A MinION-based Long-Read Sequencing Application With One-Step PCR for the Genetic Diagnosis of 21-Hydroxylase Deficiency

Eriko Adachi, Ryuichi Nakagawa, Atsumi Tsuji-Hosokawa, Maki Gau, Shizuka Kirino, Analia Yogi, Hisae Nakatani, Kei Takasawa, Tomomi Yamaguchi, Tomoki Kosho, Masanori Murakami, Toshihiro Tajima, Tomonobu Hasegawa, Tetsuya Yamada, Tomohiro Morio, Osamu Ohara, Kenichi Kashimada

Research output: Contribution to journalArticlepeer-review

Abstract

CONTEXT: Recently developed long-read sequencing (LRS) technology has been considered an option for CYP21A2 analysis. However, the clinical use of LRS for CYP21A2 analysis is limited. OBJECTIVE: This study's objective is to develop an efficient and low-cost LRS system for CYP21A2 screening. METHODS: A DNA fragment library was prepared in a single polymerase chain reaction (PCR) that covers the entire CYP21A2 gene and all known junctions caused by TNXB gene structural rearrangements, yielding a single 8-kb product of CYP21A2 or CYP21A1P/CYP21A2 chimera. After barcoding, the PCR products were sequenced on a MinION-based platform with Flongle Flow Cell R9.4.1 and R10.4.1. RESULTS: The reference genotypes of 55 patients with 21-hydroxylase deficiency (21OHD) were established using the conventional method with multiplex ligation-dependent probe amplification (MLPA) and nested PCR. LRS using Flongle Flow Cell R9.4.1 yielded consistent results. Additionally, the recently updated LRS "duplex" analysis with Flongle flow cell R10.4.1 was tested to reveal an advantage of accurately sequencing a variant located on the homopolymer region. By introducing a barcode system, the cost was reduced to be comparable to that of conventional analysis. A novel single-nucleotide variation was discovered at the acceptor site of intron 7, c.940-1G > C. We also identified a subtype of the classical chimeric junction CH2, "CH2a," in the region from the latter part of intron 5 to exon 6. CONCLUSION: We successfully established a novel low-cost and highly accurate LRS system for 21OHD genetic analysis. Our study provides insight into the feasibility of LRS for diagnosing 21OHD and other genetic diseases caused by structural rearrangements.

Original languageEnglish
Pages (from-to)750-760
Number of pages11
JournalThe Journal of clinical endocrinology and metabolism
Volume109
Issue number3
DOIs
Publication statusPublished - 2024 Feb 20

Keywords

  • 11DOF/17αOHP
  • 17α-hydroxyprogesterone (17αOHP)
  • 21-deoxycortisol (21DOF)
  • 21-hydroxylase deficiency (21OHD)
  • LC-MS/MS
  • newborn screening

ASJC Scopus subject areas

  • Endocrinology, Diabetes and Metabolism
  • Biochemistry
  • Endocrinology
  • Clinical Biochemistry
  • Biochemistry, medical

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