{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:56:01Z","timestamp":1792788961221,"version":"4.5.0"},"reference-count":25,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"King Abdulaziz University","award":["1083-611-2026"],"award-info":[{"award-number":["1083-611-2026"]}],"id":[{"id":"https:\/\/ror.org\/02ma4wv74","id-type":"ROR","asserted-by":"crossref"}]},{"award":["1083-611-2026"],"award-info":[{"award-number":["1083-611-2026"]}],"id":[{"id":"https:\/\/ror.org\/02ma4wv74","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Human orphan genes are poorly annotated and lowly expressed, which makes their behavior in disease difficult to establish. We analyzed paired normal and disease RNA-seq libraries from four cohorts, quantified against a combined reference in which 2190 of 198,507 transcripts are orphan. Cohorts were first screened for library-level differences between the two conditions, and one (GSE40419, lung adenocarcinoma) was excluded because sequencing depth, pseudoalignment rate, and submission provenance all differed by condition; it is retained throughout as a calibration. In the remaining three cohorts, comprising 151 matched pairs from psoriasis, laryngeal squamous cell carcinoma, and hepatocellular carcinoma, we measured the change in the fraction of transcripts with zero abundance, a quantity that does not depend on any transformation of expression. Orphan transcripts lose detection relative to non-orphan transcripts matched on abundance and on cross-patient detection frequency, by +0.0250\u00b10.0178, +0.0553\u00b10.0073, and +0.0659\u00b10.0122 once the global shift in detection is held fixed. The three estimates are homogeneous (p=0.163) and pool to +0.0544\u00b10.0059, whereas the same analysis applied to the excluded cohort returns thirteen times that value. We report the result at the level at which it is measured, and withdraw the patient-level and cohort-specific claims made in the first preprint version of this work.<\/jats:p>","DOI":"10.3390\/biology15191775","type":"journal-article","created":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T14:28:05Z","timestamp":1791296885000},"page":"1775","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Reduced Detection of Human Orphan Gene Transcripts in Disease Tissue Relative to Expression- and Detection- Matched Controls"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0867-8986","authenticated-orcid":false,"given":"Y.-H.","family":"Taguchi","sequence":"first","affiliation":[{"name":"Department of Physics, Chuo University, Tokyo 112-8551, Japan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9491-2435","authenticated-orcid":false,"given":"Turki","family":"Turki","sequence":"additional","affiliation":[{"name":"Department of Computer Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,10,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Lang, H., Zhang, Y., Wang, B., Li, K., and Jiang, M. (2025). Characterization and Expression Profiling of Orphan Genes in Rapeseed (Brassica napus) Provide Insights into Tissue Development and Cold Stress Adaptation. Horticulturae, 11.","DOI":"10.3390\/horticulturae11070826"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Chen, C., Vakirlis, N., Holmer, R., de Ridder, D., and Kupczok, A. (2026). Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome. bioRxiv.","DOI":"10.64898\/2026.01.16.699869"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Prabh, N., and R\u00f6delsperger, C. (2016). Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?. 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