{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T22:17:08Z","timestamp":1768515428160,"version":"3.49.0"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T00:00:00Z","timestamp":1740614400000},"content-version":"vor","delay-in-days":26,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Homologous recombination deficiency (HRD) has emerged as a critical prognostic and predictive biomarker in oncology. However, current testing methods, especially those reliant on targeted panels, are plagued by inconsistent results from the same samples. This highlights the urgent need for standardized benchmarks to evaluate HRD assay performance. In phases IIa and IIb of the Chinese HRD Harmonization Project, we developed ten pairs of well-characterized DNA reference materials derived from lung, breast, and melanoma cancer cell lines and their matched normal cell lines, keeping each paired with seven cancer-to-normal mass ratios. Reference datasets for allele-specific copy number variations (ASCNVs) and HRD scores were established and validated using three sequencing methods and nine analytical pipelines. The genomic instability scores (GISs) of the reference materials ranged from 11 to 96, enabling validation across various thresholds. The ASCNV reference datasets covered a genomic span of 2340 to 2749 Mb, equivalent to 81.2% to 95.4% of the autosomes in the 37d5 reference genome. These benchmarks were subsequently utilized to assess the accuracy and reproducibility of four HRD panel assays, revealing significant variability in both ASCNV detection and HRD scores. The concordance between panel-detected GISs and reference GISs ranged from 0.81 to 0.94, with only two assays exhibiting high overall agreement with Myriad MyChoice CDx for HRD classification. This study also identified specific challenges in ASCNV detection in HRD-related regions and the profound impact of high ploidy on consistency. The established HRD reference materials and datasets provide a robust toolkit for objective evaluation of HRD testing.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf017","type":"journal-article","created":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T16:19:49Z","timestamp":1741105189000},"source":"Crossref","is-referenced-by-count":3,"title":["Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-3665-9193","authenticated-orcid":false,"given":"Zheng","family":"Jia","sequence":"first","affiliation":[{"name":"Department of In Vitro Diagnostic Reagent, National Institutes for Food and Drug Control (NIFDC) , Beijing 100050,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9356-9164","authenticated-orcid":false,"given":"Yaqing","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University , Shanghai 200438,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7202-7160","authenticated-orcid":false,"given":"Shoufang","family":"Qu","sequence":"additional","affiliation":[{"name":"Department of In Vitro Diagnostic Reagent, National Institutes for Food and Drug Control (NIFDC) , Beijing 100050,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-9445-3421","authenticated-orcid":false,"given":"Wenbin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center\/National Clinical Research Center for Cancer\/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4606-8994","authenticated-orcid":false,"given":"Lin","family":"Gao","sequence":"additional","affiliation":[{"name":"GenePlus-Shenzhen Institute , Shenzhen 518000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1196-2446","authenticated-orcid":false,"given":"Lin","family":"Dong","sequence":"additional","affiliation":[{"name":"Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center\/National Clinical Research Center for Cancer\/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6523-0398","authenticated-orcid":false,"given":"Yun","family":"Xing","sequence":"additional","affiliation":[{"name":"GenePlus-Beijing Institute , Beijing 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102200,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9855-7226","authenticated-orcid":false,"given":"Chao","family":"Zhang","sequence":"additional","affiliation":[{"name":"GenePlus-Shenzhen Institute , Shenzhen 518000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5398-1360","authenticated-orcid":false,"given":"Yanming","family":"Xie","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University , Shanghai 200438,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2729-5618","authenticated-orcid":false,"given":"Chunli","family":"Wang","sequence":"additional","affiliation":[{"name":"Technology Development Center-Bioinformatics Group, BGI Genomics , Shenzhen 518081,","place":["China"]},{"name":"Clin Lab, BGI Genomics , Tianjin 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(NIFDC) , Beijing 100050,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7598-9015","authenticated-orcid":false,"given":"Wenxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of In Vitro Diagnostic Reagent, National Institutes for Food and Drug Control (NIFDC) , Beijing 100050,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6831-9251","authenticated-orcid":false,"given":"Xiaoping","family":"Gu","sequence":"additional","affiliation":[{"name":"Amoy Diagnostics Co ., Ltd., Xiamen 361027,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-9061-0813","authenticated-orcid":false,"given":"Shuang","family":"Yang","sequence":"additional","affiliation":[{"name":"Amoy Diagnostics Co ., Ltd., Xiamen 361027,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3079-5400","authenticated-orcid":false,"given":"Jinghua","family":"Li","sequence":"additional","affiliation":[{"name":"GeneWell Biotechnology Co ., Ltd., 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