class 1 PI3K inhibitor with predominant activity against both the δ and α isoforms in pts with PIK3CA mutations. Methods: Pts received copanlisib (60 mg IV) on days 1, 8, and 15 in 28-day cycles until progression/toxicity. Tumor assessment was every 2 cycles. The primary endpoint was objective response rate (ORR); secondary endpoints were PFS, 6-month PFS, and predictive biomarkers. Pts with KRAS mutations, HER2+ve breast cancers, lymphomas were excluded. Results: 35 pts were enrolled (from 8/2/18 to 12/27/18), of which, 28 pts were available for analysis (7 patients, not eligible or did not start therapy). Multiple histologies were enrolled with gynecologic (n = 7), gastrointestinal (n = 6), and genitourinary (n = 5) the most common tumors. Median age 61 (range 42-78). 75% of pts had ≥ 3 lines of prior therapy. 54% of PIK3CA mutations were located in the helical domain, 32% in kinase domain and 14% in other domains. Twenty-six pts had co-occurring gene alterations (median 3; range 1-9), with 9 patients having 4 or more gene alterations. The ORR was 11% (3/28, 90% CI: 3%-25%). Partial responses were seen in uterine cancer, clear cell carcinoma of anterior abdominal wall, and liposarcoma. 6 pts had > 6 months of stable disease and clinical benefit rate was 32% (9/28). Two pts are still on treatment. The most common reason for protocol discontinuation was disease progression (n = 18, 69%). Thirty pts were included for toxicity analysis. Ten pts (33%) had grade 1 or 2 toxicities, 16 pts (53%) had grade 3 toxicities, and one patient (3%) had grade 4 toxicity (CTCAE v5.0). Most common toxicities include hyperglycemia (n = 19), fatigue (n = 11), hypertension (n = 10), diarrhea (n = 10), and nausea (n = 9). Total of 5 deaths were reported, none related to treatment. Conclusions: Copanlisib showed meaningful clinical activity across various tumors with PIK3CA mutation in the late-line refractory setting. Further study either alone or in combinations in select tumors is warranted. G3/4 toxicities observed were consistent with reported toxicities for PI3K pathway inhibition. Clinical trial information: NCT02465060 .

Bioinformatics Tools and Resources for Cancer Immunotherapy Study

In recent years, cancer immunotherapy has emerged as a highly promising approach to treat patients with cancer, as the patient's own immune system is harnessed to attack cancer cells. However, the application of these approaches is still limited to a minority of patients with cancer and it is difficult to predict which patients will derive the greatest clinical benefit.One of the challenges faced by the biomedical community in the search of more effective biomarkers is the fact that translational research efforts involve collecting and accessing data at many different levels: from the type of material examined (e.g., cell line, animal models, clinical samples) to multiple data type (e.g., pharmacodynamic markers, genetic sequencing data) to the scale of a study (e.g., small preclinical study, moderate retrospective study on stored specimen sets, clinical trials with large cohorts).This chapter reviews several publicly available bioinformatics tools and data resources for high throughput molecular analyses applied to a range of data types, including those generated from microarray, whole-exome sequencing (WES), RNA-seq, DNA copy number, and DNA methylation assays, that are extensively used for integrative multidimensional data analysis and visualization.

Dabrafenib and trametinib in patients with tumors with BRAF V600E/K mutations: Results from the molecular analysis for therapy choice (MATCH) Arm H

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Background: The NCI-MATCH precision medicine trial assigns patients (pts) with solid tumors, lymphomas, or multiple myeloma with progression on prior treatment to a targeted therapy based on genetic alterations identified in pre-treatment biopsies. Arm H (EAY131-H) evaluated the combination of the BRAF inhibitor (inh) dabrafenib (DAB), and the MEK inh, trametinib (TRM), in pts with BRAF V600E/K mutations. Methods: Pts with melanoma, thyroid, or colorectal cancer were excluded. Pts with NSCLC were excluded after the U.S. Food and Drug Administration (FDA) approved DAB/TRM for this indication. Pts received DAB 150 mg po BID and TRM 2 mg PO daily on 28 day cycles until disease progression or intolerable toxicity; restaging was performed every 2 cycles. The primary endpoint was objective response rate (ORR); secondary endpoints included progression-free survival (PFS), 6-month PFS, and overall survival (OS). Results: A total of 35 pts were enrolled from 1/2016-2/2018; 2 were ineligible (CrCl below criteria; labs out of window). Over 17 distinct tumor histologies were represented. 58% of pts were female, median age was 63 (range 21-85), 94% were Caucasian, and 48% of pts had received at least 3 prior therapies (range 1- 8). The confirmed ORR was 33.3% (90% CI 19.9%, 49.1%), with a median duration of response (DoR) of 12 months (mon). Varied histologies had a DoR of > 12 mon: histiocytic sarcoma, cholangiocarcinoma and mixed adenoneuroendocrine carcinoma of unknown primary, among others. Median PFS was 9.4 mon; the 6 mon PFS rate was 70.6% (90% CI 58.2%-85.5%), and an additional 10 pts had a PFS > 5.5 mon. Median OS has not been reached. At the time of data cutoff (12/2018) 11 pts continue on treatment. Adverse events (AE) were comparable to previously reported profiles of DAB/TRM; no new AEs were identified. The most frequent grade 3 AEs were fatigue, neutropenia, hyponatremia, hypophosphatemia, and urinary tract infection; there was 1 grade 4 sepsis; no grade 5 AEs. Conclusions: In this pre-treated, mixed histology cohort, DAB and TRM showed promising activity outside of currently approved FDA indications warranting further investigations. Correlative analyses are planned. Clinical trial information: NCT02465060.

TMB standardization by alignment to reference standards: Phase II of the Friends of Cancer Research TMB Harmonization Project

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Background: Tumor mutational burden (TMB) is a predictive biomarker of response to immune checkpoint inhibitors across multiple cancers. In Phase 1 of the Friends of Cancer Research Harmonization Project, we demonstrated a robust correlation between TMB estimated using targeted next-generation sequencing (NGS) gene panels and whole exome sequencing (WES) applied to MC3-TCGA data. These findings demonstrated variability in TMB estimates across different panels. Phase 2 evaluates sustainable TMB reference standard materials for TMB alignment to assess this variability. The goal of this effort is to establish best practices for estimating TMB in order to improve consistency across panels, for the sake of optimizing clinical application and facilitating integration of datasets generated from multiple assays. Methods: Fifteen laboratories with targeted panels at different stages of development participated. We identified a set of reference standards consisting of 10 well-characterized human-derived lung and breast tumor-normal matched cell lines. WES was performed using a uniform bioinformatics pipeline agreed upon by all team members (WES-TMB). Each laboratory used their own sequencing and bioinformatics pipelines (tumor-only and tumor-normal) to estimate TMB according to genes represented in their respective panels (panel-TMB). The association between WES-TMB and each panel-TMB was investigated using regression analyses. Bias (relative to WES-TMB) and variability in TMB estimates across panels were rigorously assessed. All analyses were blinded. Results: The set of reference standards spanned a clinically meaningful TMB range (4.3 to 31.4 mut/Mb). Preliminary data from 12 laboratories shows a good correlation between panel-TMB and WES-TMB in this empirical analysis. Across panels, regression R2 values range 0.77-0.96 with slopes ranging 0.60-1.26. Calibration analyses that seek to minimize variability of TMB estimates across panels using the established set of reference standards are ongoing, as well as investigating cancer type dependence on the relationship between panel-TMB vs. WES-TMB, which will be available at the time of presentation. Conclusions: Preliminary findings demonstrate feasibility of using sustainable reference control cell lines to standardize and align estimation of TMB across different targeted NGS assays. Future studies aim to validate reference standard material as a reliable alignment tool by using formalin-fixed paraffin-embedded human tumor samples.

Abstract B080: Update on the NCI-Molecular Analysis for Therapy Choice (NCI-MATCH/EAY131) precision medicine trial

Purpose: NCI-Molecular Analysis for Therapy Choice (NCI-MATCH/EAY131), by ECOG-ACRIN (EA) and NCI, is the first national signal-finding trial to incorporate centralized NGS testing to direct patients (pts) to molecularly targeted parallel phase 2 treatment arms. We report status of accrual from opening on 08/12/15 thru 07/16/17 and future plans.

Methods: Eligible pts have advanced/refractory solid tumors, lymphoma, or myeloma. Drug treatments and molecular targets require stringent levels of evidence (LOE). Each arm (N-35) has a phase 2 dose, a molecular abnormality believed to predict response, and evidence of clinical activity. Pts must have enrolled by 05/22/17 with intent to submit fresh tissue or recent clinical biopsy. Tumor cores are shipped to the EA Central Biorepository & Pathology Facility at MD Anderson Cancer Center for evaluation of histopathology and % tumor; PTEN, MLH1, and MSH2 IHC; and RNA/DNA extraction. NGS is performed in one of 4 CLIA-accredited laboratories using the NCI-MATCH adapted Oncomine™ panel (Version 1.0; 143 genes with &gt;4000 reported variants including SNVs, indels, amplifications, and gene fusions). When an actionable mutation of interest (aMOI) or relevant IHC result is identified, the pt is assigned to treatment by a custom-designed informatics system (MATCHbox). If &gt;1 aMOI present, the pt is assigned by the variant with the highest LOE.

Results: As of 07/16/17, 5963 tumors were screened for 30 treatment arms. The assay success rate is 93%; median turnaround is 15 days (from sample receipt to return of results). 38.2% of pts have common cancers: colorectum (15.4%), breast (12.8%), lung (7.4%), and prostate (2.6%); 61.8% have less common tumors. The current overall match rate to aMOI’s is 18% (95% CI 17%, 19%); aMOI prevalence rates range from 3.47% to zero. The match rate also varies across tumor types: &lt;10% in pancreatic & SCLC; &gt;30% in bladder/urinary tract, uterine, and head/neck cancer. 998 pts have been assigned to Rx; 69% have enrolled. Of 30 arms, 8 have enrolled ≥ 35 pts; some arms with higher prevalence rates have been expanded to N=70 to accommodate pts with matching aMOIs. Arms with less frequent aMOIs will not complete accrual within the 6,000-pt central screening goal, leading to identification of pts for screening based on approved high-volume NGS labs’ assay results, verified centrally.

Conclusions: NCI-MATCH screened ~6000 pts at a rate that far exceeded expectations, and with acceptable toxicity; NGS was successful in 93%, well above the industry average of ~80%. The pace of enrollment, along with the trial’s availability at 1100+ sites, reflects the broad interest in the promise of genomics and the ability of such a trial to deliver on that promise. Lower accrual to "rare variant" arms led to use of high-volume NGS laboratories to complete the study. Follow-up will determine whether matching drugs to molecular targets results in meaningful response rates and improved patient outcome.

Citation Format: Lyndsay Harris, Alice Chen, Peter O'Dwyer, Keith Flaherty, Stanley Hamilton, Lisa McShane, Robert Gray, Shuli Li, Edith Mitchell, Diane Dragaud, Mickey Williams, Jeffrey Sklar, A. John Iafrate, David Patton, Richard F. Little, James Zweibel, Jeffrey Abrams, James Doroshow, Barbara Conley. Update on the NCI-Molecular Analysis for Therapy Choice (NCI-MATCH/EAY131) precision medicine trial [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B080.

General Biomarker Recommendations for Lymphoma

Lymphoid malignancies are a heterogeneous group of tumors that have distinctive clinical and biological behaviors. The increasing prevalence of disease reflects both treatment advances and the fact that some of these tumors are indolent. The ability to determine treatment needs at diagnosis remains problematic for some of the tumors, such as in follicular lymphomas. Major clinical advances will likely depend on precision oncology that will enable identification of specific disease entities, prognostic determination at diagnosis, and identification of precise therapeutic targets and essential pathways. However, refinement in diagnostic evaluation is an evolving science. The ability to determine prognosis at diagnosis is variable, and for many of the lymphoid malignancies prognosis can only be made after initial treatment. Clinical trials that aim to evaluate specific features of these diseases are required in order to advance clinical practice that meaningfully addresses this important public health challenge. Herein, we describe the process and general recommendation from the National Cancer Institute (NCI) clinical trials planning meeting in November 2014 to address clinical trial design and biomarker proposals in the context of NCI-supported lymphoma clinical trials in the National Clinical Trials Network.

Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer

The NCI Bladder Cancer Task Force convened a Clinical Trials Planning Meeting (CTPM) Workshop focused on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer (NMIBC). Meeting attendees included a broad and multi-disciplinary group of clinical and research stakeholders and included leaders from NCI, FDA, National Clinical Trials Network (NCTN), advocacy and the pharmaceutical and biotech industry. The meeting goals and objectives were to: 1) create a collaborative environment in which the greater bladder research community can pursue future optimally designed novel clinical trials focused on the theme of molecular targeted and immune-based therapies in NMIBC; 2) frame the clinical and translational questions that are of highest priority; and 3) develop two clinical trial designs focusing on immunotherapy and molecular targeted therapy. Despite successful development and implementation of large Phase II and Phase III trials in bladder and upper urinary tract cancers, there are no active and accruing trials in the NMIBC space within the NCTN. Disappointingly, there has been only one new FDA approved drug (Valrubicin) in any bladder cancer disease state since 1998. Although genomic-based data for bladder cancer are increasingly available, translating these discoveries into practice changing treatment is still to come. Recently, major efforts in defining the genomic characteristics of NMIBC have been achieved. Aligned with these data is the growing number of targeted therapy agents approved and/or in development in other organ site cancers and the multiple similarities of bladder cancer with molecular subtypes in these other cancers. Additionally, although bladder cancer is one of the more immunogenic tumors, some tumors have the ability to attenuate or eliminate host immune responses. Two trial concepts emerged from the meeting including a window of opportunity trial (Phase 0) testing an FGFR3 inhibitor and a second multi-arm multi-stage trial testing combinations of BCG or radiotherapy and immunomodulatory agents in patients who recur after induction BCG (BCG failure).

National Cancer Institute's Precision Medicine Initiatives for the new National Clinical Trials Network

The promise of precision medicine will only be fully realized if the research community can adapt its clinical trials methodology to study molecularly characterized tumors instead of the traditional histologic classification. Such trials will depend on adequate tissue collection, availability of quality controlled, high throughput molecular assays, and the ability to screen large numbers of tumors to find those with the desired molecular alterations. The National Cancer Institute's (NCI) new National Clinical Trials Network (NCTN) is well positioned to conduct such trials. The NCTN has the ability to seamlessly perform ethics review, register patients, manage data, and deliver investigational drugs across its many sites including both in cities and rural communities, academic centers, and private practices. The initial set of trials will focus on different questions: (1) Exceptional Responders Initiative-why do a minority of patients with solid tumors or lymphoma respond very well to some drugs even if the majority do not?; (2) NCI MATCH trial-can molecular markers predict response to targeted therapies in patients with advanced cancer resistant to standard treatment?; (3) ALCHEMIST trial-will targeted epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) inhibitors improve survival for adenocarcinoma of the lung in the adjuvant setting?; and (4) Lung Cancer Master Protocol trial for advanced squamous cell lung cancer-is there an advantage to developing drugs for small subsets of molecularly characterized tumors in a single, multiarm trial design? These studies will hopefully spawn a new era of treatment trials that will carefully select the tumors that may respond best to investigational therapy.

Abstract 304: Feasibility study of next-generation sequencing on residual formalin-fixed paraffin-embedded tissues

Next Generation Sequencing (NGS) technologies are being used for detection of somatic mutations in tumors and studies of germline variation. However, most NGS studies used DNA isolated either from whole blood or fresh frozen tissue specimens. Meanwhile, the tissue specimens available from most National Cancer Institute (NCI) funded cohorts and the Surveillance, Epidemiology and End Results (SEER) registries (http://seer.cancer.gov/biospecimen/) are primarily formalin fixed paraffin embedded (FFPE). There are limited data, on a small number of FFPE tissue samples, which suggest NGS is feasible. Much less is known about the feasibility of these technologies for large scale studies or using older FFPE specimens (e.g. 5-30 years old).

The main objective of this project was to conduct a pilot study to determine whether the DNA obtained from archival FFPE tissue is of sufficient quality and quantity to conduct NGS. Sixty high-grade serous ovarian adenocarcinomas from FFPE tissues which were between 7 and 31 years old were obtained from three SEER registries. DNA was extracted, quantified, quality assessed, and subjected to whole exome sequencing. DNA extraction (yields and quality) and whole exome sequencing (depths of coverage and exome coverage obtained) results from this study will be presented. Ultimately, data derived from this analysis could serve as the basis for determining the utility of archival FFPE biospecimens for characterization and discovery projects utilizing NGS technologies instead of relying on frozen biospecimens.

Citation Format: Danielle Mercatante Carrick, Sean Altekruse, Corrine Camalier, Wendy Cozen, Brenda Hernandez, Charles Lynch, Paul McGregor, Michele G. Mehaffey, Lisa McShane, JoyAnn Phillips Rohan, Mickey Williams, Elizabeth M. Gillanders, Leah E. Mechanic, Sheri Schully. Feasibility study of next-generation sequencing on residual formalin-fixed paraffin-embedded tissues. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 304. doi:10.1158/1538-7445.AM2014-304

Assessment of Ki67 in breast cancer: recommendations from the International Ki67 in Breast Cancer working group

Uncontrolled proliferation is a hallmark of cancer. In breast cancer, immunohistochemical assessment of the proportion of cells staining for the nuclear antigen Ki67 has become the most widely used method for comparing proliferation between tumor samples. Potential uses include prognosis, prediction of relative responsiveness or resistance to chemotherapy or endocrine therapy, estimation of residual risk in patients on standard therapy and as a dynamic biomarker of treatment efficacy in samples taken before, during, and after neoadjuvant therapy, particularly neoadjuvant endocrine therapy. Increasingly, Ki67 is measured in these scenarios for clinical research, including as a primary efficacy endpoint for clinical trials, and sometimes for clinical management. At present, the enormous variation in analytical practice markedly limits the value of Ki67 in each of these contexts. On March 12, 2010, an international panel of investigators with substantial expertise in the assessment of Ki67 and in the development of biomarker guidelines was convened in London by the co-chairs of the Breast International Group and North American Breast Cancer Group Biomarker Working Party to consider evidence for potential applications. Comprehensive recommendations on preanalytical and analytical assessment, and interpretation and scoring of Ki67 were formulated based on current evidence. These recommendations are geared toward achieving a harmonized methodology, create greater between-laboratory and between-study comparability, and allow earlier valid applications of this marker in clinical practice.

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer (unabridged version)

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in pre-analytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer (unabridged version)

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in pre-analytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in preanalytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in preanalytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College Of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in preanalytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinoma

Polymorphisms in nitrosamine metabolism, DNA repair, and immune response genes have been associated with nasopharyngeal carcinoma (NPC). Studies have suggested chromosomal regions involved in NPC. To shed light on NPC etiology, we evaluated host gene expression patterns in 31 NPC and 10 normal nasopharyngeal tissue specimens using the Affymetrix Human Genome U133 Plus 2.0 Array. We focused on genes in five a priori biological pathways and chromosomal locations. Rates of differential expression within these prespecified lists and overall were tested using a bootstrap method. Differential expression was observed for 7.6% of probe sets overall. Elevations in rate of differential expression were observed within the DNA repair (13.7%; P = 0.01) and nitrosamine metabolism (17.5%; P = 0.04) pathways. Differentially expressed probe sets within the DNA repair pathway were consistently overexpressed (93%), with strong effects observed for PRKDC, PCNA, and CHEK1. Differentially expressed probe sets within the nitrosamine metabolism pathway were consistently underexpressed (100%), with strong effects observed for NQ01, CYP2B6, and CYP2E1. No significant evidence of increases in rate of differential expression was seen within the immune/inflammatory pathway. A significant elevation in rate of differential expression was noted for chromosome 4p15.1-4q12 (13.0%; P = 0.04); both overexpression and underexpression were evident (38% and 62%, respectively). An elevation in the rate of differential expression on chromosome 14q32 was observed (11.3%; P = 0.06) with a consistent pattern of gene underexpression (100%; P < 0.0001). These effects were similar when excluding late-stage tumors. Our results suggest that nitrosamine activation and DNA repair are important in NPC. The consistent down-regulation of expression on chromosome 14q32 suggests loss of heterozygosity in this region.

Effect of protease treatment on plasma infectivity in variant Creutzfeldt-Jakob disease mice

BACKGROUND

The emergence of variant Creutzfeldt-Jakob disease (vCJD) and of a probable transmission of the disease through blood transfusion from a presymptomatic case has underlined the need for a reliable, sensitive, and specific screening test. This study was initiated to explain why attempts to identify protease-resistant prion protein (PrPres) following treatment with proteinase K (PK) in blood or blood components have so far failed.

STUDY DESIGN AND METHODS

RIII mice were inoculated intracerebrally (i.c.) with vCJD agent. As soon as some mice became ill, blood from all mice was collected, pooled, and separated into components. Aliquots of plasma were treated with either 100 and 500 microg per mL PK or left untreated. Samples were analyzed for total protein and for PrPres by Western blot with 6H4 antibodies. Infectivity in PK-treated and untreated samples was bioassayed by i.c. inoculation into healthy mice.

RESULTS

Estimated infectivity in untreated control plasma was 20.6 IU per mL. Treatment of plasma with 100 or 500 microg per mL PK resulted in estimated infectivity levels of 8.4 and 5.2 IU per mL, respectively. Coomassie staining revealed substantial changes in the protein profile after PK treatment, with massive degradation of proteins at 500 microg per mL PK. No PrPres was detected in plasma samples by Western blotting.

CONCLUSION

Infectivity in plasma of vCJD-infected mice showed a trend toward reduction following enzymatic treatment with increasing doses of PK, possibly because of activity against proteolysis-sensitive isoforms of abnormal prion protein. It is concluded that the use of PK in protocols for the detection of PrPres may decrease the sensitivity of blood-based assays.

Similar levels of infectivity in the blood of mice infected with human-derived vCJD and GSS strains of transmissible spongiform encephalopathy

BACKGROUND

The possible transmission of variant CJD (vCJD) through blood transfusion or use of plasma-derived products prompted this study comparing infectivity in murine models of vCJD and Gerstmann-Sträussler-Scheinker (GSS) disease, a non-vCJD form of transmissible spongiform encephalopathy (TSE).

STUDY DESIGN AND METHODS

RIII/Fa/Dk (RIII) or Swiss-Webster (Swiss) mice were inoculated intracerebrally (IC) with mouse-adapted strains of vCJD or GSS (Fukuoka-1) of similar infectivity. Groups of RIII mice were euthanized 17 weeks after inoculation (during the incubation period), and another 23 weeks after inoculation (when symptomatic). Blood was collected, separated into components, and inoculated into groups of healthy mice; brains and spleens from all mice were harvested and tested for the presence of PrPres by Western blot using 6H4 MoAb.

RESULTS

Levels of 20-30 infectious doses per mL were present in buffy coat and plasma during both the incubation and symptomatic stages of disease; PLT pellet infectivity was lower (10 ID/mL) and RBCs were not infectious. The disease was transmitted more efficiently by IV than IC inoculation of plasma, but there was no difference observed with inoculation of buffy coat. The incubation period was shorter after IC inoculation of GSS- than vCJD-brain inocula. The amount of PrPres in spleens was similar for both TSE agents, but was slightly lower in brains of vCJD than GSS mice.

CONCLUSION

Infectivity was detected in blood components of mice infected with a human-derived strain of vCJD during both the preclinical and clinical phases of disease in a similarly low range of concentrations as in mice infected with a human-derived nonvariant strain (GSS, Fukuoka-1). Other measures of virulence, including brain infectivity titers, incubation periods, and the accumulation of PrPres in spleens and brains, were also comparable in both experimental models.

The effect of a low-fat, high fiber, fruit and vegetable intervention on rectal mucosal proliferation

BACKGROUND

Because studies of diet and colorectal carcinoma tend to be large and complex, researchers have long been interested in the investigation of dietary exposures in relation to putative intermediate markers of large bowel malignancy, such as colorectal epithelial cell proliferation. The basic hypothesis underlying these investigations is that specific dietary components may reduce or increase the rate of cell proliferation, which, in turn, may reduce or increase neoplastic changes in the large bowel.

METHODS

The authors assessed the effects of a 4-year, low-fat, high-fiber, fruit and vegetable-enriched dietary intervention on colorectal epithelial cell proliferation among 399 participants from the Polyp Prevention Trial, a randomized multicenter trial with adenoma recurrence as the primary endpoint. Rectal biopsies were taken from flat, normal appearing mucosa on patients at baseline, after 1 year, and after 4 years. Two assays, bromodeoxyuridine (Brd U) and proliferating cell nuclear antigen (PCNA), were used to evaluate two summary measures of proliferation: the labeling index (LI) and the proliferative height (PH).

RESULTS

There were no significant differences between changes in LI and PH over the 4-year period for the intervention and control groups. This finding parallels the finding in the larger primary study, in which the dietary intervention did not alter adenoma recurrence rates.

CONCLUSIONS

A low-fat, high-fiber, fruit and vegetable-enriched dietary intervention did not alter rectal mucosal cell proliferation rates.

Iatrogenic Creutzfeldt-Jakob disease at the millennium

The causes and geographic distribution of 267 cases of iatrogenic Creutzfeldt-Jakob disease (CJD) are here updated at the millennium. Small numbers of still-occurring cases result from disease onsets after longer and longer incubation periods following infection by cadaveric human growth hormone or dura mater grafts manufactured and distributed before the mid-1980s. The proportion of recipients acquiring CJD from growth hormone varies from 0.3 to 4.4% in different countries, and acquisition from dura mater varies between 0.02 and 0.05% in Japan (where most cases occurred). Incubation periods can extend up to 30 years, and cerebellar onsets predominate in both hormone and graft recipients (in whom the site of graft placement had no effect on the clinical presentation). Homozygosity at codon 129 of the PRNP gene is over-represented in both forms of disease; it has no effect on the incubation period of graft recipients, but may promote shorter incubation periods in hormone cases. Knowledge about potential high-risk sources of contamination gained during the last quarter century, and the implementation of methods to circumvent them, should minimize the potential for iatrogenic contributions to the current spectrum of CJD.

Colposcopy Quality Control: Establishing Colposcopy Criterion Standards for the National Cancer Institute ALTS Trial Using Cervigrams

OBJECTIVES

The colposcopy quality control (QC) group of the Atypical Squamous Cells of Undetermined Significance-Low-Grade Squamous Intraepithelial Lesions (ASCUS/ LSIL) Triage Study (ALTS) monitors colposcopists at four clinical centers by direct observation and indirectly by assessment of digitized computer colposcopic images transferred nightly by modem. The purpose of this preclinical study was to determine the agreement among colposcopy QC monitors' colposcopic impressions and biopsy site placement through evaluation of cervical photographic images.

MATERIALS AND METHODS

A nonparticipant selected 100 Cervigram slides representing four pathologically confirmed categories: cervical intraepihelial neoplasia 1(CIN), CIN2 and CIN3, normal, and cancer. our colposcopy QC monitors and two certified Cervigram evaluators independently interpreted the images for colpocopic impression on two separate occasions. Measures of agreement were calculated for intraobserver, pairwise interobserver, and observer versus histological diagnoses. Participants also indicated the most severe biopsy site by marking an χ on a 4 × 6-inch color print duplication. Mean distances between biopsy site annotations for each pair of evaluators were calculated.

RESULTS

The ALTS observer agreement with histology ranged from 75.3% (K = .66) to 47.4% (K = .36) for the first evaluation and 71.1 % (K = .63) to 50.5% (K = .38) for the second evaluation. ALTS interobserver agreement varied between 71 % and 57% for the first interpretation and 76% and I2% for the second evaluation. ALTS intraobserver agreement varied from 86% (K = .86) to 68.0% (K = .60). The mean listances between biopsy site annotations for each pair of ALTS observers varied from 0.99 ± 0.93 mm to 1.44 ± 1.19 nm.

CONCLUSIONS

The ALTS colposcopy QC monitors achieved poor to good observer agreement with histology, fair to excellent interobserver agreement, and good to excellent intraobserver agreement in assessing the severity of cervical images. These levels of agreement are similar to many reported by pathologists for cervical cytology and histology interpretations. Monitors also demonstrated a very narrow variation of distance (< 2 mm) for ideal biopsy site placement.

Creutzfeldt-Jakob disease in a husband and wife

A 53-year-old man died of sporadic Creutzfeldt-Jakob disease (CJD) after a 1.5-year clinical course. Four and a half years later, his then 55-year-old widow died from CJD after a 1-month illness. Both patients had typical clinical and neuropathologic features of the disease, and pathognomonic proteinase-resistant amyloid protein ("prion" protein, or PrP) was present in both brains. Neither patient had a family history of neurologic disease, and molecular genetic analysis of their PrP genes was normal. No medical, surgical, or dietary antecedent of CJD was identified; therefore, we are left with the unanswerable alternatives of human-to-human transmission or the chance occurrence of sporadic CJD in a husband and wife.

Using and interpreting surrogate end-points in cancer research

Researchers have proposed a broad range of molecular, cellular and histological markers as surrogate end-points for cancer (SECs). The effect of an intervention on a 'valid' SEC is concordant with its effect on cancer incidence. The validity of a potential SEC is determined primarily by the extent to which the marker is a necessary event on the causal pathway to cancer. Colorectal adenomatous polyp formation is an example of a reasonably valid SEC because these lesions are obligate precursors of most large bowel malignancies. However, the existence of a plausible major alternative causal pathway--one bypassing the potential SEC--weakens inferences from that marker to cancer. Moreover, unless the pathway to cancer operates nearly exclusively through the SEC, an SEC that is valid for one intervention or exposure may not be valid for another. Metabolic, ecological, observational epidemiological and intervention studies may yield data that are useful in revealing these causal interrelations of intervention (exposure), SEC and cancer. Empirical studies of three questions are pertinent: (1) What is the relation of the SEC to cancer? (2) What is the relation of the intervention (exposure) to the SEC? (3) To what extent does the SEC mediate the relation between the intervention (exposure) and cancer? Data on SEC measurement error are important in ascertaining the extent to which marker results have been attenuated by such error. It is essential to carry out these studies to evaluate potential SECs (such as epithelial cell hyperproliferation) with plausible major alternative pathways to cancer. At the present time, definitive evidence on etiology and prevention will emerge only from studies with cancer end-points or SECs that are, by and large, necessary steps on the causal pathway to malignant disease.

A mismatch between kinesthetic and visual perception in Parkinson's disease

Kinesthesia may be defective in patients with Parkinson's disease (PD), and this defect conceivably has a role in parkinsonian hypokinetic symptoms. In the present study, PD patients used kinesthetic perception to estimate the amplitude of passive angular displacements of the index finger about the metacarpophalangeal joint and to scale them as a percentage of a reference stimulus. The reference stimulus was either a standard kinesthetic stimulus preceding each test stimulus (task K) or a visual representation of the standard kinesthetic stimulus (task V). In task V, the PD patients' underestimation of the amplitudes of finger perturbations was significantly greater than that of normal subjects, but not for task K. PD patients' underestimation was also greater in task V than in task K; the difference between the underestimations was significantly greater than for normal subjects. These results suggest that, when kinesthesia is used to match a visual target, distances are perceived to be shorter by the PD patients. Assuming that visual perception is normal, kinesthesia is "reduced" in PD patients. This reduced kinesthesia, when combined with the well-known reduced motor output and probably reduced corollary discharges, implies that the sensorimotor apparatus is "set" smaller in PD patients than in normal subjects.

Use of buspirone for treatment of cerebellar ataxia. An open-label study

OBJECTIVE

To evaluate the efficacy of buspirone hydrochloride, a serotonin (5-hydroxytryptamine1A) agonist, in treating patients with cerebellar ataxia.

DESIGN

Open-label study in which 20 patients (14 with cerebellar cortical atrophy and six with olivopontocerebellar atrophy) received buspirone hydrochloride, up to 60 mg/d, for 8 weeks.

SETTING

Research hospital.

MAIN OUTCOME MEASURES

Clinical, physiological, and psychological assessment.

RESULTS

Nine patients with mild or moderate cerebellar dysfunction who completed the study showed significant improvement in clinical and self-assessment ratings, but not in a motor performance test, posturography (data were incomplete), State-Trait Anxiety Inventory, and Beck Depression Inventory. Seven patients with severe cerebellar dysfunction who completed the study had no improvement on any measure.

CONCLUSIONS

Buspirone may be effective in treating mild to moderate cerebellar ataxia. A double-blind study of the efficacy of buspirone in cerebellar ataxia is warranted.

Disturbances of kinaesthesia in patients with cerebellar disorders

We studied the ability of patients with cerebellar degeneration to perceive differences in kinaesthetic stimuli and compared it with that of normal subjects. All participants were tested for duration, amplitude and velocity sensation. In separate experiments, the responses of muscle spindle afferents and slowly adapting cutaneous mechanoreceptors to the kinaesthetic stimuli were recorded. The performance of patients with cerebellar degeneration was significantly worse than that of normal subjects on the tasks testing for duration and velocity perception. Although both spindle afferents and slowly adapting cutaneous mechanoreceptors were able to provide relevant sensory information during the kinaesthetic tasks, spindle afferents were superior in detecting velocity changes. These results suggest that the cerebellum may be involved in processing sensory signals that are involved in motor control as well as in conscious perception.

Abnormal facilitation of the response to transcranial magnetic stimulation in patients with Parkinson's disease

We studied the facilitation of the motor evoked potential (MEP) elicited with transcranial magnetic stimulation by increasing the stimulus intensity and the degree of voluntary activation of the target muscle in patients with Parkinson's disease (PD) and in normal volunteers. The threshold intensity for eliciting MEPs with the muscle at rest did not differ in PD patients and normal subjects. At rest, stimuli of similar intensity, related to the individual's threshold, elicited MEPs with amplitudes consistently larger in patients than in normal subjects, although when we compared the averaged MEP amplitude across all stimulus intensities, the differences reached only borderline statistical significance. Voluntary muscle activation elicited a smaller increase in the MEP area in PD patients than in normal subjects. Increasing the degree of voluntary muscle activation at fixed stimulus intensities elicited a smaller increase of MEP amplitude, duration, and area in PD patients than in normal subjects. These results suggest that control of the excitability of the motor system is abnormal in PD patients, with enhancement of excitability at rest and weak energization during voluntary muscle activation.