{"doi":"10.1002/mef2.62","title":"Survey of commercial antibodies targeting Y chromosome‐encoded genes","abstract":"Although immunoassays are an indispensable tool for scientific research, antibody specificity has been recognized as a major challenge to the rigor and reproducibility of research findings. A 2016 proposal published by the International Working Group for Antibody Validation identified five pillars of antibody validation.1 Among these is genetic validation, in which “The expression of the target protein is eliminated or significantly reduced by genome editing or RNA interference.” Y chromosome-encoded genes present unique opportunities and challenges to validate antibodies on this genetic principle. Fortunately, readily available female-derived cells and tissues can serve as a target-negative source material, which is far more convenient than typical sources of genetic validation, which require knockout or knockdown approaches to a target gene. However, an additional challenge for the specificity of these antibodies is that many Y chromosome proteins have “gametologs,” or highly homologous genes encoded on the X chromosome. As gametologs can share over 90% amino acid identity, these protein targets present unique specificity challenges. However, this obstacle has not impeded commercial antibody suppliers who market hundreds of antibodies with purported specificity for Y chromosome-encoded genes. We performed an analysis of the extent to which Y chromosome gene-targeted commercial antibodies recognize female-derived materials using data provided in their marketing materials (a detailed methodology is provided in the Supporting Information). Table 1 lists 65 antibodies purporting to target a Y chromosome-encoded gene with company-supplied marketing demonstrating immunoreactivity in female-derived tissues. Product page URLs are provided in Supporting Information: Table S1. For one example, an antibody targeting sex-determining region chromosome Y marketed by MyBioSource (catalog # MBS8513980) presents validation data in HeLa cells, which is a cervical cancer cell line with no Y chromosomes.2 Among these antibodies, frequently used female-derived cell lines were HeLa, 30/65 (46%), HEK293T, female human embryonic kidney cells used in 14 (22%), and MCF-7 breast cancer cells used in 7 (11%). One antibody, a rabbit polyclonal raised against the “N terminus” of DEAD-box helicase 3 Y-linked (DDX3Y) (LS Biosciences, catalog # LS-C355991) presented positive immunohistochemistry in human breast cancer tissue. While not definitively a Y-chromosome absent tissue, we included this as a likely female-positive tissue, based on the prevalence of breast cancer in females compared to males being roughly 99-to-1 in the United States.3 Among 65 antibodies, we noted just two that had disclaimers warning that the antibody may cross-react with homologous X chromosome-encoded proteins. No validation data was provided (16/30, 56%). Validation data was provided indicating a positive signal in female or likely female tissue (see discussion below) with or without positive data in male tissue (9/30, 30%). Validation data was provided indicating a positive signal in male or likely male tissue, but no data on female tissue (4/30, 13%). Validation data was provided indicating a positive signal in male or likely male tissue, and affirmatively negative data in female tissue (1/30, 3%). This survey provides evidence of widespread off-target antigen recognition in commercial antibodies purporting to recognize Y chromosome-encoded proteins. Some important caveats should be noted. First, many antibodies provided no primary data on female tissues. For example, 20/30 (67%) of DDX3Y antibodies provided no data in female tissues. Therefore, it seems likely that the 65 antibodies listed in Table 1 are a significant underrepresentation of Y chromosome-targeted antibodies lacking specificity. Second, this analysis assumes that the identities of the listed cell types provided in marketing materials are accurate and not subject to cell line contamination, conceivably with Y ch","journal":"MedComm – Future Medicine","year":2023,"id":385443,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9625,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1153901,"name":"Dionne A. Argyle","orcid":null,"position":1,"is_corresponding":false},{"id":1117764,"name":"Joseph J. Olivieri","orcid":null,"position":2,"is_corresponding":false},{"id":320295,"name":"Jayakrishna Ambati","orcid":"0000-0003-1622-6365","position":3,"is_corresponding":false},{"id":320313,"name":"Bradley D. Gelfand","orcid":"0000-0003-4619-9409","position":0,"is_corresponding":true}],"reference_count":3,"raw_metadata":null,"created_at":"2026-07-19T01:17:52.636565Z","pmid":"38645476","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}