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Breast cancer (BC) patients with a germline CHEK2 c.1100delC variant have an increased risk of contralateral BC (CBC) and worse BC-specific survival (BCSS) compared to non-carriers. We aimed to assess the associations of CHEK2 c.1100delC, radiotherapy, and systemic treatment with CBC risk and BCSS. Analyses were based on 82,701 women diagnosed with invasive BC including 963 CHEK2 c.1100delC carriers; median follow-up was 9.1 years. Differential associations of treatment by CHEK2 c.1100delC status were tested by including interaction terms in a multivariable Cox regression model. A multi-state model was used for further insight into the relation between CHEK2 c.1100delC status, treatment, CBC risk and death. There was no evidence for differential associations of therapy with CBC risk by CHEK2 c.1100delC status The strongest association with reduced CBC risk was observed for the combination of chemotherapy and endocrine therapy [HR(95%CI): 0.66 (0.55–0.78)]. No association was observed with radiotherapy. Results from the multi-state model showed shorter BCSS for CHEK2 c.1100delC carriers versus non-carriers also after accounting for CBC occurrence [HR(95%CI) :1.30 (1.09–1.56)]. In conclusion, systemic therapy was associated with reduced CBC risk irrespective of CHEK2 c.1100delC status. Moreover, CHEK2 c.1100delC carriers had shorter BCSS, which appears not to be fully explained by their CBC risk. (Main MS: 3201 words)

Background There is evidence for an inherited contribution to primary brain cancer. Linkage analysis of high-risk brain cancer pedigrees has identified candidate regions of interest in which brain cancer predisposition genes are likely to reside. Methods Genome-wide linkage analysis was performed in a unique set of 11 informative, extended, high-risk primary brain cancer pedigrees identified in a population genealogy database, which include from 2 to 6 sampled, related primary brain cancer cases. Access to formalin-fixed paraffin embedded tissue samples archived in a biorepository allowed analysis of extended pedigrees. Results Individual high-risk pedigrees were singly informative for linkage at multiple regions. Suggestive evidence for linkage was observed on chromosomes 2, 3, 14, and 16. The chromosome 16 region in particular contains a promising candidate gene, pyridoxal-dependent decarboxylase domain-containing 1 (PDXDC1), with prior evidence for involvement with glioblastoma from other previously reported experimental settings, and contains the lead single nucleotide polymorphism (rs3198697) from the linkage analysis of the chromosome 16 region. Conclusions Pedigrees with a statistical excess of primary brain cancers have been identified in a unique genealogy resource representing the homogeneous Utah population. Genome-wide linkage analysis of these pedigrees has identified a potential candidate predisposition gene, as well as multiple candidate regions that could harbor predisposition loci, and for which further analysis is suggested.

Background: Previously, family-based designs and high-risk pedigrees have illustrated value for the discovery of high- and intermediate-risk germline breast cancer susceptibility genes. However, genetic heterogeneity is a major obstacle hindering progress. New strategies and analytic approaches will be necessary to make further advances. One opportunity with the potential to address heterogeneity via improved characterization of disease is the growing availability of multisource databases. Specific to advances involving family-based designs are resources that include family structure, such as the Utah Population Database (UPDB). To illustrate the broad utility and potential power of multisource databases, we describe two different novel family-based approaches to reduce heterogeneity in the UPDB. Methods: Our first approach focuses on using pedigree-informed breast tumor phenotypes in gene mapping. Our second approach focuses on the identification of families with similar pleiotropies. We use a novel network-inspired clustering technique to explore multi-cancer signatures for high-risk breast cancer families. Results: Our first approach identifies a genome-wide significant breast cancer locus at 2q13 [P = 1.6 × 10−8, logarithm of the odds (LOD) equivalent 6.64]. In the region, IL1A and IL1B are of particular interest, key cytokine genes involved in inflammation. Our second approach identifies five multi-cancer risk patterns. These clusters include expected coaggregations (such as breast cancer with prostate cancer, ovarian cancer, and melanoma), and also identify novel patterns, including coaggregation with uterine, thyroid, and bladder cancers. Conclusions: Our results suggest pedigree-informed tumor phenotypes can map genes for breast cancer, and that various different cancer pleiotropies exist for high-risk breast cancer pedigrees. Impact: Both methods illustrate the potential for decreasing etiologic heterogeneity that large, population-based multisource databases can provide. See all articles in this CEBP Focus section, “Modernizing Population Science.”

Context.—The adoption of digital capture of pathology slides as whole slide images (WSI) for educational and research applications has proven utility.Objective.—To compare pathologists' primary diagnoses derived from WSI versus the standard microscope. Because WSIs differ in format and method of observation compared with the current standard glass slide microscopy, this study is critical to potential clinical adoption of digital pathology.Design.—The study enrolled a total of 2045 cases enriched for more difficult diagnostic categories and represented as 5849 slides were curated and provided for diagnosis by a team of 19 reading pathologists separately as WSI or as glass slides viewed by light microscope. Cases were reviewed by each pathologist in both modalities in randomized order with a minimum 31-day washout between modality reads for each case. Each diagnosis was compared with the original clinical reference diagnosis by an independent central adjudication review.Results.—The overall major discrepancy rates were 3.64% for WSI review and 3.20% for manual slide review diagnosis methods, a difference of 0.44% (95% CI, −0.15 to 1.03). The time to review a case averaged 5.20 minutes for WSI and 4.95 minutes for glass slides. There was no specific subset of diagnostic category that showed higher rates of modality-specific discrepancy, though some categories showed greater discrepancy than others in both modalities.Conclusions.—WSIs are noninferior to traditional glass slides for primary diagnosis in anatomic pathology.

Background: Breast tumor subtyping has failed to provide impact in susceptibility genetics. The PAM50 assay categorizes breast tumors into: Luminal A, Luminal B, HER2-enriched and Basal-like. However, tumors are often more complex than simple categorization can describe. The identification of heritable tumor characteristics has potential to decrease heterogeneity and increase power for gene finding. Methods: We used 911 sporadic breast tumors with PAM50 expression data to derive tumor dimensions using principal components (PC). Dimensions in 238 tumors from high-risk pedigrees were compared with the sporadic tumors. Proof-of-concept gene mapping, informed by tumor dimension, was performed using Shared Genomic Segment (SGS) analysis. Results: Five dimensions (PC1-5) explained the majority of the PAM50 expression variance: three captured intrinsic subtype, two were novel (PC3, PC5). All five replicated in 745 TCGA tumors. Both novel dimensions were significantly enriched in the high-risk pedigrees (intrinsic subtypes were not). SGS gene-mapping in a pedigree identified a 0.5 Mb genome-wide significant region at 12q15. This region segregated through 32 meioses to 8 breast cancer cases with extreme PC3 tumors (P = 2.6 × 10−8). Conclusions: PC analysis of PAM50 gene expression revealed multiple independent, quantitative measures of tumor diversity. These tumor dimensions show evidence for heritability and potential as powerful traits for gene mapping. Impact: Our study suggests a new approach to describe tumor expression diversity, provides new avenues for germline studies, and proposes a new breast cancer locus. Similar reparameterization of expression patterns may inform other studies attempting to model the effects of tumor heterogeneity. Cancer Epidemiol Biomarkers Prev; 27(6); 644–52. ©2018 AACR.

Interstitial cystitis/painful bladder syndrome is a chronic pelvic pain condition of unknown etiology. We hypothesized that related interstitial cystitis/painful bladder syndrome cases were more likely to have a genetic etiology. The purpose of this study was to perform a genetic linkage analysis.We identified interstitial cystitis/painful bladder syndrome cases using diagnostic codes linked to the Utah Population Database genealogy resource and to electronic medical records. For this analysis we used 13 high risk pedigrees, defined as having a statistical excess number of interstitial cystitis/painful bladder syndrome cases among descendants compared to matched hospital population rates. Case status was confirmed in medical records using natural language processing. DNA was obtained from stored, nonneoplastic, formalin fixed, paraffin embedded tissue blocks. Each pedigree had at least 2 cases with DNA available. Parametric linkage analysis was performed.Pedigrees ranged in size from 2 to 12 genotyped cases for a total of 48 cases. Significant genome wide linkage evidence was found under a dominant model on chromosome 3p13-p12.3 (maximum heterogeneity θ logarithm of odds 3.56). Two pedigrees showed at least nominal linkage evidence in this region (logarithm of odds greater than 0.59). The most informative pedigree included 12 interstitial cystitis/painful bladder syndrome cases (pedigree θ logarithm of odds 2.1). Other regions with suggestive linkage evidence included 1p21-q25, 3p21.1-p14.3, 4q12-q13, 9p24-p22 and 14q24-q31, all under a dominant model.While the etiology of interstitial cystitis/painful bladder syndrome is unknown, this study provides evidence that a genetic variant(s) on chromosome 3 and possibly on chromosomes 1, 4, 9 and 14 contribute to an interstitial cystitis/painful bladder syndrome predisposition. Sequence analysis of affected cases in identified pedigrees may provide insight into genes contributing to interstitial cystitis/painful bladder syndrome.

Chronic myelomonocytic leukemia (CMML) is a rare malignant neoplasm of the blood-forming cells in bone marrow characterized by persistent monocytosis. Although most patients with CMML show clonal genetic aberrations, there is no known cytogenetic or molecular genetic finding that is specific to CMML. We report a patient who had a clinical and morphological presentation consistent with CMML. The genetic work-up showed an ETV6-ABL1 fusion consequent to a 9;12 translocation, and a missense mutation in SMC1A (c.1757G>A, p.Arg586Gln). The SMC1A mutations are recurrent, albeit rare, in myeloid malignancies, without an established clinical significance in CMML. ETV6-ABL1 fusion is a rare but recurrent genetic aberration found in various hematologic malignancies involving both the lymphoid and myeloid lineage, but to the best of our knowledge, CMML is an exceptionally rare presentation of ETV6-ABL1 rearranged neoplasm. ETV6-ABL1 fusion is often formed through complex rearrangements, and usually cryptic by routine G-banded chromosome analysis. The diseases associated with this rearrangement generally have an aggressive course, hence detecting or excluding this rearrangement during diagnostic work-up is critical for treatment planning.

Background: Artificial intelligence (AI) is fast becoming the tool of choice for scalable and reliable analysis of medical images. However, constraints in sharing medical data outside the institutional or geographical space, as well as difficulties in getting AI models and modeling platforms to work across different environments, have led to a “reproducibility crisis” in digital medicine. Methods: This study details the implementation of a web platform that can be used to mitigate these challenges by orchestrating a digital pathology AI pipeline, from raw data to model inference, entirely on the local machine. We discuss how this federated platform provides governed access to data by consuming the Application Program Interfaces exposed by cloud storage services, allows the addition of user-defined annotations, facilitates active learning for training models iteratively, and provides model inference computed directly in the web browser at practically zero cost. The latter is of particular relevance to clinical workflows because the code, including the AI model, travels to the user's data, which stays private to the governance domain where it was acquired. Results: We demonstrate that the web browser can be a means of democratizing AI and advancing data socialization in medical imaging backed by consumer-facing cloud infrastructure such as Box.com. As a case study, we test the accompanying platform end-to-end on a large dataset of digital breast cancer tissue microarray core images. We also showcase how it can be applied in contexts separate from digital pathology by applying it to a radiology dataset containing COVID-19 computed tomography images. Conclusions: The platform described in this report resolves the challenges to the findable, accessible, interoperable, reusable stewardship of data and AI models by integrating with cloud storage to maintain user-centric governance over the data. It also enables distributed, federated computation for AI inference over those data and proves the viability of client-side AI in medical imaging. Availability: The open-source application is publicly available at https://episphere.github.io/path , with a short video demonstration at https://youtu.be/z59jToy2TxE .

The major types of non-small cell lung cancer, squamous cell carcinoma and adenocarcinoma, have distinct tumor immune microenvironments. Understanding the mechanisms underlying these differences is of particular importance given the success and current limitations of immunotherapy. We developed multiple mouse models of lung cancer to demonstrate that NKX2-1 potently suppresses SOX2-driven squamous tumorigenesis by repressing adeno-to-squamous transdifferentiation. Furthermore, SOX2 recruits, whereas NKX2-1 suppresses, tumor-associated neutrophils (TANs) at least partly through inverse regulation of the chemoattractant CXCL5/6. Single-cell RNA sequencing revealed that TANs exhibit tumor-promoting features and distinct gene expression profiles compared to blood neutrophils. Finally, TANs cooperate with squamous-associated genetic alterations to promote squamous tumors. These data reveal how transcription factors with key functions in normal development dictate not only cancer cell identity but also distinct tumor immune microenvironments. Citation Format: Gurkan Mollaoglu, Alex Jones, Sarah Wait, Anandaroop Mukhopadhyay, Sangmin Jeong, Rahul Arya, Soledad Camolotto, Timothy Mosbruger, Chris Stubben, Christopher Conley, Arjun Bhutkar, Jeffery Vahrenkamp, Kristofer Berrett, Melissa Cessna, Thomas Lane, Benjamin Witt, Mohamed Salama, Jason Gertz, Kevin Jones, Eric Snyder, Trudy Oliver. Lineage specifiers SOX2 and NKX2-1 inversely regulate tumor cell fate and neutrophil recruitment in lung cancer [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B72.

Nearly all patients with small cell lung cancer (SCLC) eventually relapse with chemoresistant disease. The molecular mechanisms driving chemoresistance in SCLC remain un-characterized. Here, we describe whole-exome sequencing of paired SCLC tumor samples procured at diagnosis and relapse from 12 patients, and unpaired relapse samples from 18 additional patients. Multiple somatic copy number alterations, including gains in ABCC1 and deletions in MYCL, MSH2, and MSH6, are identifiable in relapsed samples. Relapse samples also exhibit recurrent mutations and loss of heterozygosity in regulators of WNT signaling, including CHD8 and APC. Analysis of RNA-sequencing data shows enrichment for an ASCL1-low expression subtype and WNT activation in relapse samples. Activation of WNT signaling in chemosensitive human SCLC cell lines through APC knockdown induces chemoresistance. Additionally, in vitro-derived chemoresistant cell lines demonstrate increased WNT activity. Overall, our results suggest WNT signaling activation as a mechanism of chemoresistance in relapsed SCLC.

Background & Aims Post-colonoscopy colorectal cancers (PCCRCs) may arise from missed lesions or due to molecular features of tumors that allow them to grow rapidly. We aimed to compare clinical, pathology, and molecular features of PCCRCs (those detected within 6–60 months of colonoscopy) and detected CRCs (those detected within 6 months of a colonoscopy). Methods Within a population-based cross-sectional study of incident CRC cases in Utah (from 1995 through 2009), we identified PCCRCs (those cancers that developed within 5 years of a colonoscopy) and matched the patients by age, sex, and hospital site to patients with detected CRC. Archived specimens were retrieved and tested for microsatellite instability (MSI), CpG island methylation, and mutations in KRAS and BRAF. There were 2659 cases of CRC diagnosed within the study window; 6% of these (n = 159) were defined as PCCRCs; 84 of these cases had tissue available and were matched to 84 subjects with detected CRC. Results Higher proportions of PCCRCs than detected CRCs formed in the proximal colon (64% vs 44%; P = .016) and were of an early stage (86% vs 69%; P = .040). MSI was observed in 32% of PCCRCs compared with 13% of detected CRCs (P = .005). The other molecular features were found in similar proportions of PCCRCs and detected CRCs. In a multivariable logistic regression, MSI (odds ratio, 4.20; 95% CI, 1.58–11.14) was associated with PCCRC. There was no difference in 5-year survival between patients with PCCRCs vs detected CRCs. Conclusion In this population-based cross-sectional study of incident CRC cases in Utah, we found PCCRCs to be more likely to arise in the proximal colon and demonstrate MSI, so PCCRCs and detected CRC appear to have different features or processes of tumorigenesis. Additional studies are needed to determine if post-colonoscopy cancers arise through a specific genetic pathway.

The major types of non-small-cell lung cancer (NSCLC)-squamous cell carcinoma and adenocarcinoma-have distinct immune microenvironments. We developed a genetic model of squamous NSCLC on the basis of overexpression of the transcription factor Sox2, which specifies lung basal cell fate, and loss of the tumor suppressor Lkb1 (SL mice). SL tumors recapitulated gene-expression and immune-infiltrate features of human squamous NSCLC; such features included enrichment of tumor-associated neutrophils (TANs) and decreased expression of NKX2-1, a transcriptional regulator that specifies alveolar cell fate. In Kras-driven adenocarcinomas, mis-expression of Sox2 or loss of Nkx2-1 led to TAN recruitment. TAN recruitment involved SOX2-mediated production of the chemokine CXCL5. Deletion of Nkx2-1 in SL mice (SNL) revealed that NKX2-1 suppresses SOX2-driven squamous tumorigenesis by repressing adeno-to-squamous transdifferentiation. Depletion of TANs in SNL mice reduced squamous tumors, suggesting that TANs foster squamous cell fate. Thus, lineage-defining transcription factors determine the tumor immune microenvironment, which in turn might impact the nature of the tumor.

BACKGROUND: Breast tumor subtyping has failed to provide impact in susceptibility genetics. The PAM50 assay categorizes breast tumors into: Luminal A, Luminal B, HER2-enriched and Basal-like. However, tumors are often more complex than simple categorization can describe. The identification of heritable tumor characteristics has potential to decrease heterogeneity and increase power for gene-finding. METHODS: We used 911 sporadic breast tumors with PAM50 expression data to derive tumor dimensions using principal components (PC). Dimensions in 238 tumors from high-risk pedigrees were compared to the sporadic tumors. Proof-of-concept gene mapping, informed by tumor dimension, was performed using Shared Genomic Segment (SGS) analysis. RESULTS: Five dimensions (PC1-5) explained the majority of the PAM50 expression variance: three captured intrinsic subtype, two were novel (PC3, PC5). All five replicated in 745 TCGA tumors. Both novel dimensions were significantly enriched in the high-risk pedigrees (intrinsic subtypes were not). SGS gene-mapping in a pedigree identified a 0.5 Mb genomewide significant region at 12q15. This region segregated through 32 meioses to 8 breast cancer cases with extreme PC3 tumors (p=2.6×10(−8)). CONCLUSIONS: Principal component analysis of PAM50 gene expression revealed multiple independent, quantitative measures of tumor diversity. These tumor dimensions show evidence for heritability and potential as powerful traits for gene-mapping. IMPACT: Our study suggests a new approach to describe tumor expression diversity, provides new avenues for germline studies, and proposes a new breast cancer locus. Similar reparameterization of expression patterns may inform other studies attempting to model the effects of tumor heterogeneity.

B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL, but data regarding genetic prognostic biomarkers are much more limited for adult patients. We identified 70 adult B-ALL patients from three institutions and performed genome-wide analysis via single nucleotide polymorphism (SNP) arrays on DNA isolated from their initial diagnostic sample and, when available, relapse bone marrow specimens to identify recurring copy number alterations (CNA). As B-cell developmental genes play a crucial role in this leukemia, we assessed such for recurrent deletions in diagnostic and relapse samples. We confirmed previous findings that the most prevalent deletions of these genes occur in CDKN2A, IKZF1, and PAX5, with several others at lower frequencies. Of the 16 samples having paired diagnostic and relapse samples, 5 showed new deletions in these recurrent B-cell related genes and 8 showed abolishment. Deletion of EBF1 heralded a significant negative prognostic impact on relapse free survival in univariate and multivariate analyses. The combination of both a CDKN2A/B deletion and an IKZF1 alteration (26% of cases) also showed a trend toward predicting worse overall survival compared to having only one or neither of these deletions. These findings add to the understanding of genomic influences on this comparably understudied disease cohort that upon further validation may help identify patients who would benefit from upfront treatment intensification.

Tissue microarrays (TMAs) are becoming more common in pathology. With the costs of validating instruments or optimizing antibodies and control tissues on the rise, the best way to cut costs would be to use TMAs. Good laboratory techniques for constructing TMAs are essential for the technician. Tissue samples are extremely valuable and often depleted because of specialized histologic testing. The costs saved using TMAs outweigh the expense of purchasing a TMA instrument. A sound method for optimizing tissue samples for TMA construction would be beneficial to the medical and research community. Advanced or radical-tissue microarray (R-TMA) techniques require only minute tissue samples that were not amenable to TMA construction in the past.

The Job or hyper-immunoglobulinemia E syndrome is a primary immunodeficiency that is usually inherited in an autosomal dominant fashion. With the discovery of mutations in the STAT3 gene in the majority of autosomal dominant cases, it is now possible to make a molecular diagnosis of hyper-IgE syndrome. Both primary and secondary immunodeficiencies, including hyper-IgE syndrome, may predispose for malignancies, especially lymphomas, mainly mature B cell lymphomas, and classical Hodgkin lymphoma. Here, we report of a 48-year-old male with hyper-IgE syndrome who developed a primary parotid gland diffuse large B cell lymphoma. Analysis for STAT3 mutations demonstrated that the causal mutation of hyper-IgE syndrome, R382Q, arose de novo in the patient and it was transmitted to three of his five children, all three of whom are clinically affected. We review the literature regarding lymphoma in hyper-IgE syndrome and the possible etiologic relationship with STAT3 mutations.

Hairy cell leukemia variant (HCL-V) is a poorly described, rare B-cell lymphoproliferative disorder typically positive for CD103 and CD11c, while lacking CD25. Splenic marginal zone lymphomas (SMZL) also have this unusual phenotype in 15% to 25% of cases, have other overlapping clinical or morphologic features, and are more common than HCL-V. The purpose of our study was to better characterize HCL-V and determine whether most cases could be distinguished from SMZL. Cases with an HCL-V phenotype were identified from our flow cytometry service, and 10 were selected for further study based on bone marrow or splenic tissue availability. All cases had cytologic features consistent with HCL-V, and 9 of 10 patients had lymphocytosis. Bone marrow involvement was mostly interstitial and/or sinusoidal without lymphoid nodules. Coexpression of preswitched with postswitched heavy chain isotypes, an unusual feature of HCL, was seen in 2 of 4 cases. This study better defines HCL-V and establishes that most cases do not represent SMZL.

The primary tumors that typically cause carcinomatous meningitis include lung cancer, breast cancer, leukemia, lymphoma and melanoma. A variety of neurological signs and symptoms can be seen depending on the extent and location of the meningeal metastasis. Once the diagnosis of carcinomatous meningitis is confirmed, the search for the primary tumor can be a challenge and at times may require extensive radiographic or even surgical evaluation to obtain specimen for pathological confirmation. Here we report a patient who presented with bilateral cranial nerve VIII and cerebellar symptoms, and was diagnosed with carcinomatous meningitis. Only after an exploratory laporatomy did it become clear that the initial symptoms were related to a metastatic gallbladder carcinoma.

Background The issue of which specific antibodies need to be used when evaluating acute leukemias by flow cytometry is controversial. Methods Recent studies have suggested that antibodies against CD117 or c-kit are not essential for the assignment of blast lineage by flow cytometry, even though CD117 appears to be a very specific marker for myeloid lineage acute leukemias. We report a case of acute myeloid leukemia M2 subtype with an 8:21 translocation, where the leukemic blasts expressed CD117, CD19, and CD15 but did not show definitive expression of the myeloid markers CD13 or CD33. Results and Conclusions This study highlights the importance of CD117 when evaluating acute leukemias by flow cytometry, which was necessary in this case to suggest that the blasts were phenotypically abnormal myeloblasts. In addition, this case presented an unusual acute myeloid leukemia phenotype that will likely be encountered by others and could be difficult to interpret. Cytometry Part B (Clin. Cytometry) 52B:40–43, 2003. © 2003 Wiley-Liss, Inc.

Abnormalities of chromosome 2p23 with expression of ALK1 and p80 occur in both inflammatory myofibroblastic tumor (IMT) and anaplastic large cell lymphoma. This immunohistochemical study investigates whether the ALK family of neoplasms includes fibroblastic-myofibroblastic, myogenic, and spindle cell tumors. Formalin-fixed paraffin-embedded archival tissues from 10 IMTs and 125 other soft tissue tumors were stained for ALK1 and p80 with standard immunohistochemistry. ALK1 and/or p80 reactivity was observed in a cytoplasmic pattern in IMT (4/10; 40%), malignant peripheral nerve sheath tumor (4/10; 40%), rhabdomyosarcoma (6/31; 19%), leiomyosarcoma (1/10; 10%), and malignant fibrous histiocytoma (1/11; 9%). No staining was observed in nodular fasciitis, desmoid, infantile myofibromatosis, infantile fibrosarcoma, synovial sarcoma, leiomyoma, or myofibrosarcoma. Alveolar rhabdomyosarcomas (4/16; 25%) displayed a distinctive dot-like cytoplasmic positivity. No cases displayed nuclear reactivity. Fluorescent in situ hybridization on 12 of the positive cases revealed a combination of abnormalities including ALK break-apart signals, nucleophosmin (NPM)/ALK fusions, or extra copies of 2p23. This study demonstrates that in addition to IMT, abnormalities of ALK1 and p80 expression with a variety of structural chromosomal changes are found in several sarcomas, especially rhabdomyosarcoma and malignant peripheral nerve sheath tumor. Although immunoreactivity in non-IMTs cannot distinguish between structural abnormalities involving 2p23 or additional copies of 2p23, it supports the concept of ALK involvement in a larger group of neoplasms, some of which have other documented clonal abnormalities. In IMT, immunohistochemistry for ALK1 and p80 is useful as an indicator of a 2p23 abnormality, but it must be interpreted in the context of histologic and other clinicopathologic data if used as an adjunct to differential diagnosis.

Rhabdomyosarcoma (RMS), the most common soft tissue sarcoma of childhood, displays a variety of histologic patterns. Immunohistochemistry is used extensively to distinguish RMS from its mimics. Myogenin and MyoD1, myogenic transcriptional regulatory proteins expressed early in skeletal muscle differentiation, are considered sensitive and specific markers for RMS and are more specific than desmin and muscle-specific actin and more sensitive than myoglobin. Previous studies have focused on expression of myogenin and MyoD1 in small round cell tumors. This study assesses myogenin and MyoD1 in rhabdomyosarcoma subtypes and spindle cell tumors considered in the differential diagnosis of RMS. Formalin-fixed, paraffin-embedded archival tissue from 32 RMS, 107 non-RMS, and 11 benign skeletal muscle samples was stained for myogenin and MyoD1 with standard immunohistochemical techniques. Nuclear positivity was scored on a three-tiered scale. All RMSs expressed myogenin. Alveolar RMS (ARMS) showed strong nuclear staining, especially in tumor cells lining fibrous septae and perivascular regions. In cases with a subtle alveolar architecture on routinely stained sections, myogenin highlighted and enhanced visualization of the alveolar morphologic pattern. Embryonal RMSs (ERMSs) were more variable in myogenin staining pattern and intensity. No cases of nodular fasciitis, malignant fibrous histiocytoma, malignant peripheral nerve sheath tumor, inflammatory myofibroblastic tumor, myofibrosarcoma, leiomyoma, leiomyosarcoma, or alveolar soft part sarcoma stained for myogenin. Focal nuclear reactivity was seen in desmoid (2 of 10), infantile myofibromatosis (2 of 10), synovial sarcoma (1 of 10), and infantile fibrosarcoma (2 of 10). Non-neoplastic skeletal muscle fiber nuclei stained positively for myogenin in both tumor-associated samples (25 of 40) and benign skeletal muscle samples (5 of 11). Although all RMSs were immunoreactive for MyoD1, cytoplasmic and nonspecific background staining and reactivity of nonmyoid tissues hindered its practical utility in paraffin-embedded samples in this study. Although myogenin is a highly sensitive and specific marker for RMS, it is rarely seen in other spindle cell soft tissue tumors. As previously reported, ARMS stained more strongly than ERMS. In contrast to previous studies, rare non-RMS (7 of 107) displayed focal nuclear reactivity, and entrapped atrophic or regenerative skeletal muscle fibers also stained positively. Although these are potential pitfalls in the interpretation of myogenin, careful attention to morphology and other features, to the relative paucity of myogenin-positive nuclei in non-RMS. and to the presence of entrapped muscle fibers should prevent incorrect interpretation. Because the extent of myogenin expression in RMS is much greater than in non-RMS, it is a very useful marker when interpreted in the context of other clinicopathologic data.

B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL, but data regarding prognostic biomarkers are much more limited for adult patients. Microarray-based genome-wide profiling studies in pediatric B-ALL patients have revealed recurrent abnormalities in B-cell development and cell cycle regulation. IKZF1 alterations convey a negative prognostic impact in pediatric B-ALL, but their significance is not well characterized in adult B-ALL. CDKN2A alterations have been associated with a poorer prognosis in adult Ph+ ALL, possibly by mediating resistance to targeted therapy. The copy number landscape of adult B-ALL has not been fully assessed and is likely distinct from its pediatric counterpart. In addition, the copy number changes in relapsed adult B-ALL, including comparison with initial diagnostic samples, have not been characterized. We identified 70 adult B-ALL patients (median age 45 years, range 18-83) from 1998-2013 at three institutions. DNA was isolated from formalin-fixed, paraffin-embedded (FFPE) diagnostic bone marrow clots, as well as relapse samples when available, and assessed with the OncoScan FFPE Express genome-wide single nucleotide polymorphism (SNP) assay (Affymetrix). Copy number alteration (CNA) and loss of heterozygosity (LOH) analysis was performed using Nexus Software V7 (Biodiscovery) and in-house coding. For cases with adequate DNA, IKZF1 sequencing was also performed. Clinical data included age, gender, hematologic laboratory values at presentation, CSF involvement, receipt of allogeneic transplant, cytogenetic profile, presence of t(9;22), event-free survival (EFS), and overall survival (OS). Recurrent deletions in the diagnostic samples were noted at several loci, including CDKN2A (48.6%), IKZF1 (40%), ICR (38.6%), PAX5 (24.2%), BTG1 (17.1%), ETV6 (15.7%), BTLA (14.3%), RB1 (5.7%), EBF1 (5.7%), LEF1 (2.9%), and TCF3 (2.9%). Recurrent gains were identified at the following loci: ERG (30%), ETS2 (21.4%), MYB (20%), UBASH3B (20%), PTEN (20%), PRKCH (18.6%), CDK6 (17.1%), and ETV6 (12.9%). In addition, LOH was observed in all loci with recurrent CNAs named above. 27 samples obtained at the time of relapse were screened for the recurrent CNAs identified in the diagnostic samples. The cumulative incidence of CNAs at these genes was lower in the relapse cohort than the initial diagnostic cohort, although there was a higher frequency of CNAs at PAX5, BTLA, ETS2, RB1, LEF1, PTEN, and TCF3 in the relapse samples. 16 patients had samples available at both the time of diagnosis and time of relapse. The average number of CNAs at diagnosis and relapse was the same, but analysis of paired samples revealed frequent changes at the previously defined loci of CNAs. There were a number of new CNAs at these loci in relapse samples, but there was also a similar incidence of reversion to the copy neutral state in loci that previously had CNAs in the diagnostic samples. Sequencing data was available on 26 diagnostic samples for the IKZF1 gene. Only two samples had mutations corresponding to amino acid changes. One of these two had a heterozygous deletion at IKZF1, indicating that the mutated isoform was the only one expressed. 11 other samples had a SNP without a corresponding amino acid change. 14 relapse samples were sequenced, two of which harbored a point mutation in IKZF1. Neither of these samples had a CNA at this locus. 10 of the remaining 12 relapse samples had a SNP without a corresponding amino acid change. When correlated with outcomes, no individual CNA heralded a significant prognostic impact in the entire cohort or in subgroup analyses stratified by presence of t(9;22) for either EFS or OS. However, the combination of both CDK2NA and IKZF1 deletions (26%) correlated with a significantly worse OS than having only one or neither of these deletions (both vs. CDKN2A only: p=0.028, both vs. IKZF1 only: p=0.027, both vs. neither deleted: p=0.048). Age was the only other covariate significant in univariate analyses for OS, yet IKZF1/CDKN2A co-deletion remained significant in multivariate analysis adjusting for age. Adult B-ALL demonstrates recurrent copy number changes, and the pattern of CNAs is often different at relapse than at diagnosis indicating clonal evolution. When identified in diagnostic samples, co-deletion of CDKN2A /IKZF1 is a negative prognostic marker in adult B-ALL. Disclosures South: Illumina: Consultancy, Honoraria; Affymetrix: Consultancy, Honoraria; ARUP Laboratories: Employment; Lineagen Corporation: Consultancy. Bixby:Seattle Genetics, Inc.: Research Funding. Gastier-Foster:Bristol-Myers Squibb: Research Funding.

B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL. Prognostic biomarkers are needed for better risk-stratification and therapy selection. Microarray-based genome-wide profiling studies in pediatric patients have revealed recurrent abnormalities in B-cell development and cell cycle regulation. IKZF1 alterations convey a negative prognostic impact in pediatric B-ALL, but their significance is not well characterized in adult B-ALL. CDKN2A alterations have also been associated with a poorer prognosis in adult Ph+ ALL, possibly by mediating resistance to targeted therapy. The copy number landscape of adult B-ALL has not been fully assessed, and given its inferior prognosis, may be distinct from its pediatric counterpart. We identified 70 adult B-ALL patients (median age 45 years, range 18-83) from 1998-2013 at three institutions. DNA was isolated from formalin-fixed, paraffin-embedded (FFPE) diagnostic bone marrow clots and assessed with the OncoScan FFPE Express genome-wide single nucleotide polymorphism (SNP) assay (Affymetrix). Copy number alteration (CNA) analysis was performed using Nexus Software V7 (Biodiscovery) and in-house coding. The most frequent CNAs called by the software were manually verified for probe evidence. Clinical data available on this cohort included age, gender, hematologic laboratory values at presentation, CSF involvement, receipt of allogeneic transplant, cytogenetic profile, presence of t(9;22), event-free survival (EFS), and overall survival (OS). Estimated median survival time of the entire adult B-ALL patient cohort was 29 months. Recurrent deletions in the diagnostic samples were noted at several loci, including CDKN2A (47%), IKZF1 (40%), PAX5 (24%), BTG1 (17%), and BTLA (14%). Recurrent gains were identified at the following loci: ERG (30%), ETS2 (21%), MYB (20%), UBASH3B (20%), PRKCH (19%), CDK6 (17%), and ETV6 (16%). No individual CNA heralded a significant prognostic impact in the entire cohort or in subgroup analyses stratified by presence of t(9;22) for either EFS or OS, though this could be due to our relatively smaller sample size in contrast to pediatric studies that have observed a prognostic impact at some of these loci. However, the combination of both CDK2NA and IKZF1 deletions (26%) correlated with a significantly worse overall survival than having only one or neither of these deletions (both vs CDKN2A only: p = 0.028, both vs IKZF1 only: p = 0.027, both vs neither deleted: p = 0.048). Age was the only other covariate significant in univariate analyses for OS, yet IKZF1/CDKN2A co-deletion remained significant in multivariate analysis adjusting for age. Adult B-ALL demonstrates frequent CDKN2A deletions, IKZF1 deletions, and CDKN2A/IKZF1 co-deletions. To our knowledge, the negative prognostic impact of the CDKN2A/IKZF1 co-deletion is a novel finding in adult B-ALL and requires further validation in larger cohorts. Citation Format: Shiven Patel, Clinton C. Mason, Martha J. Glenn, Christian N. Paxton, Sara T. South, Melissa H. Cessna, Julie Asch, Erin F. Cobain, Dale L. Bixby, Lauren B. Smith, Joshua D. Schiffman, Rodney R. Miles. IKZF1/CDKN2A co-deletion predicts shorter survival in adult B-ALL. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1723. doi:10.1158/1538-7445.AM2015-1723