American journal of clinical pathology最新文献

{"title":"Systematic comparison of GPT models for the analysis of pathology reports in a low-resource language: A case study for Turkish.","authors":"Omer Faruk Dilbaz, Muhammet Nusret Ozates, Beyza Bolat, Cigdem Gunduz-Demir, Ibrahim Kulac","doi":"10.1093/ajcp/aqaf091","DOIUrl":"https://doi.org/10.1093/ajcp/aqaf091","url":null,"abstract":"<p><strong>Objective: </strong>Large language models (LLMs) can process text for various applications, including surgical pathology reports, but studies primarily focus on English. Their performance has not been systematically studied for a low-resource language. To analyze the performance of various LLMs, 759 Turkish pathology reports from 5 different procedures were selected.</p><p><strong>Methods: </strong>We used 10 examples from every procedure to optimize prompts for OpenAI's GPT-3.5 Turbo, GPT-4o mini, and GPT-4o. The rest was used to test generalizability.</p><p><strong>Results: </strong>The GPT-4o model performed superior in processing Turkish reports (12%-25% over GPT-3.5 Turbo, 3%-16% over GPT-4o mini). English-translated versions of the reports have been demonstrated to enhance accuracy, especially for GPT-3.5 Turbo and GPT-4o mini. GPT4-o showed comparable results for Turkish and English. A 12% to 22% performance gap was observed between GPT-4o and GPT-3.5 Turbo for English-translated reports. Domain-related tips in prompts increased accuracy. Results of larger test sets were parallel for all models with the validation set. The GPT-4o model yielded the most accurate results, while the GPT-4o mini model demonstrated intermediate performance. The GPT-3.5 Turbo model exhibited the least accuracy.</p><p><strong>Conclusions: </strong>To our knowledge, for the first time in the literature, we have demonstrated the performance of GPT models in Turkish surgical pathology reports, and results indicate that data extracted by GPT-4o are almost ready for direct application.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IGL::CCND1 detected by optical genome mapping revises diagnosis of a B-cell lymphoma.","authors":"Soma R Chakraborty, Michelle A Bickford, Narcisa A Smuliac, Kyle A Tonseth, Farzana Murad, Jing Bao, Devon N Wilson, Heather B Steinmetz, Lauren M Wainman, Liam L Donnely, Swaroopa PonnamReddy, Jeremiah X Karrs, Prabhjot Kaur, Wahab A Khan","doi":"10.1093/ajcp/aqaf096","DOIUrl":"https://doi.org/10.1093/ajcp/aqaf096","url":null,"abstract":"<p><strong>Objective: </strong>Differentiating between the repertoire of immunoglobulin rearrangements is important in guiding diagnoses and management of B-cell lymphoma processes. A subset of these disease entities, such as chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL), can show distinct genomic profiles with a shared cell of origin. In this report, we describe a rare case in which differentiating between the immunoglobulin family of rearrangements (IGH, IGK, IGL) with optical genome mapping (OGM) helped revise the clinical suspicion of CLL.</p><p><strong>Methods: </strong>We present a 50-year-old woman with a lymphoproliferative disorder. Her clinical laboratory genetics workup included chromosomal banding analysis, fluorescence in situ hybridization, next-generation sequencing, and OGM. Optical genome mapping was performed on the bone marrow specimen, starting with the ultra-high molecular weight DNA mapped on the Saphyr system. Structural variants with OGM were detected using rare variant analysis set to default parameters.</p><p><strong>Results: </strong>In 2021, flow cytometry performed on the peripheral blood detected a monotypic CD5+/CD23+ B-cell population. A subsequent bone marrow in 2024 detected similar findings by flow with κ light chain restriction. Chromosomal banding analysis found a translocation between the long arms of chromosomes 11 and 22. Optical genome mapping demonstrated that this translocation involved the CCND1 locus juxtaposed to the regulatory immunoglobulin λ (IGL) gene cluster.</p><p><strong>Conclusions: </strong>We present a case of CD5+/CD10- small B-cell lymphoma that immunophenotypically resembled CLL but showed positive immunostaining for cyclin D1. The combination of the clinicopathologic findings and the CCND1 translocation involving IGL, detected by OGM, supported a revised diagnosis of MCL.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abnormal choline transporter immunohistochemical staining in older children with chronic constipation not associated with Hirschsprung disease.","authors":"Erin L J Alston, Alejandro Flores, Samuel Nurko, Christopher Schottmiller, Lisa Teot, Jeffrey D Goldsmith","doi":"10.1093/ajcp/aqaf095","DOIUrl":"https://doi.org/10.1093/ajcp/aqaf095","url":null,"abstract":"<p><strong>Objective: </strong>Choline transporter (ChT) immunohistochemistry (IHC) is a new ancillary test that aids in the diagnosis of Hirschsprung disease in newborns and infants. The behavior of this stain in older children (greater than 1 year of age) with chronic constipation, where Hirschsprung disease is clinically unlikely, has not been investigated. The aim of our study was to determine the behavior of ChT IHC in rectal biopsies performed on older children with chronic constipation.</p><p><strong>Methods: </strong>We performed ChT IHC on 54 endoscopically obtained mucosal biopsies from 41 patients with chronic constipation. For comparison, ChT IHC was also performed on 12 endoscopically obtained mucosal biopsies from 8 nonconstipated children, 11 rectal suction biopsies from 9 infants, and 6 full-thickness biopsies from 5 older children with confirmed Hirschsprung disease. We reviewed the ChT IHC staining and quantified the number of positive staining neurites in the muscularis mucosae.</p><p><strong>Results: </strong>Of the 54 rectal biopsies from children with chronic constipation, 13 (24%) showed an aganglionic staining pattern, and 7 (13%) showed equivocal staining. The number of immunoreactive neurites in the muscularis mucosae in constipated children without Hirschsprung disease, however, was substantially lower than seen in patients with Hirschsprung disease. In comparison, in children without constipation, most biopsies showed a ganglionic pattern (11/12 [92%]). All biopsies from the Hirschsprung disease group demonstrated an aganglionic pattern.</p><p><strong>Conclusions: </strong>In our cohort, ChT IHC showed an abnormal/aganglionic or equivocal pattern in 37% of patients with chronic constipation. As such, ChT IHC results should be interpreted with caution when performed on rectal biopsies in chronically constipated children.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of gastric Helicobacter pylori infection on duodenal mucosa: New evidence on the alteration of intraepithelial lymphocytes.","authors":"Fatih Yilmaz, Kadri Atay, Gül Çirkin, Erkan Sanmak","doi":"10.1093/ajcp/aqaf071","DOIUrl":"10.1093/ajcp/aqaf071","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to elucidate the effect of gastric Helicobacter pylori (HP) colonization on the duodenal mucosa, focusing on intraepithelial lymphocyte (IEL) numbers and localizations.</p><p><strong>Methods: </strong>The paired gastric and duodenal tissues from 132 patients with celiac disease (CD) and 190 individuals without CD were examined. Gastric HP status (presence and intensity) was compared with IEL counts per 100 enterocytes (IEL/100), localizations (basal-apical), and endoscopic, serologic, and clinicopathologic parameters.</p><p><strong>Results: </strong>H pylori was detected in 176 (54.7%) gastric tissues, and its presence did not significantly change the duodenal IEL/100 counts in either CD (P = .121) or non-CD (P = .400) cases. It was seen in older individuals (P = .003), and age was also associated with HP intensity (P = .027). In non-CD cases, duodenal intraepithelial lymphocytosis (DIL) in HP-positive and HP-negative samples was 37 (33.9%) and 31 (38.3%), respectively (P = .538). Although a slight increase was observed with sparse HP colonization (+), intense colonization (+++) was significantly associated with less scalloping (P = .037), lower IEL/100 (P = .003), and antiendomysial antibody IgA (P = .048). A similar pattern was also observed in tissue transglutaminase IgA titers (P = .053).</p><p><strong>Conclusions: </strong>Considering the effect of gastric HP on duodenal IELs, endoscopic and serologic parameters, depending on its intensity, will provide a more accurate estimation in cases where the cause of DIL is investigated.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"443-454"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of TP53 mutations by immunohistochemistry in acute myeloid leukemia varies with interpreter expertise and mutation status.","authors":"Lee P Richman, Brianna F Waller, Scott B Lovitch, Ashwini Jambhekar","doi":"10.1093/ajcp/aqaf047","DOIUrl":"10.1093/ajcp/aqaf047","url":null,"abstract":"<p><strong>Objective: </strong>TP53 mutations, including missense and inactivating (frameshift, splice site, and nonsense) mutations, occur in approximately 10% of myeloid neoplasms and confer adverse outcomes. Classification of myeloid neoplasms by World Health Organization and International Consensus Classification standards recognizes the importance of early detection of TP53 mutations. p53 immunohistochemistry (IHC) is a widely accessible method used to detect mutations; however, previous studies have demonstrated variable accuracy, especially for inactivating TP53 mutations. Recently, sequencing using targeted panels has seen increased use. Although highly accurate, sequencing is resource intensive and not universally available.</p><p><strong>Methods: </strong>Using 134 bone marrow samples from patients with acute myeloid leukemia evaluated for TP53 mutation by sequencing, we assessed the concordance of p53 IHC with sequencing as well as the interrater-reliability for IHC intensity and percent positivity.</p><p><strong>Results: </strong>Consistent with previous studies, we found that p53 IHC was strongly specific and modestly sensitive for missense mutations and that overall performance improved with dedicated hematopathology training. We also found that IHC performed poorly for inactivating mutations and was even variable between cases harboring identical amino acid changes. Low predicted transcriptional activity of p53 missense proteins correlated with a mutant pattern of IHC staining. The status of the second allele and variant allele frequency also affected the accuracy of p53 IHC as a surrogate for TP53 allele status.</p><p><strong>Conclusion: </strong>Cases of acute myeloid leukemia with TP53 mutations predicted to have low transcriptional activity showed reduced overall survival. Our results demonstrate limited practical utility of p53 IHC for accurate evaluation of TP53 mutation status because of multifactorial confounders.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"331-341"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Concurrent or subsequent lymphomatous effusion in large B-cell lymphoma portends a dismal prognosis: A multi-institutional study.","authors":"Savanah D Gisriel, Ji Yuan, Haiming Tang, Jie Xu, Hong Fang, Shaoying Li, Jenna McCracken, Peng Li, Ryan C Braunberger, Zijun Y Xu-Monette, Xiaojun Wu, Endi Wang, Qian-Yun Zhang, Lorinda A Soma, Samuel G Katz, Jing Jing Zhang, Nana P Matsumoto, Ken H Young, Mina L Xu, Zenggang Pan","doi":"10.1093/ajcp/aqaf057","DOIUrl":"10.1093/ajcp/aqaf057","url":null,"abstract":"<p><strong>Objective: </strong>Rare large B-cell lymphomas (LBCLs) present with concurrent or subsequent lymphomatous effusion (solid-effusion LBCL, SE-LBCL), which may have an inferior prognosis compared with their noneffusion counterpart. In addition, the relationship between SE-LBCL and human herpesvirus 8-negative effusion-based LBCL (EB-LBCL) remains unclear.</p><p><strong>Methods: </strong>We collected 141 cases of SE-LBCL and a control cohort of 101 cases of stage IV solid-only LBCL. The clinicopathologic features were analyzed and compared between SE-LBCL and solid-only LBCL.</p><p><strong>Results: </strong>Patients with SE-LBCL had a median age of 67 years with a male-to-female ratio of 1.3:1. Eighty-six patients had concurrent solid lymphoma and lymphomatous effusion, whereas 55 developed lymphomatous effusion subsequently. Most cases involved the pleural cavities (79%, 112/141), followed by the peritoneal (21%, 29/141) and pericardial (11%, 16/141) cavities. BCL6, CD10, and MUM1 were expressed in 77% (90/117), 46% (60/130), and 61% (58/95) of cases, respectively, and 58% (71/123) were subclassified into the germinal center B-cell (GCB) subtype. Rearrangements of BCL2, BCL6, and MYC were detected in 42% (31/73), 35% (22/63), and 40% (35/88), respectively, and 22% (19/87) had both MYC and BCL2 rearrangements. The patients with SE-LBCL had a dismal prognosis, with a median survival of 5.7 months, which was significantly worse than solid-only LBCL (147.5 months; P < .0001).</p><p><strong>Conclusions: </strong>The pathologic features of SE-LBCL were similar to those of solid-only LBCL but distinct from those of EB-LBCL; in particular, lymphomatous effusion was an independently adverse prognostic factor in LBCL. Our study underscores the need for surveillance of lymphomatous effusion during LBCL staging and development of effective therapeutic regimens for SE-LBCL.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"390-401"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishing a comprehensive artificial intelligence lifecycle framework for laboratory medicine and pathology: A series introduction.","authors":"Christopher A Garcia, Katelyn A Reed, Eric Lantz, Patrick Day, Mark D Zarella, Steven N Hart, Eric Will, John G Skiffington, Melinda Rice, Debra A Novak, David S McClintock","doi":"10.1093/ajcp/aqaf069","DOIUrl":"10.1093/ajcp/aqaf069","url":null,"abstract":"<p><strong>Objective: </strong>Despite exponential growth in artificial intelligence (AI) research for laboratory medicine and pathology, a significant gap exists between model development and clinical AI implementation. This article introduces a structured framework, the Clinical AI Readiness Evaluator (CARE), to bridge this gap and support the responsible adoption of AI in clinical laboratory settings.</p><p><strong>Methods: </strong>Building upon the Machine Learning Technology Readiness Levels framework, we developed CARE specifically for the clinical laboratory environment by incorporating health care-specific requirements, regulatory considerations, and workflow integration needs. This framework was iteratively refined through practical application across diverse AI use cases within laboratory medicine and pathology.</p><p><strong>Results: </strong>The CARE framework provides a systematic approach to AI development and implementation through 8 component workstreams: clinical use case, data, data pipeline, code, clinical user experience, clinical technology infrastructure, clinical orchestration, and regulatory compliance. Unlike generic AI frameworks, CARE distinguishes itself by emphasizing both health care and laboratory workflow integration, regulatory requirements, ethical considerations, and comprehensive validation for clinical contexts. The framework accommodates both internally developed models and commercial AI solutions, providing clear guidance through technology readiness levels and structured review processes.</p><p><strong>Conclusions: </strong>The CARE framework addresses the unique challenges of implementing AI in laboratory medicine and pathology by providing a comprehensive roadmap from initial concepts through clinical deployment and maintenance. This article, the first in a series of 4, establishes the foundational AI lifecycle framework, while subsequent articles will explore data documentation, ethical AI considerations, and governance structures. By adopting this structured approach, laboratories can responsibly harness AI's potential to enhance diagnostic accuracy and operational efficiencies and, ultimately, improve patient care.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"424-437"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning neural network of adenocarcinoma detection in effusion cytology.","authors":"Katsuhide Ikeda, Nanako Sakabe, Kenta Fukuda, Shouichi Sato, Toshiaki Hara, Harumi Kobayashi, Masato Nakaguro, Kennosuke Karube, Kohzo Nagata","doi":"10.1093/ajcp/aqaf067","DOIUrl":"10.1093/ajcp/aqaf067","url":null,"abstract":"<p><strong>Objective: </strong>Cytologic examination, which confirms the presence or absence of malignant cells, detects malignant cells from various organs, with adenocarcinoma as the most common histologic type. We developed a deep learning model to detect malignant cells in images obtained following effusion cytology.</p><p><strong>Methods: </strong>The deep learning model was created using the YOLOv8 object detection algorithm (Roboflow, Inc) and 275 cases of adenocarcinoma comprising 12 182 images and 29 245 labels as well as 188 cases negative for malignancy comprising 1980 images.</p><p><strong>Results: </strong>The adenocarcinoma test dataset exhibited Precision, Recall, F1, and mean average Precision scores of 0.909, 0.911, 0.910, and 0.955, respectively. The number of adenocarcinoma test images in which 1 or more malignant cells were detected was 2710 of 2731. The sensitivity in the nonadenocarcinoma dataset was 97.1%, and the false-positive rate in the negative-for-malignancy dataset was 7.3%. The accuracy, sensitivity, and specificity of the model using all the test datasets were 96.3%, 98.5%, and 92.7%, respectively.</p><p><strong>Conclusions: </strong>Although some issues regarding cell annotation when creating an object detection model remain, the accuracy is sufficient to assist cancer screening in effusion cytology. It is vital to reliably detect malignant cells in effusion cytology, and the further development of automated systems to reduce false-negative results is expected.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"415-423"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resident in-service examination first-year trainee survey results: Comparison of US and international medical graduates' perceived preparedness for pathology residency.","authors":"Alisha M Maltos, Jodi Gedallovich, Rebecca K Miller-Kuhlmann, Kimberly W Sanford, Ali Brown, Jay Wagner, Kelly Ernst","doi":"10.1093/ajcp/aqaf065","DOIUrl":"10.1093/ajcp/aqaf065","url":null,"abstract":"<p><strong>Objective: </strong>This study investigates the academic backgrounds and medical school pathology exposure among first-year pathology residents, comparing graduates from the United States and international medical schools.</p><p><strong>Methods: </strong>A survey was administered as part of the Resident In-Service Examination First, offered by the American Society for Clinical Pathology, which assessed academic background, preparedness for residency, and prior exposure to pathology education. Associations between undergraduate pathology exposure, timing of residency selection, reported preparedness, and examination performance were analyzed.</p><p><strong>Results: </strong>Of the 417 residents who completed the survey, 39.3% had graduated from international medical institutions. International medical graduates reported higher rates of medical school curricula that included required pathology rotations (33.5% vs 3.6%, P = .001) and greater perceived preparedness for anatomic pathology residency (28.7% vs 15.8%, P = .002), with no significant difference in examination performance. Additionally, 22.5% of US medical student respondents selected pathology before medical school, compared to only 10.4% of international medical graduates (P = .002).</p><p><strong>Conclusions: </strong>This study highlights differences in educational exposure and perceived preparedness for pathology residency between US and international medical graduates, with international medical graduates reporting more preresidency exposure to pathology and higher perceived confidence at the start of residency. These findings suggest potential areas for curricular improvement in US medical schools to enhance pathology exposure.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"402-408"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment of the Veterans Affairs SeqFORCE (Sequencing for Research Clinical and Epidemiology) program for SARS-CoV-2 whole-genome sequencing.","authors":"Mark Holodniy, Ying Pei, Gary Stack, Christopher Wade, Yashpal Agrawal, Nicholas Barasch, Fady Baddoura, Carmen Kletecka, Patrick Adegboyega, Christina Trevino, Joel Mewton, Vafa Bayat, Anosh Mostaghimi, James S Klutts, Jessica Wang-Rodriguez","doi":"10.1093/ajcp/aqaf064","DOIUrl":"10.1093/ajcp/aqaf064","url":null,"abstract":"<p><strong>Objective: </strong>We sought to establish the US Department of Veterans Affairs (VA) Veterans Health Administration (VHA) Sequencing for Research Clinical and Epidemiology (SeqFORCE) multilaboratory consortium for SARS-CoV-2 whole-genome sequencing (WGS).</p><p><strong>Methods: </strong>Clinical criteria were established for sending patient and employee samples from 145 VHA medical centers to 10 VHA clinical laboratories using 4 different WGS platforms. A linked pipeline among laboratories for SARS-CoV-2 clade and lineage interpretation, result transmission to electronic health records, and data storage was developed.</p><p><strong>Results: </strong>The SeqFORCE program went live on July 1, 2021. As of December 15, 2024, 51 307 samples have been analyzed by WGS for SARS-CoV-2. The median participant age was 60 years, 76.6% were male, and 13.5% were inpatients; 96.5% were Delta, Omicron, and Recombinant sublineages; and 78.5% represented SARS-CoV-2 postvaccination samples among patients and staff.</p><p><strong>Conclusions: </strong>Establishment of VA SeqFORCE enabled national population analysis for use in epidemiologic response and population health policy as well as expanded SARS-CoV-2 sequencing capacity to meet the demand for clinical and public health sequencing. The program consolidated operations using standardized procedures, test setup, analysis, reporting, and tracking. It also improved oversight and governance of VA contributions to global databases, mitigated system inefficiencies, and prepared VHA for future genomic challenges.</p>","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"302-309"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}