CC BY-NC-ND 4.0 · Thromb Haemost 2024; 124(04): 374-385
DOI: 10.1055/a-2217-9837
Stroke, Systemic or Venous Thromboembolism

Complete F9 Gene Deletion, Duplication, and Triplication Rearrangements: Implications for Factor IX Expression and Clinical Phenotypes

YuXin Ma*
1   Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
2   Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
Yang Li*
2   Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
Jie Sun
3   Haemophilia Comprehensive Care Center, Capital Medical University, Beijing Children's Hospital, Beijing, China
Qian Liang
2   Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
Runhui Wu
3   Haemophilia Comprehensive Care Center, Capital Medical University, Beijing Children's Hospital, Beijing, China
Qiulan Ding
2   Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
4   Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
Jing Dai
2   Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
5   Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
› Author Affiliations
Funding This study was supported by the National Natural Science Foundation of China (grant numbers 81970126, 81970127, 82170128, and 82270128).


Background Factor IX (FIX) plays a critical role in blood coagulation. Complete deletion of F9 results in severe hemophilia B, whereas the clinical implications of complete F9 duplication and triplication remain understudied.

Objective To investigate the rearrangement mechanisms underlying complete F9 deletion (cases 1 and 2), duplication (cases 3 and 4), and triplication (case 5), and to explore their association with FIX expression levels and clinical impacts.

Methods Plasma FIX levels were detected using antigen and activity assays. CNVplex technology, optical genome mapping, and long-distance polymerase chain reaction were employed to characterize the breakpoints of the chromosomal rearrangements.

Results Cases 1 and 2 exhibited FIX activities below 1%. Case 3 displayed FIX activities within the reference range. However, cases 4 and 5 showed a significant increase in FIX activities. Alu-mediated nonallelic homologous recombination was identified as the cause of F9 deletion in case 1; FoSTeS/MMBIR (Fork Stalling and Template Switching/microhomology-mediated break-induced replication) contributed to both F9 deletion and tandem duplication observed in cases 2 and 3; BIR/MMBIR (break-induced replication/microhomology-mediated break-induced replication) mediated by the same pair of low-copy repeats results in similar duplication–triplication/inversion–duplication (DUP–TRP/INV–DUP) rearrangements in cases 4 and 5, leading to complete F9 duplication and triplication, respectively.

Conclusion Large deletions involving the F9 gene exhibit no apparent pattern, and the extra-hematologic clinical phenotypes require careful analysis of other genes within the deletion. The impact of complete F9 duplication and triplication on FIX expression might depend on the integrity of the F9 upstream sequence and the specific rearrangement mechanisms. Notably, DUP–TRP/INV–DUP rearrangements significantly elevate FIX activity and are closely associated with thrombotic phenotypes.

Authors' Contribution

Y.M. and Y.L. designed and performed the experiments and contributed to the writing of the manuscript. J.S., Q.L., and R.W., collected and organized the clinical cases. Q.D. and J.D. analyzed the data, reviewed and revised the manuscript, and provided supervision for the entire project.

* These authors contributed equally as co-first authors.

Supplementary Material

Publication History

Received: 08 September 2023

Accepted: 21 November 2023

Accepted Manuscript online:
27 November 2023

Article published online:
26 December 2023

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