Associations of Multiparametric Breast MRI Features, Tumor-Infiltrating Lymphocytes, and Immune Gene Signature Scores Following a Single Dose of Trastuzumab in HER2-Positive Early-Stage Breast Cancer.

Dynamic biomarkers that permit the real-time monitoring of the tumor microenvironment response to therapy are an unmet need in breast cancer. Breast magnetic resonance imaging (MRI) has demonstrated value as a predictor of pathologic complete response and may reflect immune cell changes in the tumor microenvironment. The purpose of this pilot study was to investigate the value of breast MRI features as early markers of treatment-induced immune response. Fourteen patients with early HER2+ breast cancer were enrolled in a window-of-opportunity study where a single dose of trastuzumab was administered and both tissue and MRIs were obtained at the pre- and post-treatment stages. Functional diffusion-weighted and dynamic contrast-enhanced MRI tumor measures were compared with tumor-infiltrating lymphocytes (TILs) and RNA immune signature scores. Both the pre-treatment apparent diffusion coefficient (ADC) and the change in peak percent enhancement (DPE) were associated with increased tumor-infiltrating lymphocytes with trastuzumab therapy (r = -0.67 and -0.69, p < 0.01 and p < 0.01, respectively). Low pre-treatment ADC and a greater decrease in PE in response to treatment were also associated with immune-activated tumor microenvironments as defined by RNA immune signatures. Breast MRI features hold promise as biomarkers of early immune response to treatment in HER2+ breast cancer.

The next phase in patient safety education: Towards a standardized, tools-based pathology patient safety curriculum: A call to action from the Association of Pathology Chairs' Residency Program Directors Section Training Residents in Patient Safety Workgroup.

Patient safety education is a mandated Common Program Requirement of the Accreditation Council for Graduate Medical Education and for the Royal College of Physicians and Surgeons of Canada in all medical residency and fellowship programs. Although many hospitals and healthcare environments have general patient safety education tools for trainees, few to none focus on the unique training milieu of pathologists, including a mix of highly automated and manual error-prone processes, frequent multiplicity of events, and lack of direct patient relationships for error disclosure. We established a national Association of Pathology Chairs-Program Directors Section Workgroup focused on patient safety education for pathology trainees entitled Training Residents in Patient Safety (TRIPS). TRIPS included diverse representatives from across the United States, as well as representatives from pathology organizations including the American Board of Pathology, the American Society for Clinical Pathology, the United States and Canadian Academy of Pathology, the College of American Pathologists, and the Society to Improve Diagnosis in Medicine. Objectives of the workgroup included developing a standardized patient safety curriculum, designing teaching and assessment tools, and refining them with pilot sites. Here we report the establishment of TRIPS as well as data from national needs assessment of Program Directors across the country, who confirmed the need for a standardized patient safety curriculum.

Multiresolution nondestructive 3D pathology of whole lymph nodes for breast cancer staging.

SIGNIFICANCE: For breast cancer patients, the extent of regional lymph node (LN) metastasis influences the decision to remove all axillary LNs. Metastases are currently identified and classified with visual analysis of a few thin tissue sections with conventional histology that may underrepresent the extent of metastases. AIM: We sought to enable nondestructive three-dimensional (3D) pathology of human axillary LNs and to develop a practical workflow for LN staging with our method. We also sought to evaluate whether 3D pathology improves staging accuracy in comparison to two-dimensional (2D) histology. APPROACH: We developed a method to fluorescently stain and optically clear LN specimens for comprehensive imaging with multiresolution open-top light-sheet microscopy. We present an efficient imaging and data-processing workflow for rapid evaluation of H&E-like datasets in 3D, with low-resolution screening to identify potential metastases followed by high-resolution localized imaging to confirm malignancy. RESULTS: We simulate LN staging with 3D and 2D pathology datasets from 10 metastatic nodes, showing that 2D pathology consistently underestimates metastasis size, including instances in which 3D pathology would lead to upstaging of the metastasis with important implications on clinical treatment. CONCLUSIONS: Our 3D pathology method may improve clinical management for breast cancer patients by improving staging accuracy of LN metastases.

Medical Education in Pathology: General Concepts and Strategies for Implementation.

CONTEXT.­: Pathology education must evolve as medical knowledge expands and disruptive technologies emerge. The evolution in pathology teaching practices accelerated as traditional teaching modalities were suspended in March 2020 during the coronavirus disease 2019 (COVID-19) pandemic. OBJECTIVES.­: To provide pathologists an overview of established teaching paradigms and practical examples of how these paradigms may be applied to pathology education, emphasizing differences in graduate and undergraduate medical education as well as the challenges and promises of remote learning, as revealed by the COVID-19 pandemic. DATA SOURCES.­: Selected peer-reviewed publications representing the field of educational social science. CONCLUSIONS.­: Evidence-based methods described in education and social sciences can be effectively deployed in pathology education and especially remote learning, as necessitated by the current COVID-19 pandemic. Understanding established principles, such as cognitive load, competency-based learning, peer-assisted learning, and flipped classrooms may prove useful in developing effective, learner-centric content for pathology education.

Quantitative chemical imaging of breast calcifications in association with neoplastic processes.

Calcifications play an essential role in early breast cancer detection and diagnosis. However, information regarding the chemical composition of calcifications identified on mammography and histology is limited. Detailed spectroscopy reveals an association between the chemical composition of calcifications and breast cancer, warranting the development of novel analytical tools to better define calcification types. Previous investigations average calcification composition across broad tissue sections with no spatially resolved information or provide qualitative visualization, which prevents a robust linking of specific spatially resolved changes in calcification chemistry with the pathologic process. Method: To visualize breast calcification chemical composition at high spatial resolution, we apply hyperspectral stimulated Raman scattering (SRS) microscopy to study breast calcifications associated with a spectrum of breast changes ranging from benign to neoplastic processes, including atypical ductal hyperplasia, ductal carcinoma in situ, and invasive ductal carcinoma. The carbonate content of individual breast calcifications is quantified using a simple ratiometric analysis. Results: Our findings reveal that intra-sample calcification carbonate content is closely associated with local pathological processes. Single calcification analysis supports previous studies demonstrating decreasing average carbonate level with increasing malignant potential. Sensitivity and specificity reach >85% when carbonate content level is used as the single differentiator in separating benign from neoplastic processes. However, the average carbonate content is limiting when trying to separate specific diagnostic categories, such as fibroadenoma and invasive ductal carcinoma. Second harmonic generation (SHG) data can provide critical information to bridge this gap. Conclusion: SRS, combined with SHG, can be a valuable tool in better understanding calcifications in carcinogenesis, diagnosis, and possible prognosis. This study not only reveals previously unknown large variations of breast microcalcifications in association with local malignancy but also corroborates the clinical value of linking microcalcification chemistry to breast malignancy. More importantly, it represents an important step in the development of a label-free imaging strategy for breast cancer diagnosis with tremendous potential to address major challenges in diagnostic discordance in pathology.

Rapid pathology of lumpectomy margins with open-top light-sheet (OTLS) microscopy.

Open-top light-sheet microscopy is a technique that can potentially enable rapid ex vivo inspection of large tissue surfaces and volumes. Here, we have optimized an open-top light-sheet (OTLS) microscope and image-processing workflow for the comprehensive examination of surgical margin surfaces, and have also developed a novel fluorescent analog of H&E staining that is robust for staining fresh unfixed tissues. Our tissue-staining method can be achieved within 2.5 minutes followed by OTLS microscopy of lumpectomy surfaces at a rate of up to 1.5 cm2/minute. An image atlas is presented to show that OTLS image quality surpasses that of intraoperative frozen sectioning and can approximate that of gold-standard H&E histology of formalin-fixed paraffin-embedded (FFPE) tissues. Qualitative evidence indicates that these intraoperative methods do not interfere with downstream post-operative H&E histology and immunohistochemistry. These results should facilitate the translation of OTLS microscopy for intraoperative guidance of lumpectomy and other surgical oncology procedures.

Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins.

Intraoperative assessment of breast surgical margins will be of value for reducing the rate of re-excision surgeries for lumpectomy patients. While frozen-section histology is used for intraoperative guidance of certain cancers, it provides limited sampling of the margin surface (typically <1 % of the margin) and is inferior to gold-standard histology, especially for fatty tissues that do not freeze well, such as breast specimens. Microscopy with ultraviolet surface excitation (MUSE) is a nondestructive superficial optical-sectioning technique that has the potential to enable rapid, high-resolution examination of excised margin surfaces. Here, a MUSE system is developed with fully automated sample translation to image fresh tissue surfaces over large areas and at multiple levels of defocus, at a rate of ∼5 min / cm2. Surface extraction is used to improve the comprehensiveness of surface imaging, and 3-D deconvolution is used to improve resolution and contrast. In addition, an improved fluorescent analog of conventional H&E staining is developed to label fresh tissues within ∼5 min for MUSE imaging. We compare the image quality of our MUSE system with both frozen-section and conventional H&E histology, demonstrating the feasibility to provide microscopic visualization of breast margin surfaces at speeds that are relevant for intraoperative use.

Unexpected PAX8 Immunoreactivity in Metastatic High-grade Breast Cancer.

Immunohistochemistry (IHC) is often critical for distinction between metastatic carcinomas of Mullerian organ and breast origin. Paired box family protein 8 (PAX8) has been described as a transcription factor highly specific to neoplasms derived from Mullerian organs, thyroid, and kidney. PAX8 IHC with polyclonal and monoclonal antibody reagents was performed on 27 primary and 22 metastatic breast carcinomas. Eight of 27 primary breast carcinomas (30%) were positive for PAX8 with the monoclonal antibody reagent only; 0 of 22 were polyclonal anti-PAX8 immunoreactive. Substantial numbers of metastases had positive immunoreactivity for polyclonal anti-PAX8 (23%). Each of these metastases and additional cases (45% total) also had positive immunoreactivity for monoclonal anti-PAX8, including 5 of 7 brain metastases. IHC with monoclonal anti-PAX8 was positive on 6 of 7 primary breast carcinomas corresponding to PAX8-positive metastases. Together, these results indicate a significant fraction of breast carcinoma metastases and corresponding primary neoplasms have immunoreactivity for PAX8, and positivity rates depend on the antibody used. Diagnoses of metastatic breast carcinoma were achieved with the aid of clinical history and additional IHC in cases of PAX8 immunoreactivity. Contextual interpretation is imperative for PAX8 IHC, particularly when the differential diagnosis includes metastatic breast carcinoma with limited diagnostic material available.

Real-time Visualization of Breast Carcinoma in Pathology Specimens From Patients Receiving Fluorescent Tumor-Marking Agent Tozuleristide.

CONTEXT.­: Resection of breast carcinoma with adequate margins reduces the risk of local recurrence and reoperation. Tozuleristide (BLZ-100) is an investigational peptide-fluorophore agent that may aid in intraoperative tumor detection and margin assessment. In this study, fluorescence imaging was conducted ex vivo on gross breast pathology specimens. OBJECTIVES.­: To determine the potential of tozuleristide to detect breast carcinoma in fresh pathology specimens and the feasibility of fluorescence-guided intraoperative pathology assessment of surgical margins. DESIGN.­: Twenty-three patients received an intravenous bolus dose of 6 or 12 mg of tozuleristide at least 1 hour before surgery. Fifteen lumpectomy and 12 mastectomy specimens were evaluated for fluorescence by the site's clinical pathology staff using the SIRIS, an investigational near-infrared imaging device. The breast tissue was then processed per usual procedures. Fluorescent patterns were correlated with the corresponding hematoxylin-eosin-stained sections. Clinical pathology reports were used to correlate fluorescent signal to grade, histotype, prognostic marker status, and margin measurements. RESULTS.­: Tozuleristide fluorescence was readily observed in invasive and in situ breast carcinoma specimens. Most invasive carcinomas were bright and focal, whereas in situ lesions demonstrated a less intense, more diffuse pattern. Tozuleristide was detected in ductal and lobular carcinomas with a similar fluorescent pattern. Fluorescence was detected in high- and low-grade lesions, and molecular marker/hormone receptor status did not affect signal. Fluorescence could be used to identify the relationship of carcinoma to margins intraoperatively. CONCLUSIONS.­: Tumor targeting with tozuleristide allowed visual real-time distinction between pathologically confirmed breast carcinoma and normal tissue.

Disclosure of Harmful Medical Error to Patients: A Review With Recommendations for Pathologists.

Harmful error is an infrequent but serious challenge in the pathology laboratory. Regulatory bodies and advocacy groups have mandated and encouraged disclosure of error to patients. Many pathologists are interested in participating in disclosure of harmful error but are ill-equipped to do so. This review of the literature with recommendations examines the current state of the patient safety movement and error disclosure as it pertains to pathology and provides a practical and explicit guide for pathologists for who, when, and how to disclose harmful pathology error to patients. The authors provide a definition of harmful pathology error, and the rationale and principles behind effective disclosure are discussed. The changing culture of medicine and its effect on pathology is examined including the trend towards increasing transparency and patient engagement. Related topics are addressed including the management of expected adverse events, barriers to disclosure, and additional resources for the implementation of disclosure programs in pathology.

Raman-Encoded Molecular Imaging with Topically Applied SERS Nanoparticles for Intraoperative Guidance of Lumpectomy.

Intraoperative identification of carcinoma at lumpectomy margins would enable reduced re-excision rates, which are currently as high as 20% to 50%. Although imaging of disease-associated biomarkers can identify malignancies with high specificity, multiplexed imaging of such biomarkers is necessary to detect molecularly heterogeneous carcinomas with high sensitivity. We have developed a Raman-encoded molecular imaging (REMI) technique in which targeted nanoparticles are topically applied on excised tissues to enable rapid visualization of a multiplexed panel of cell surface biomarkers at surgical margin surfaces. A first-ever clinical study was performed in which 57 fresh specimens were imaged with REMI to simultaneously quantify the expression of four biomarkers HER2, ER, EGFR, and CD44. Combined detection of these biomarkers enabled REMI to achieve 89.3% sensitivity and 92.1% specificity for the detection of breast carcinoma. These results highlight the sensitivity and specificity of REMI to detect biomarkers in freshly resected tissue, which has the potential to reduce the rate of re-excision procedures in cancer patients. Cancer Res; 77(16); 4506-16. ©2017 AACR.

Pathologists' Perspectives on Disclosing Harmful Pathology Error.

CONTEXT: - Medical errors are unfortunately common. The US Institute of Medicine proposed guidelines for mitigating and disclosing errors. Implementing these recommendations in pathology will require a better understanding of how errors occur in pathology, the relationship between pathologists and treating clinicians in reducing error, and pathologists' experiences with and attitudes toward disclosure of medical error. OBJECTIVE: - To understand pathologists' attitudes toward disclosing pathology error to treating clinicians and patients. DESIGN: - We conducted 5 structured focus groups in Washington State and Missouri with 45 pathologists in academic and community practice. Participants were questioned about pathology errors, how clinicians respond to pathology errors, and what roles pathologists should play in error disclosure to patients. RESULTS: - These pathologists believe that neither treating physicians nor patients understand the subtleties and limitations of pathologic diagnoses, which complicates discussions about pathology errors. Pathologists' lack of confidence in communication skills and fear of being misrepresented or misunderstood are major barriers to their participation in disclosure discussions. Pathologists see potential for their future involvement in disclosing error to patients, but at present advocate reliance on treating clinicians to disclose pathology errors to patients. Most group members believed that going forward pathologists should offer to participate more actively in error disclosure to patients. CONCLUSIONS: - Pathologists lack confidence in error disclosure communication skills with both treating physicians and patients. Improved communication between pathologists and treating physicians could enhance transparency and promote disclosure of pathology errors. Consensus guidelines for best practices in pathology error disclosure may be useful.

'Non-classical' HER2 FISH results in breast cancer: a multi-institutional study.

The 2013 CAP/ASCO HER2 Testing Guidelines Update modified HER2 FISH categories such that some cases with 'monosomy', 'co-amplification/polysomy', low-level increased HER2 signals or clustered heterogeneity now are considered amplified or equivocal. This study examines the frequency and clinico-pathologic characteristics of breast cancers with equivocal or 'non-classical' HER2 FISH results. Breast cancers (2001-2014) with HER2 FISH results, HER2 immunohistochemistry, ER, grade, and age from three institutions (Stanford, UCSF, UWMC) were collected. HER2 FISH was interpreted using the updated recommendations. Amplified cases with non-classical results were grouped into the following categories: (1) 'monosomy' (ratio ≥2.0, mean HER2/cell<4.0); (2) 'co-amplified' (ratio<2.0, mean HER2/cell ≥6.0); (3) 'low amplified' (ratio ≥2.0, mean HER2/cell 4.0-5.9). Heterogeneous cases with clustered HER2-positive cells were also included. Of 8068 cases, 5.2% were equivocal and 4.6% had a 'non-classical' HER2 amplified result; 1.4% 'monosomy', 0.8% 'co-amplified', 2.1% 'low amplified', and 0.3% clustered heterogeneity. These cancers had a high frequency of ER positive (80.4%), Nottingham grade 3 (52.1%) results. The highest percentage of grade 3 cancers (66.7%) and positive HER2 immunohistochemistry (31.7%) was in the 'co-amplified' group. The 'monosomy' group had the highest percent grade 1 cancers (13.3%) and was most frequently HER2 immunohistochemistry negative (30.1%). Equivocal cases had very similar characteristics to the 'low-amplified' category. Cases with non-classical HER2 amplification or equivocal results are typically ER positive, higher grade cancers. 'Co-amplified' cases have the highest frequencies of aggressive characteristics and 'monosomy' cases the highest frequencies of lower risk features. With little clinical outcomes data currently available on these non-classical HER2 results, these results support the current classification scheme for HER2 FISH, with case-by-case correlation with additional clinical-pathologic factors when evaluating whether to offer HER2-targeted therapies in these non-classical cases.

Surgical Specimen Management: A Descriptive Study of 648 Adverse Events and Near Misses.

CONTEXT: - Surgical specimen adverse events can lead to delays in treatment or diagnosis, misdiagnosis, reoperation, inappropriate treatment, and anxiety or serious patient harm. OBJECTIVES: - To describe the types and frequency of event reports associated with the management of surgical specimens, the contributing factors, and the level of harm associated with these events. DESIGN: - A retrospective review was undertaken of surgical specimen adverse events and near misses voluntarily reported in the University HealthSystem Consortium Safety Intelligence Patient Safety Organization database by more than 50 health care facilities during a 3-year period (2011-2013). Event reports that involved surgical specimen management were reviewed for patients undergoing surgery during which tissue or fluid was sent to the pathology department. RESULTS: - Six hundred forty-eight surgical specimen events were reported in all stages of the specimen management process, with the most common events reported during the prelaboratory phase and, specifically, with specimen labeling, collection/preservation, and transport. The most common contributing factors were failures in handoff communication, staff inattention, knowledge deficit, and environmental issues. Eight percent of the events (52 of 648) resulted in either the need for additional treatment or temporary or permanent harm to the patient. CONCLUSIONS: - All phases of specimen handling and processing are vulnerable to errors. These results provide a starting point for health care organizations to conduct proactive risk analyses of specimen handling procedures and to design safer processes. Particular attention should be paid to effective communication and handoffs, consistent processes across care areas, and staff training. In addition, organizations should consider the use of technology-based identification and tracking systems.

NDER: A novel web application using annotated whole slide images for rapid improvements in human pattern recognition.

CONTEXT: Whole-slide images (WSIs) present a rich source of information for education, training, and quality assurance. However, they are often used in a fashion similar to glass slides rather than in novel ways that leverage the advantages of WSI. We have created a pipeline to transform annotated WSI into pattern recognition training, and quality assurance web application called novel diagnostic electronic resource (NDER). AIMS: Create an efficient workflow for extracting annotated WSI for use by NDER, an attractive web application that provides high-throughput training. MATERIALS AND METHODS: WSI were annotated by a resident and classified into five categories. Two methods of extracting images and creating image databases were compared. Extraction Method 1: Manual extraction of still images and validation of each image by four breast pathologists. Extraction Method 2: Validation of annotated regions on the WSI by a single experienced breast pathologist and automated extraction of still images tagged by diagnosis. The extracted still images were used by NDER. NDER briefly displays an image, requires users to classify the image after time has expired, then gives users immediate feedback. RESULTS: The NDER workflow is efficient: annotation of a WSI requires 5 min and validation by an expert pathologist requires An additional one to 2 min. The pipeline is highly automated, with only annotation and validation requiring human input. NDER effectively displays hundreds of high-quality, high-resolution images and provides immediate feedback to users during a 30 min session. CONCLUSIONS: NDER efficiently uses annotated WSI to rapidly increase pattern recognition and evaluate for diagnostic proficiency.

Lobular in-situ neoplasia on breast core needle biopsy: imaging indication and pathologic extent can identify which patients require excisional biopsy.

BACKGROUND: The surgical management of lobular in-situ neoplasia (LN) identified by core needle biopsy (CNB) is currently variable. Our institution has routinely excised LN on CNB since 2003, allowing for an unbiased assessment of upgrade rates. METHODS: Cases of LN on CNB, including atypical lobular hyperplasia (ALH) and lobular carcinoma-in-situ (LCIS), were identified in our pathology database. CNBs with concurrent pleomorphic LCIS, ductal carcinoma-in-situ (DCIS), and invasive carcinoma were excluded. Imaging indication/modality, biopsy indication, and radiologic concordance were determined. Pathology review included scoring total foci of LN in each CNB. Upgrade rates to invasive carcinoma or DCIS at excision were calculated. RESULTS: A total of 106 cases of LN (73 ALH and 33 LCIS) on CNB were identified. Thirty patients had concurrent atypical ductal hyperplasia (ADH) and 76 had LN alone; 93 (88%) of the patients had available surgical follow-up (25 LN + ADH and 68 LN alone). The upgrade rate at excision was 16% (4 of 25) for LN + ADH and 4.4% (3 of 68) for LN alone. Patients with LN alone and discordant imaging, imaging for high-risk indications, or extensive LCIS (>4 foci) accounted for all the upgrades. Normal-risk patients who underwent biopsy to assess calcifications found by routine mammographic screening with LN alone did not result in upgrade. CONCLUSIONS: Women with a CNB diagnosis of LN for calcifications found on routine, normal-risk mammographic screening have a negligible risk of upgrade and may not require excisional biopsy. However, excisional biopsy should be offered to women undergoing imaging for other indications or with >4 foci of LN on CNB.

Frequency of HER2 heterogeneity by fluorescence in situ hybridization according to CAP expert panel recommendations: time for a new look at how to report heterogeneity.

In 2009, a College of American Pathologists expert panel published supplemental HER2 testing recommendations suggesting that cases with between 5% and 50% individual cells amplified by fluorescence in situ hybridization be reported as "heterogeneous for HER2 gene amplification." We examined the implications of applying these recommendations to clinical practice in 1,329 consecutive breast cancer cases. By ratio criteria, 23.2% of cases met the proposed criteria for heterogeneity, of which 81.6% were not amplified and 15.5% were equivocal by standard criteria. In contrast, the proposed criteria based on HER2 signals per cell classified only 6.5% of cases as heterogeneous, of which only 8% (7/87) were not amplified and 79% (69/87) were equivocal by standard criteria. These results show that the 2 proposed criteria sets are not equivalent and that the ratio-based definition results in large numbers of nonamplified cases being classified as heterogeneous. Further definition of optimal criteria with clinical relevance is needed before HER2 heterogeneity reporting is adopted in routine practice.

Communicating pathology and laboratory errors: anatomic pathologists' and laboratory medical directors' attitudes and experiences.

Physicians are urged to communicate more openly following medical errors, but little is known about pathologists' attitudes about reporting errors to their institution and disclosing them to patients. We undertook a survey to characterize pathologists' and laboratory medical directors' attitudes and experience regarding the communication of errors with hospitals, treating physicians, and affected patients. We invited 260 practicing pathologists and 81 academic hospital laboratory medical directors to participate in a self-administered survey. This survey included questions regarding estimated error rates and barriers to and experience with error disclosure. The majority of respondents (~95%) reported having been involved with an error, and respondents expressed near unanimous belief that errors should be disclosed to hospitals, colleagues, and patients; however, only about 48% thought that current error reporting systems were adequate. In addition, pathologists expressed discomfort with their communication skills in regard to error disclosure. Improving error reporting systems and developing robust disclosure training could help prevent future errors, improving patient safety and trust.

Biome representational in silico karyotyping.

Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping-biome representational in silico karyotyping (BRISK)-as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery.

Achieving 95% cross-methodological concordance in HER2 testing: causes and implications of discordant cases.

We were interested in determining our concordance between fluorescence in situ hybridization (FISH) and a previously validated immunohistochemical HER2 assay to identify possible reasons for discordance and to determine if all reasons for discordance were addressed by the American Society of Clinical Oncology/College of American Pathologists guidelines. We reviewed 697 cases (2004-2007) in which HER2 immunohistochemical and FISH testing were concurrently done. Overall concordance between nonequivocal immunohistochemical and FISH results was 96%. Of the 19 discordant cases, 13 (68%) were interpreted as positive immunohistochemically but negative by FISH. The primary reason for this discordance was immunohistochemical interpretation. Weak stain intensity, granular staining, and interpretation in areas of crush artifact were identified as the most common issues. Of the 6 cases interpreted as immunohistochemically negative and FISH-positive, 2 were from patients known to be receiving trastuzumab at the time of biopsy, 1 was very close to the FISH equivocal category, and 4 cases had fewer than 1.5 CEP17 signals per cell (1 patient in this group was also receiving trastuzumab). Focusing on issues with HER2 immunohistochemical interpretation can improve concordance rates for immunohistochemically positive cases, but biologic reasons may explain some discordant immunohistochemically negative cases.