SVA retrotransposition in exon 6 of the coagulation factor IX gene causing severe hemophilia B

International Journal of Hematology
Yuki NakamuraTetsuhito Kojima

Abstract

Hemophilia B is an X-linked recessive bleeding disorder caused by abnormalities of the coagulation factor IX gene (F9). Insertion mutations in F9 ranging from a few to more than 100 base pairs account for only a few percent of all hemophilia B cases. We investigated F9 to elucidate genetic abnormalities causing severe hemophilia B in a Japanese subject. We performed PCR-mediated analysis of F9 and identified a large insertion in exon 6. Next, we carried out direct sequencing of a PCR clone of the whole insert using nested deletion by exonuclease III and S1 nuclease. We identified an approximately 2.5-kb SINE-VNTR-Alu (SVA)-F element flanked by 15-bp duplications in the antisense orientation in exon 6. Additionally, we carried out exontrap analysis to assess the effect of this retrotransposition on mRNA splicing. We observed that regular splicing at exons 5 and 6 of F9 was disturbed by the SVA retrotransposition, suggesting that abnormal FIX mRNA may be reduced by nonsense-mediated mRNA decay. In conclusion, this is the first report of SVA retrotransposition causing severe hemophilia B; only five cases of LINE-1 or Alu retrotranspositions in F9 have been reported previously.

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Citations

May 10, 2016·Mobile DNA·Dustin C Hancks, Haig H Kazazian
Dec 13, 2017·Proceedings of the National Academy of Sciences of the United States of America·D Cristopher BraggLaurie J Ozelius
Sep 14, 2019·Nature Reviews. Genetics·Lindsay M Payer, Kathleen H Burns
Jul 8, 2021·Analytical Chemistry·Lahari UppuluriMing Xiao
Nov 5, 2021·BMC Genomics·Matias I AutioShyam Prabhakar

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