title: A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations.
abstract: Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (~97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis.
authors: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors: Fuyuki
authors: F
authors: Miya
authors: Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, Japan.
authors: Mitsuhiro
authors: M
authors: Kato
authors: Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan.
authors: Tadashi
authors: T
authors: Shiohama
authors: Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan.
authors: Nobuhiko
authors: N
authors: Okamoto
authors: Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.
authors: Shinji
authors: S
authors: Saitoh
authors: Department of Pediatric Neurosurgery, Takatsuki General Hospital, Osaka, Japan.
authors: Mami
authors: M
authors: Yamasaki
authors: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors: Daichi
authors: D
authors: Shigemizu
authors: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors: Tetsuo
authors: T
authors: Abe
authors: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors: Takashi
authors: T
authors: Morizono
authors: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors: Keith A
authors: KA
authors: Boroevich
authors: Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
authors: Kenjiro
authors: K
authors: Kosaki
authors: 1] Division of Regenerative Medicine, Institute for Clinical Research, Osaka National Hospital, National Hospital Organization, Osaka, Japan [2] Department of Neurosurgery, Osaka National Hospital, National Hospital Organization, Osaka, Japan.
authors: Yonehiro
authors: Y
authors: Kanemura
authors: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors: Tatsuhiko
authors: T
authors: Tsunoda
mesh_terms: D001921:Brain / Q000473:pathology; D019295:Computational Biology / Q000379:methods; D059472:Exome; D005260:Female; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008831:Microcephaly / Q000235:genetics; D009154:Mutation; D009419:Nerve Tissue Proteins / Q000235:genetics; D010375:Pedigree
chemical_list: C467202:ASPM protein, human; D009419:Nerve Tissue Proteins