Development of a Body of Knowledge for the Clinical Bioinformatician: Perspectives from the Association for Molecular Pathology's Clinical Genomics Bioinformatician Body of Knowledge Steering Committee.

The use of next-generation sequencing and other high-throughput technologies in the clinical molecular diagnostics laboratory requires the application of bioinformatics pipelines and other computational tools to analyze, visualize, and store these clinical data. Clinical bioinformaticians, individuals with the skills to develop, validate, and deploy these tools in a clinical setting, are needed to ensure that these molecular diagnostic technologies can be appropriately used for clinical care. Building on existing expertise in informatics, next-generation sequencing, and clinical molecular diagnostics, the Association for Molecular Pathology has generated a series to establish an initial clinical bioinformatician body of knowledge.

Dabrafenib and trametinib in Langerhans cell histiocytosis and other histiocytic disorders.

The standard treatment for Langerhans cell histiocytosis (LCH) is chemotherapy, although the failure rates are high. Since MAP-kinase activating mutations are found in most cases, BRAF- and MEK-inhibitors have been used successfully to treat patients with refractory or relapsed disease. However, data on long-term responses in children are limited and there are no data on the use of these inhibitors as first-line therapy.

Current clinical practices and challenges in molecular testing: a GOAL Consortium Hematopathology Working Group report.

While molecular testing of hematologic malignancies is now standard of care, there is variability in practice and testing capabilities between different academic laboratories, with common questions arising on how to best meet clinical expectations. A survey was sent to hematopathology subgroup members of the Genomics Organization for Academic Laboratories consortium to assess current and future practice and potentially establish a reference for peer institutions. Responses were received from 18 academic tertiary-care laboratories regarding next-generation sequencing (NGS) panel design, sequencing protocols and metrics, assay characteristics, laboratory operations, case reimbursement, and development plans.

Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines: A Report from the Association for Molecular Pathology.

To assess the clinical implementation of the 2017 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, identify content that may result in classification inconsistencies, and evaluate implementation barriers, an Association for Molecular Pathology Working Group conducted variant interpretation challenges and a guideline implementation survey. A total of 134 participants participated in the variant interpretation challenges, consisting of 11 variants in four cancer cases. Results demonstrate 86% (range, 54% to 94%) of the respondents correctly classified clinically significant variants, variants of uncertain significance, and benign/likely benign variants; however, only 59% (range, 39% to 84%) of responses agreed with the working group's consensus intended responses regarding both tiers and categories of clinical significance.

Recommendations for the Use of in Silico Approaches for Next-Generation Sequencing Bioinformatic Pipeline Validation: A Joint Report of the Association for Molecular Pathology, Association for Pathology Informatics, and College of American Pathologists.

In silico approaches for next-generation sequencing (NGS) data modeling have utility in the clinical laboratory as a tool for clinical assay validation. In silico NGS data can take a variety of forms, including pure simulated data or manipulated data files in which variants are inserted into existing data files. In silico data enable simulation of a range of variants that may be difficult to obtain from a single physical sample.

Principles and Validation of Bioinformatics Pipeline for Cancer Next-Generation Sequencing.

Clinical bioinformatics plays a key role in the implementation of clinical next-generation sequencing (NGS) testing infrastructure. Bioinformatics workflows in a clinical laboratory are complex and therefore need to be validated as part of an end-to-end NGS assay validation before clinical use. The validation cohort should be representative of the types of samples, types of variants, lower limits of detection of the assay, as well as sequence context of the panel.

Lineage switching of the cellular distribution of BRAFV600E in multisystem Langerhans cell histiocytosis.

Most children with high-risk Langerhans cell histiocytosis (LCH) have BRAFV600E mutation. BRAFV600E alleles are detectable in myeloid mononuclear cells at diagnosis but it is not known if the cellular distribution of mutation evolves over time. Here, the profiles of 16 patients with high-risk disease were analyzed.

Containers in Bioinformatics: Applications, Practical Considerations, and Best Practices in Molecular Pathology.

Systematic implementation of bioinformatics resources for next generation sequencing (NGS)-based clinical testing is an arduous undertaking. One of the key challenges involves developing an ecosystem of information technology infrastructure for enabling scalable and reproducible bioinformatics services that is resilient and secure for handling genetic and protected health information, often embedded in an existing non-bioinformatics-oriented infrastructure. Container technology provides an ideal and infrastructure-agnostic solution for molecular laboratories developing and using bioinformatics pipelines, whether on-premise or using the cloud.

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).

Purpose: Several professional societies have published guidelines for the clinical interpretation of somatic variants, which specifically address diagnostic, prognostic, and therapeutic implications. Although these guidelines for the clinical interpretation of variants include data types that may be used to determine the oncogenicity of a variant (eg, population frequency, functional, and in silico data or somatic frequency), they do not provide a direct, systematic, and comprehensive set of standards and rules to classify the oncogenicity of a somatic variant. This insufficient guidance leads to inconsistent classification of rare somatic variants in cancer, generates variability in their clinical interpretation, and, importantly, affects patient care.

ALK-positive histiocytosis: a new clinicopathologic spectrum highlighting neurologic involvement and responses to ALK inhibition.

ALK-positive histiocytosis is a rare subtype of histiocytic neoplasm first described in 2008 in 3 infants with multisystemic disease involving the liver and hematopoietic system. This entity has subsequently been documented in case reports and series to occupy a wider clinicopathologic spectrum with recurrent KIF5B-ALK fusions. The full clinicopathologic and molecular spectra of ALK-positive histiocytosis remain, however, poorly characterized.

Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group.

The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as several other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians, and patients in the ability to generate, communicate, consume, and use genomic test results.

Molecular characterization of pleomorphic mesothelioma: a multi-institutional study.

The molecular alterations of pleomorphic mesotheliomas are largely unknown. In the present study, we performed whole-exome sequencing (WES) on 24 pleomorphic mesotheliomas in order to better characterize the molecular profile of this rare histologic variant. BAP1 protein expression and CDKN2A deletion by FISH were also evaluated.

The Utility of Next-Generation Sequencing in Advanced Breast and Gynecologic Cancers.

Objectives: Next-generation sequencing (NGS) has the potential to identify genetic alterations that are actionable with targeted therapy. Our objective was to identify the impact of NGS testing on advanced breast and gynecologic malignancies.

Methods: A retrospective review of 108 patients who underwent NGS testing between 2015 and 2019 was performed.

The Ethics of Artificial Intelligence in Pathology and Laboratory Medicine: Principles and Practice.

Growing numbers of artificial intelligence applications are being developed and applied to pathology and laboratory medicine. These technologies introduce risks and benefits that must be assessed and managed through the lens of ethics. This article describes how long-standing principles of medical and scientific ethics can be applied to artificial intelligence using examples from pathology and laboratory medicine.

Whole exome sequencing reveals BAP1 somatic abnormalities in mesothelioma in situ.

Objectives: We have recently described the first cases of mesothelioma in situ, identified as a pure surface population of mesothelial cells that have lost BAP1 nuclear staining, in the setting of no clinically/radiologically demonstrable mesothelial tumor. These cases have a high propensity to develop invasive mesothelioma. The genetic events that lead to the development of mesothelioma in situ are unknown, nor is it known whether mesothelioma in situ cases carry somatic or germline mutations.

Is Next-Generation Sequencing Alone Sufficient to Reliably Diagnose Gliomas?

The power and widespread use of next-generation sequencing (NGS) in surgical neuropathology has raised questions as to whether NGS might someday fully supplant histologic-based examination. We therefore sought to determine the feasibility of relying on NGS alone for diagnosing infiltrating gliomas. A total of 171 brain lesions in adults, all of which had been analyzed by GlioSeq NGS, comprised the study cohort.

KRAS amplification in metastatic colon cancer is associated with a history of inflammatory bowel disease and may confer resistance to anti-EGFR therapy.

Mutations in RAS occur in 30-50% of metastatic colorectal carcinomas (mCRCs) and correlate with resistance to anti-EGFR therapy. Consequently, mCRC biomarker guidelines state RAS mutational testing should be performed when considering EGFR inhibitor treatment. However, a small subset of mCRCs are reported to harbor RAS amplification.

An institutional experience evaluating hTERT immunostaining in 100 consecutive ThinPrep urine specimens.

Introduction: Studies have shown that expression of human telomerase reverse transcriptase (hTERT) in mature urothelial cells indicates an increased risk of urothelial carcinoma. We evaluated the utility of immunocytochemistry with a commercially available anti-hTERT antibody (SCD-A7) in 100 consecutive urine cytology specimens using ThinPrep processing.

Materials And Methods: ThinPrep slides prepared from 100 consecutive urine specimens were stained using anti-hTERT antibody (SCD-A7) after staining optimization had been successfully completed.

Interactive Browser-Based Genomics Data Visualization Tools for Translational and Clinical Laboratory Applications.

Visualization-driven data exploration is a highly effective modality for interpreting and discovering insights from high-throughput genomics data sets; however, it is vastly underutilized in routine workflows in clinical and translation settings. We have developed three open-source, browser-based, interactive genomics data visualization widgets that can be used as intuitive stand-alone applications or integrated with existing web-based laboratory information solutions. The widgets were developed in JavaScript using the D3.

Clinical Utility of GlioSeq Next-Generation Sequencing Test in Pediatric and Young Adult Patients With Brain Tumors.

Brain tumors are the leading cause of death in children. Establishing an accurate diagnosis and therapy is critical for patient management. This study evaluated the clinical utility of GlioSeq, a next-generation sequencing (NGS) assay, for the diagnosis and management of pediatric and young adult patients with brain tumors.

Real-Time Targeted Genome Profile Analysis of Pancreatic Ductal Adenocarcinomas Identifies Genetic Alterations That Might Be Targeted With Existing Drugs or Used as Biomarkers.

Background & Aims: It has been a challenge to select treatment for patients with pancreatic ductal adenocarcinomas (PDACs) based on genome alterations. We performed targeted genomic profile analyses of a large number of PDACs to assess the full spectrum of actionable genomic alterations.

Methods: We performed targeted genomic profile analyses of 3594 PDAC samples from an international cohort, including capture-based targeted genomic profiling of as many as 315 cancer-associated genes and intron regions of 28 genes that are rearranged in cancer cells.

GLIS Rearrangement is a Genomic Hallmark of Hyalinizing Trabecular Tumor of the Thyroid Gland.

Background: Hyalinizing trabecular tumor (HTT) is a rare thyroid neoplasm with a characteristic trabecular growth pattern and hyalinization. This lesion has been the subject of long-term controversy surrounding its genetic mechanisms, relationship to papillary thyroid carcinoma (PTC), and malignant potential. Due to the presence of nuclear features shared with PTC, HTT frequently contributes to a false-positive cytology, which hampers patient management.

Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing-Based Assays for Cancer.

Human Genome Variation Society (HGVS) nomenclature is a de facto clinical standard for reporting DNA sequence variants. With increasing use of high-throughput sequencing, manual generation of HGVS nomenclatures for all variants is impractical and error-prone. It is therefore beneficial to include one or more HGVS generator tools in next-generation sequencing (NGS) bioinformatics pipelines to enable automated, consistent, and accurate generation of HGVS nomenclature after appropriate validation.