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
{"title":"建立退伍军人事务SeqFORCE（临床和流行病学研究测序）项目，进行SARS-CoV-2全基因组测序。","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":null,"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":1.9000,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"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\":null,\"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\":1.9000,\"publicationDate\":\"2025-09-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"American journal of clinical pathology\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1093/ajcp/aqaf064\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"PATHOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"American journal of clinical pathology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1093/ajcp/aqaf064","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"PATHOLOGY","Score":null,"Total":0}
Establishment of the Veterans Affairs SeqFORCE (Sequencing for Research Clinical and Epidemiology) program for SARS-CoV-2 whole-genome sequencing.
Objective: 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).
Methods: 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.
Results: 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.
Conclusions: 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.
期刊介绍：
The American Journal of Clinical Pathology (AJCP) is the official journal of the American Society for Clinical Pathology and the Academy of Clinical Laboratory Physicians and Scientists. It is a leading international journal for publication of articles concerning novel anatomic pathology and laboratory medicine observations on human disease. AJCP emphasizes articles that focus on the application of evolving technologies for the diagnosis and characterization of diseases and conditions, as well as those that have a direct link toward improving patient care.
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