Abstract: SA-PO0594
Validation of a Targeted Region-Based Sliding Window (TRSW) Approach for Copy Number Variation Detection in a Large Cohort of Patients with ADPKD
Session Information
- Cystic Kidney Diseases: Clinical Research
November 08, 2025 | Location: Exhibit Hall, Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Genetic Diseases of the Kidneys
- 1201 Genetic Diseases of the Kidneys: Monogenic Kidney Diseases
Authors
- Carriazo Julio, Sol Maria, University of Toronto, Toronto, Ontario, Canada
- Sarie, Yasmina, University of Toronto, Toronto, Ontario, Canada
- Song, Xuewen, University of Toronto, Toronto, Ontario, Canada
- Haghighi, Amirreza, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Khowaja, Saima, University Health Network, Toronto, Ontario, Canada
- Pei, York, University of Toronto, Toronto, Ontario, Canada
Background
With advances in next-generation sequencing(NGS), targeted NGS(tNGS) is widely used in ADPKD, showing excellent diagnostic yield for single-nucleotide variants and indels. However, copy number variations(CNVs) are often missed but can be detected by multiplex ligation-dependent probe amplification(MLPA) as an additional follow-up test. Recently, sequence-based CNV detection from tNGS has emerged as a potential approach for CNV detection, but has not been systematically evaluated large PKD cohorts. Here, we report our results on the diagnostic accuracy of a TRSW-based method for CNV detection in a large PKD cohort.
Methods
We retrospectively analyzed patients with exome-based gene panels from the Toronto Genetic Epidemiology Study of PKD(TGSEP) using TRSW. In this computational method, average read depths from tNGS are compared to those of a normal pool to generate a potential CNV call. After filtering(Figure 1), patients with potential CNVs in PKD1/2 exons were reviewed in Integrative Genomics Viewer(IGV) to classify calls as likely positive(LP) or negative(LN) and compared with MLPA when available.
Results
Among 2365 patients from TGESP, 934 had tNGS data(Figure 1). After filtering, review of 448 potential CNVs in PKD1/2 on the IGV identified 44 LP and 404 LN cases. In the LP group, MLPA confirmed 40/43 CNVs; 3 were missed by MLPA but confirmed by other methods. In the LN group, MLPA was also negative in 156/166 cases; 9 had false positives by MLPA, and 1 CNV was false negative by TRSW.
Conclusion
TRSW provides a sensitive and accurate method for CNV detection from NGS data with high concordance to MLPA, although it requires extensive filtering and manual review. A combined TRSW-MLPA approach may enhance CNV diagnostic yield in ADPKD.