Table 1.
Characteristics of data sets provided by participating centers of the German Consortium for Hereditary Breast & Ovarian Cancer (GC-HBOC), namely the Institute of Medical Genetics and Applied Genomics (IMGAG), University Hospital Tübingen, the Institute for Clinical Genetics (ICG), University Hospital Carl Gustav Carus Dresden, the Department of Medical Genetics (DMG), University Hospital Münster, the Center for Familial Breast and Ovarian Cancer (CFBOC), University Hospital Cologne, and the Institute of Human Genetics (IHG) at the University of Regensburg.
| IMGAG | ICG | DMG | CFBOC | IHG | ||
|---|---|---|---|---|---|---|
| Sample size | Set 1 | 348 | 585 | 545 | 412 | 251 |
| Set 2 | 1410 | |||||
| Testing indication | Various | Cancer-related | Familial BC/OC | Familial BC/OC | Familial BC/OC | |
| Considered PRS | BCAC 313 | BCAC 313 | BRIDGES 306 | BRIDGES 306 | BRIDGES 306 | |
| BRIDGES 306 | ||||||
| NGS approach | WGS |
Twist Custom Cancer Panel |
Twist Custom Panel | Agilent TruRisk v3 | Agilent TruRisk v3 | |
| Reference | hg38 | hg19 | hg19 | hg19 | hg38 | |
| Variant caller | Set 1 | DRAGEN v4.0.3 | freebayes v1.3.6 | DRAGEN v4.2.4 | freebayes v1.3.6 | CLC LightSpeed v23.0.2 |
| Set 2 | freebayes v1.3.6 | GATK v4.2.6 HaplotypeCaller | GATK v4.4.0 HaplotypeCaller | GATK v4.3.2 HaplotypeCaller | GATK v4.2.6 HaplotypeCaller | |
| Calling mode | Set 1 | Unforced | Forced | Forced | Forced | Unforced |
| Set 2 | Forced | |||||
| Quality filter | DP ≥ 15 | DP ≥ 20 | DP ≥ 20 | DP ≥ 30 | DP ≥ 10 | |
Each center provided two data sets.
BC/OC breast/ovarian cancer, DP sequencing depth, PRS polygenic risk score.