Improved detection of SBDS gene mutation by a new method of next-generation sequencing analysis based on the Chinese mutation spectrum

• Published in: PloS one Vol. 17; no. 12; p. e0269029
• Main Authors: Wu, Dong, Zhang, Li, Qiang, Yuzhen, Wang, Kaiyu
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 13.12.2022; Public Library of Science (PLoS)
• Subjects: Analysis; Biology and Life Sciences; Carrier frequencies; Data analysis; Diamonds; Diploids; DNA sequencing; East Asian People; Exons; Gene mutations; Genes; Genetic disorders; Genetic screening; Genetic testing; Genomes; High-Throughput Nucleotide Sequencing; Humans; Misalignment; Mutation; Next-generation sequencing; Nucleotide sequencing; Point mutation; Proteins - genetics; Pseudogenes; Research and analysis methods; Sequence analysis; China; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0269029

Next-generation sequencing (NGS) is a useful molecular diagnostic tool for genetic diseases. However, due to the presence of highly homologous pseudogenes, it is challenging to use short-read NGS for analyzing mutations of the Shwachman-Bodian-Diamond syndrome ( SBDS ) gene. The SBDS mutation spectrum was analyzed in the Chinese population, which revealed that SBDS variants were primarily from sequence exchange between SBDS and its pseudogene at the base-pair level, predominantly in the coding region and splice junction of exon two. The c.258+2T>C and c.185_184TA>GT variants were the two most common pathogenic SBDS variants in the Chinese population, resulting in a total carrier frequency of 1.19%. When analyzing pathogenic variants in the SBDS gene from the NGS data, the misalignment was identified as a common issue, and there were different probabilities of misalignment for different pathogenic variants. Here, we present a novel mathematical method for identifying pathogenic variants in the SBDS gene from the NGS data, which utilizes read-depth of the paralogous sequence variant (PSV) loci of SBDS and its pseudogene. Combined with PCR and STR orthogonal experiments, SBDS gene mutation analysis results were improved in 40% of clinical samples, and various types of mutations such as homozygous, compound heterozygous, and uniparental diploid were explored. The findings effectively reduce the impact of misalignment in NGS-based SBDS mutation analysis and are helpful for the clinical diagnosis of SBDS -related diseases, the research into population variation, and the carrier screening.