biostudies-literatureKaschta DM.S. is a DZHK principal investigator and is supported by grants from the Deutsche ForschungsgemeinschaftUniversität zu Lübeck100https://www.ebi.ac.uk/biostudies/studies/S-EPMC12445032biostudies-literatureUnknown17(1)<h4>Background</h4>Short-read genome sequencing (GS) is among the most comprehensive genetic testing methods available, capable of detecting single-nucleotide variants, copy-number variants, mitochondrial variants, repeat expansions, and structural variants in a single assay. Despite its technical advantages, the full clinical utility of GS in real-world diagnostic settings remains to be fully established.<h4>Methods</h4>This study systematically compared singleton GS (sGS), trio GS (tGS), and exome sequencing-based standard-of-care (SoC) genetic testing in 416 patients with rare diseases in a blinded, prospective study. Three independent teams with divergent baseline expertise evaluated the diagnostic yield of GS as a unifying first-tier test and directly compared its variant detection caGenome medicineEvaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.PMC12445032(DFG; SP1532/13-1, SP1532/3-2 and SP1532/5-1)Franzenburg SWilson SNagel Ivan der Ven ATHoffmann BHandler KWoitschach RKaschta DHornig NGehring BSchlein CMunchau AGreiten BRosenstiel PYumiceba VHerrmann GPozojevic JUtermann-Thusing CBerge VCaliebe ASpielmann MPapingi DHellenbroich YPost CBirgel FHerget TSchau-Romer KHoff KDalski ADittmar MLisfeld JRust FGaass FArriens VSreenivasan VKAWehnert JVolk AEFranke ALoscher BSGembicki RGrohte KMuhle HBruggemann NRecke AKautza-Lucht MRosler LHiort OPenas EMMZuhlke CFuß JBalachandran SHarder LVater IMargraf NGToutouna LAl-Tawil MSalewski MBLiegmann ASMeyenborg MMollring ANommels HHuning IBaumer TKohler JRoberts KHanker BPoggenburg IfalseEvaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.<h4>Background</h4>Short-read genome sequencing (GS) is among the most comprehensive genetic testing methods available, capable of detecting single-nucleotide variants, copy-number variants, mitochondrial variants, repeat expansions, and structural variants in a single assay. Despite its technical advantages, the full clinical utility of GS in real-world diagnostic settings remains to be fully established.<h4>Methods</h4>This study systematically compared singleton GS (sGS), trio GS (tGS), and exome sequencing-based standard-of-care (SoC) genetic testing in 416 patients with rare diseases in a blinded, prospective study. Three independent teams with divergent baseline expertise evaluated the diagnostic yield of GS as a unifying first-tier test and directly compared its variant detection ca2025-01-01T00:00:00Z2025 Sep2026-06-03T14:36:09.991Z2026-04-28T03:11:42.156ZS-EPMC124450324096312010.1186/s13073-025-01516-7