title: A Specially Designed Multi-Gene Panel Facilitates Genetic Diagnosis in Children with Intrahepatic Cholestasis: Simultaneous Test of Known Large Insertions/Deletions.
abstract: OBJECTIVE
  Large indels are commonly identified in patients but are not detectable by routine Sanger sequencing and panel sequencing. We specially designed a multi-gene panel that could simultaneously test known large indels in addition to ordinary variants, and reported the diagnostic yield in patients with intrahepatic cholestasis.
  
  
  METHODS
  The panel contains 61 genes associated with cholestasis and 25 known recurrent large indels. The amplicon library was sequenced on Ion PGM system. Sequencing data were analyzed using a routine data analysis protocol and an internal program encoded for large indels test simultaneously. The validation phase was performed using 54 patients with known genetic diagnosis, including 5 with large insertions. At implement phase, 141 patients with intrahepatic cholestasis were evaluated.
  
  
  RESULTS
  At validation phase, 99.6% of the variations identified by Sanger sequencing could be detected by panel sequencing. Following the routine protocol, 99.8% of false positives could be filtered and 98.8% of retained variations were true positives. Large insertions in the 5 patients with known genetic diagnosis could be correctly detected using the internal program. At implementation phase, 96.9% of the retained variations, following the routine protocol, were confirmed to be true. Twenty-nine patients received a potential genetic diagnosis when panel sequencing data were analyzed using the routine protocol. Two additional patients, who were found to harbor large insertions in SLC25A13, obtained a potential genetic diagnosis when sequencing data were further analyzed using the internal program. A total of 31 (22.0%) patients obtained a potential genetic diagnosis. Nine different genetic disorders were diagnosed, and citrin deficiency was the commonest.
  
  
  CONCLUSIONS
  Specially designed multi-gene panel can correctly detect large indels simultaneously. By using it, we assigned a potential genetic diagnosis to 22.0% of patients with intrahepatic cholestasis.
authors.affiliation: Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China.
authors.forename: Neng-Li
authors.initials: NL
authors.lastname: Wang
authors.affiliation: The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.
authors.forename: Yu-Lan
authors.initials: YL
authors.lastname: Lu
authors.affiliation: The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China.
authors.forename: Mei-Hong
authors.initials: MH
authors.lastname: Zhang
authors.affiliation: Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China.
authors.forename: Jing-Yu
authors.initials: JY
authors.lastname: Gong
authors.affiliation: The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Lu
authors.affiliation: The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China.
authors.forename: Xin-Bao
authors.initials: XB
authors.lastname: Xie
authors.affiliation: The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China.
authors.forename: Yi-Ling
authors.initials: YL
authors.lastname: Qiu
authors.affiliation: Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China.
authors.forename: Yan-Yan
authors.initials: YY
authors.lastname: Yan
authors.affiliation: The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.
authors.forename: Bing-Bing
authors.initials: BB
authors.lastname: Wu
authors.affiliation: The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China.
authors.forename: Jian-She
authors.initials: JS
authors.lastname: Wang
mesh_terms: D002648:Child; D002780:Cholestasis, Intrahepatic / Q000235:genetics*; D042241:Early Diagnosis; D005260:Female; D015723:Gene Library; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D033681:Mitochondrial Membrane Transport Proteins / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D033681:Mitochondrial Membrane Transport Proteins; C119629:SLC25A13 protein, human