FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort

Eyyüp Üçtepe; Hilal Yildiz Er; Hanifenur Mancılar; Fatma Nisa Esen; Sait Tümer; Vehap Topçu; Ant Uzay; Ali Bülent Antmen; Aziz Polat; Ahmet Yeşilyurt

doi:10.31067/acusaglik.1855530

FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort

Abstract

Purpose: To investigate the molecular basis of FA in patients with unresolved genetic diagnoses and to highlight diagnostic pitfalls related to pseudogene interference and autozygosity. Methods: Seven patients presenting with bone marrow failure and clinical features compatible with FA were evaluated. All underwent whole-exome sequencing (WES), FA-targeted gene panel analysis, copy-number variation (CNV) assessment, and runs of homozygosity (ROH) mapping. In cases with inconclusive NGS results, targeted Sanger sequencing was performed for candidate regions. Results: Four patients harbored clearly pathogenic or likely pathogenic biallelic variants in FANCA, including truncating, splice-site, and exon-deletion variants, establishing a definitive molecular diagnosis. In contrast, three unrelated patients (P5–P7) from consanguineous families remained without a confirmed genetic diagnosis for several years despite positive chromosomal breakage tests. All three shared the same intronic FANCD2 splice-site variant, c.1948-16T>G, located within a genomic region of high homology to flanking FANCD2 pseudogenes. Initial external WES analyses either failed to detect this variant or reported it with low allelic balance, precluding confident interpretation. Re-analysis incorporating ROH mapping identified a shared autozygous region on chromosome 3 encompassing FANCD2. Subsequent gene-specific Sanger sequencing confirmed homozygosity for the c.1948-16T>G variant in all three patients, establishing FANCD2 as the causative gene. Conclusion: This study demonstrates that pseudogene interference can obscure pathogenic variants in standard exome sequencing pipelines and lead to prolonged diagnostic odysseys in FA. Integrating chromosomal breakage testing with pseudogene-aware NGS analysis, ROH and structural-variant assessment, and targeted Sanger confirmation is essential for accurate FA diagnosis, particularly in consanguineous populations and for genes embedded in complex genomic regions.

Keywords

Ethical Statement

This study did not require formal ethics committee approval according to national and institutional regulations, as it involved only the retrospective analysis of routine clinical genetic testing results and anonymized clinical data. No additional procedures, interventions, or sample collection were performed for research purposes, and no identifiable personal information was used. All patients (or their legal guardians) had previously provided written informed consent at the time of their clinical evaluation, permitting the use of their anonymized clinical and genetic data for scientific and educational purposes in accordance with institutional policy. All procedures were conducted in accordance with the principles of the Declaration of Helsinki.

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Details

Primary Language

English

Subjects

Haematology

Journal Section

Research Article

Authors

Eyyüp Üçtepe
0000-0002-1820-9094
Türkiye

Hilal Yildiz Er
0000-0002-9932-5643
Türkiye

Hanifenur Mancılar
0000-0003-2338-5436
Türkiye

Fatma Nisa Esen
0000-0002-8267-3721
Türkiye

Sait Tümer
0000-0002-1347-1958
Türkiye

Vehap Topçu
0000-0001-7224-5697
Türkiye

Ant Uzay
0000-0003-1381-4188
Türkiye

Ali Bülent Antmen
0000-0001-6058-6021
Türkiye

Aziz Polat
0000-0002-3454-9849
Türkiye

Ahmet Yeşilyurt ^*
0000-0003-1289-7866
Türkiye

Publication Date

March 24, 2026

Submission Date

January 9, 2026

Acceptance Date

February 16, 2026

Published in Issue

Year 2026 Volume: 17 Number: January, February, March 2026

DOI

https://doi.org/10.31067/acusaglik.1855530

IZ

https://izlik.org/JA83BE94NH

Cite

RIS / Bibtex

APA

Üçtepe, E., Yildiz Er, H., Mancılar, H., Esen, F. N., Tümer, S., Topçu, V., Uzay, A., Antmen, A. B., Polat, A., & Yeşilyurt, A. (2026). FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort. Acıbadem Üniversitesi Sağlık Bilimleri Dergisi, 17(January, February, March 2026). https://doi.org/10.31067/acusaglik.1855530

AMA

1.Üçtepe E, Yildiz Er H, Mancılar H, et al. FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort. Acibadem Univ Saglik Bilim Derg. 2026;17(January, February, March 2026). doi:10.31067/acusaglik.1855530

Chicago

Üçtepe, Eyyüp, Hilal Yildiz Er, Hanifenur Mancılar, et al. 2026. “FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort”. Acıbadem Üniversitesi Sağlık Bilimleri Dergisi 17 (January, February, March 2026). https://doi.org/10.31067/acusaglik.1855530.

EndNote

Üçtepe E, Yildiz Er H, Mancılar H, Esen FN, Tümer S, Topçu V, Uzay A, Antmen AB, Polat A, Yeşilyurt A (March 1, 2026) FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort. Acıbadem Üniversitesi Sağlık Bilimleri Dergisi 17 January, February, March 2026

IEEE

[1]E. Üçtepe et al., “FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort”, Acibadem Univ Saglik Bilim Derg, vol. 17, no. January, February, March 2026, Mar. 2026, doi: 10.31067/acusaglik.1855530.

ISNAD

Üçtepe, Eyyüp - Yildiz Er, Hilal - Mancılar, Hanifenur - Esen, Fatma Nisa - Tümer, Sait - Topçu, Vehap - Uzay, Ant - Antmen, Ali Bülent - Polat, Aziz - Yeşilyurt, Ahmet. “FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort”. Acıbadem Üniversitesi Sağlık Bilimleri Dergisi 17/January, February, March 2026 (March 1, 2026). https://doi.org/10.31067/acusaglik.1855530.

JAMA

1.Üçtepe E, Yildiz Er H, Mancılar H, Esen FN, Tümer S, Topçu V, Uzay A, Antmen AB, Polat A, Yeşilyurt A. FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort. Acibadem Univ Saglik Bilim Derg. 2026;17. doi:10.31067/acusaglik.1855530.

MLA

Üçtepe, Eyyüp, et al. “FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort”. Acıbadem Üniversitesi Sağlık Bilimleri Dergisi, vol. 17, no. January, February, March 2026, Mar. 2026, doi:10.31067/acusaglik.1855530.

Vancouver

1.Eyyüp Üçtepe, Hilal Yildiz Er, Hanifenur Mancılar, Fatma Nisa Esen, Sait Tümer, Vehap Topçu, Ant Uzay, Ali Bülent Antmen, Aziz Polat, Ahmet Yeşilyurt. FANCD2 Pseudogene Interference in Fanconi Anemia: Lessons from a Seven-Patient Turkish Cohort. Acibadem Univ Saglik Bilim Derg. 2026 Mar. 1;17(January, February, March 2026). doi:10.31067/acusaglik.1855530