RNA sequencing and target long-read sequencing reveal an intronic transposon insertion causing aberrant splicing.
Journal
Journal of human genetics
ISSN: 1435-232X
Titre abrégé: J Hum Genet
Pays: England
ID NLM: 9808008
Informations de publication
Date de publication:
15 Dec 2023
15 Dec 2023
Historique:
received:
09
08
2023
accepted:
01
12
2023
revised:
28
11
2023
medline:
16
12
2023
pubmed:
16
12
2023
entrez:
15
12
2023
Statut:
aheadofprint
Résumé
More than half of cases with suspected genetic disorders remain unsolved by genetic analysis using short-read sequencing such as exome sequencing (ES) and genome sequencing (GS). RNA sequencing (RNA-seq) and long-read sequencing (LRS) are useful for interpretation of candidate variants and detection of structural variants containing repeat sequences, respectively. Recently, adaptive sampling on nanopore sequencers enables target LRS more easily. Here, we present a Japanese girl with premature chromatid separation (PCS)/mosaic variegated aneuploidy (MVA) syndrome. ES detected a known pathogenic maternal heterozygous variant (c.1402-5A>G) in intron 10 of BUB1B (NM_001211.6), a known responsive gene for PCS/MVA syndrome with autosomal recessive inheritance. Minigene splicing assay revealed that almost all transcripts from the c.1402-5G allele have mis-splicing with 4-bp insertion. GS could not detect another pathogenic variant, while RNA-seq revealed abnormal reads in intron 2. To extensively explore variants in intron 2, we performed adaptive sampling and identified a paternal 3.0 kb insertion. Consensus sequence of 16 reads spanning the insertion showed that the insertion consists of Alu and SVA elements. Realignment of RNA-seq reads to the new reference sequence containing the insertion revealed that 16 reads have 5' splice site within the insertion and 3' splice site at exon 3, demonstrating causal relationship between the insertion and aberrant splicing. In addition, immunoblotting showed severely diminished BUB1B protein level in patient derived cells. These data suggest that detection of transcriptomic abnormalities by RNA-seq can be a clue for identifying pathogenic variants, and determination of insert sequences is one of merits of LRS.
Identifiants
pubmed: 38102195
doi: 10.1038/s10038-023-01211-8
pii: 10.1038/s10038-023-01211-8
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ek01099674
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ek0109637
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ek0109549
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP20H03641
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23H02875
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : 23K14944
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : 22K20852
Informations de copyright
© 2023. The Author(s), under exclusive licence to The Japan Society of Human Genetics.
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