CAP TODAY and the Association for Molecular Pathology have teamed up to bring molecular case reports to CAP TODAY readers. AMP members write the reports using clinical cases from their own practices that show molecular testing’s important role in diagnosis, prognosis, and treatment. The following report comes from Washington University School of Medicine in St. Louis. If you would like to submit a case report, please send an email to the AMP at amp@amp.org. For more information about the AMP and all previously published case reports, visit www.amp.org.
Read More »Pathology navigators bring molecular test efficiencies
November 2023—Few things in the laboratory can do so much at once: boost histotechnologist productivity, safeguard tissue, offer a career path and help retain staff, keep watch on test utilization, and reduce the number of calls to pathologists and turnaround time, all while advocating for the patient.
Read More »For infectious disease, what tests and at what time in disease course
September 2023—For the tickborne and mosquito-borne arboviruses, which are frequently more transient in blood and tissue than other pathogens, both molecular and serologic testing have a place in the diagnostic toolkit.
Read More »Genetic counseling within the laboratory: For oncology cases, lab’s consult service plugs gap
September 2023—What happens when an oncologist cannot confidently determine what type of genetic test to order for their patient? Where can a provider turn if they do not know whether a genetic variant is clinically actionable? As genetic testing becomes a more integral part of personalized medicine and health care in general, there is a growing need to bridge the gap between those skilled in molecular diagnostics and those on the patient-facing side of care. In response to this need, the Center for Integrated Diagnostics (CID), a high-complexity molecular diagnostics laboratory at Massachusetts General Hospital, created its Consultation Service.
Read More »Growing pains put gene panels in a pinch
April 2023—After years of excitement and scientific breakthroughs, the use of molecular testing to guide cancer therapeutics finally is coming into its own. Unfortunately, it appears to have landed in the wrong place at the right time. That place is a lonely spot, surrounded by gaps in economics and coverage, as well as knowledge, guidelines, ordering patterns, turnaround times, reporting, and the like. So plentiful are the gaps that, put together, they could form a vast, inhospitable space, a veritable Colorado Plateau, with molecular testing as a majestic, enticing but remote rocky pinnacle in the middle. Think Monument Valley. It’s worth the trek. The evidence in support of genomic profiling continues to grow. Simply put, “Patients with the right markers who get the right drugs do better,” says Neal Lindeman, MD, vice chair, laboratory medicine and molecular pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine/New York Presbyterian Hospital. But as numerous studies are showing, the lag in testing is growing as well.
Read More »No time to wait: How rapid NGS changed cancer care
November 2022—Rapid next-generation sequencing in a community hospital setting, performed by histotechnologists and interpreted by anatomic pathologists, is possible and paying off, and it “makes the pathologist a much more meaningful part of the precision oncology team,” says Brandon Sheffield, MD, of the Department of Laboratory Medicine, William Osler Health System, Brampton/Etobicoke, Ontario. “It has changed practice at our hospitals,” he says.
Read More »Resistance targets: blood culture ID panel pitfalls
May 2021—Most of the time, bloodstream infection antimicrobial resistance results achieved with blood culture molecular ID panels will be accurate. When and why they might not be was the focus of an AMP 2020 virtual session. “I don’t want to lead anyone to believe that these are not good, accurate, and important types of tests,” Richard E. Davis, PhD, D(ABMM), MLS(ASCP)CM, said of the panels.
Read More »NGS in more labs? IFCC group aims to ease the way
May 2021—When it comes to next-generation sequencing, don’t count out community hospital labs, especially as black-box solutions come on the market. That’s the hope of members of an International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) working group that aims to help clinical labs develop in-house NGS programs. Large-scale genomic testing won’t be necessary or practical at the community hospital level. But hospital-based genomic testing programs should set out to meet the NCCN guideline targets and provide testing for which a wide range of sample input and quality can be accepted, says Robyn Sussman, PhD, a member of the IFCC working group and molecular development assistant director, Penn Precision and Computational Diagnostics, University of Pennsylvania Perelman School of Medicine.
Read More »Seeking stability in gene nomenclature
April 2021—Human first names are not necessarily known for being meaningful—or unique for that matter. When Shakespeare’s Juliet muses, “What’s in a name?” she’s observing that her lover’s name is more or less an arbitrary label without relevance to the essence of Romeo.
Read More »Problems, solutions at core of UTI, C. diff modules
April 2021—Urinary tract infections and Clostridioides (Clostridium) difficile testing are the topics of two of the modules released recently in the CAP Test Ordering Program. The Laboratory Workup for Urinary Tract Infections module became available online in January, and C. difficile Testing in October 2020 (www.cap.org/member-resources/test-ordering-program). The program is free to CAP members.
Read More »AMP case report: Adult B-lymphoblastic leukemia/lymphoma, BCR-ABL1-like
April 2021—A 71-year-old female with a history of asthma and hypertension initially presented to her local hospital complaining of shortness of breath. She was found to be pancytopenic with severe anemia (hemoglobin 5 g/dL). She was subsequently transferred to a tertiary care facility for further evaluation. Bone marrow biopsy revealed a hypercellular marrow composed of 72 percent blasts. Flow cytometric analysis revealed a B-lymphoblast immunophenotype with expression of CD34, dim CD45, CD19, CD79a, CD22, HLA-DR, TDT, CD200, CD33, and dim CD13.
Read More »For POC molecular, pauses, plans, and testing precautions
January 2021—The use of molecular assays at the point of care is exciting but a bit scary. That’s how Raquel Martinez, PhD, D(ABMM), described the state of the science for molecular infectious disease POC testing when she spoke in a virtual AMP session in November with Omai Garner, PhD, D(ABMM), of UCLA Health.
Read More »AMP case report: Role of lymphoma sequencing panel in diagnosis of pediatric-type follicular lymphoma
November 2020—Pediatric-type follicular lymphoma (PTFL) is a rare form of lymphoma that was recognized as a new diagnostic entity in the revised 2016 WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. The classic features of PTFL include male predominance, localized stage I lymphadenopathy, blastoid morphology, high proliferation index, and exceedingly good response rate to local excision.
Read More »Molecular methods shown to push cases forward: Case studies in hematopathology
October 2020—B-ALL with aberrant expression of myeloid markers should be investigated further for specific gene abnormalities, including ZNF384 rearrangements, and microarray analysis may play an important role.
Read More »AMP case report: TET2TET— reconciling conflicting genomic reports
October 2020—After 20 years of CAP advocacy, synoptic reporting in surgical pathology is ubiquitous. This came about in part by fiat and in part by all parties agreeing on the importance of standardization for patient care. The merits of some elements remain controversial. Molecular pathology, a newer discipline, does not offer the scope for creative writing once available in surgical pathology.
Read More »MGMT promoter methylation: assays, implications
October 2020—With MGMT gene promoter methylation observed in about 50 percent of glioblastomas, it remains a biomarker of strong clinical interest in routine practice, even though it’s not the sole determinant in decisions related to therapy. PCR and pyrosequencing are the most commonly used assays, and there’s a technique that is not yet mainstream but gaining interest, said Tejus A. Bale, MD, PhD, assistant attending pathologist in the Department of Neuropathology and Diagnostic Molecular Pathology, Memorial Sloan Kettering Cancer Center. Dr. Bale spoke June 30 in the first of a series of Association for Molecular Pathology webinars on emerging and evolving biomarkers.
Read More »Steps to verifying SARS-CoV-2 antibody assays and what’s known about protective immunity
August 2020—The CAP treats emergency use authorization assays similar to FDA-cleared assays and thus requires full verification. In a June 4 CAP webinar, Neil Anderson, MD, D(ABMM), assistant director of clinical microbiology, Washington University School of Medicine in St. Louis, walked through how to approach verification for SARS-CoV-2 assays. Co-presenter Elitza Theel, PhD, D(ABMM), director of the infectious diseases serology laboratory at Mayo Clinic, reported what’s known about protective immunity against SARS-CoV-2.
Read More »AMP case report: Burkitt-like lymphoma with 11q aberration
August 2020—Burkitt-like lymphoma with 11q aberration (BLL-11q) is a new provisional entity in the revised 2016 WHO classification of hematopoietic and lymphoid tumors.1 It refers to a subset of high-grade B-cell lymphomas that resemble Burkitt lymphoma with similar morphology, phenotype, and gene expression profiling, but lack MYC gene rearrangements. Instead, these lymphomas carry chromosome 11q proximal gains and telomeric losses, suggesting co-dysregulation of oncogenes and tumor suppressor genes.
Read More »Outbreak detection of novel pathogens: Is AI the answer?
July 2020—A machine learning algorithm, used in conjunction with BioFire’s Syndromic Trends, demonstrated a mechanism for near real-time outbreak detection of enterovirus D68, says a study reported in the Journal of Clinical Virology.
Read More »AMP case report: CCND1/IGH fusion amplification in a case of plasma cell myeloma
June 2020—A middle-aged adult presented with shortness of breath and bruising and was found to have leukopenia (WBC 4.16 K/mcL; normal range 4.50–11.00 K/mcL) and anemia (Hgb 7.6 g/dL; normal range 12–16 g/dL) with rouleaux. The hypercellular bone marrow core biopsy (80–90 percent cellularity) contained 90 percent plasma cells of variable morphology, some with prominent nucleoli and occasional binucleate forms.
Read More »Carcinoma of unknown primary case reviewed in tumor board session
January 2020—A molecular oncology tumor board session at CAP19 explored a case of cancer of unknown primary, presented by medical oncologist Alexander Drilon, MD, research director of early drug development at Memorial Sloan Kettering Cancer Center, and Rondell P. Graham, MBBS, head of GI/liver pathology at Mayo Clinic Rochester.
Read More »AMP case report: Diagnostic pitfalls of testing rare molecular aberrations in lung adenocarcinomas
February 2019—Lung cancer is the second most commonly diagnosed malignancy and results in the most cancer-related deaths each year in the United States, but actionable aberrations in EGFR, ALK, ROS1, and other oncogenes are improving outcomes for a subset of patients.
Read More »Molecular ‘bucket list’ for renal cancer
September 2018—Leo Tolstoy is not listed as a coauthor on the most recent iteration of The Cancer Genome Atlas on renal cell carcinoma, which focuses on molecular characterization of RCC.
Read More »Next step? The switch from stool culture to PCR
September 2018—The advantages of moving from stool culture to a molecular platform are many: faster time to results, more accurate pathogen identification, a savings of space and staff time. For Jose Alexander, MD, D(ABMM), SM, MB(ASCP), and colleagues at Florida Hospital Orlando, another plus is being able to adhere to the Infectious Diseases Society of America guideline suggestion that labs use a diagnostic approach that can distinguish O157 from non-O157 E. coli and Shiga toxin 1 from Shiga toxin 2 E. coli.
Read More »PGx testing: recommended alleles for CYP2C19 panels
August 2018—After more than a year of gathering information and deliberating, members of the Association for Molecular Pathology Pharmacogenomics Working Group have issued the first in what will be a series of recommendations to standardize pharmacogenetic testing.
Read More »Molecular lung cancer testing: from guideline to practice
August 2018—Testing turnaround times can affect whether non-small cell lung cancer patients receive an EGFR or ALK tyrosine kinase inhibitor when indicated. At disease progression on an EGFR TKI, integrating circulating tumor DNA and tissue-based testing may lessen some of the limitations of each form of testing.
Read More »Pharmacogenomics advocates make case for wider use
May 2018—Use of pharmacogenomic testing is still limited, despite ample research, the existence of guidelines, and the emerging evidence it can help patients. Panels can be costly and insurance coverage variable, and providers need guidance—from pharmacists, the lab, decision support alerts—in knowing what and when to order and in understanding the results. Plus, patients move.
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