Genome Analysis in Sick Neonates and Infants: High-yield Phenotypes and Contribution of Small Copy Number Variations

Hisato Suzuki, Masatoshi Nozaki, Hiroshi Yoshihashi, Kazuo Imagawa, Daigo Kajikawa, Mamiko Yamada, Yu Yamaguchi, Naoya Morisada, Mayuko Eguchi, Shoko Ohashi, Shinsuke Ninomiya, Toshiyuki Seto, Tomoharu Tokutomi, Mariko Hida, Katsuaki Toyoshima, Masatoshi Kondo, Ayano Inui, Kenji Kurosawa, Rika Kosaki, Yushi ItoNobuhiko Okamoto, Kenjiro Kosaki, Toshiki Takenouchi

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


Objective: To delineate the diagnostic efficacy of medical exome, whole exome, and whole genome sequencing according to primary symptoms, the contribution of small copy number variations, and the impact of molecular diagnosis on clinical management. Study design: This was a prospective study of 17 tertiary care centers in Japan, conducted between April 2019 and March 2021. Critically ill neonates and infants less than 6 months of age were recruited in neonatal intensive care units and in outpatient clinics. The patients underwent medical exome, whole exome, or whole genome sequencing as the first tier of testing. Patients with negative results after medical exome or whole exome sequencing subsequently underwent whole genome sequencing. The impact of molecular diagnosis on clinical management was evaluated through contacting primary care physicians. Results: Of the 85 patients, 41 (48%) had positive results. Based on the primary symptoms, patients with metabolic phenotypes had the highest diagnostic yield (67%, 4/6 patients), followed by renal (60%, 3/5 patients), and neurologic phenotypes (58%, 14/24 patients). Among them, 4 patients had pathogenic small copy number variations identified using whole genome sequencing. In the 41 patients with a molecular diagnosis, 20 (49%) had changes in clinical management. Conclusions: Genome analysis for critically ill neonates and infants had a high diagnostic yield for metabolic, renal, and neurologic phenotypes. Small copy number variations detected using whole genome sequencing contributed to the overall molecular diagnosis in 5% of all the patients. The resulting molecular diagnoses had a significant impact on clinical management.

Original languageEnglish
Pages (from-to)38-48.e1
JournalJournal of Pediatrics
Publication statusPublished - 2022 May


  • congenital disorders
  • copy number variations
  • exome sequencing
  • infant
  • intensive care
  • metabolic disorders
  • neonate
  • whole genome sequencing

ASJC Scopus subject areas

  • Pediatrics, Perinatology, and Child Health


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