Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Cohorts and Patients
2.2. The Determination of Pathogenicity for Somatic Variant Calls
2.3. Groupwise Association Test, Outlier Detection Analysis, and Variant Annotation
2.4. HRD Score Calculation
2.5. Statistical Analysis
2.6. Survival Analysis
3. Results
3.1. Distribution of the TCGA Pan-Cancer Atlas Cohort across Racial Groups
3.2. Association of HRD Scores with Survival across Cancer Types
3.3. Synergistic Effects between Genome-Wide HRD and Global TMB among Cancers
3.4. Racial Differences of Genome-Wide HRD and Global TMB across Cancers
3.5. Predisposing HRD-Related Genes That Are Specific to Race
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Asian | African American/Black | White | Total | |
---|---|---|---|---|
BLCA | 42 | 22 | 319 | 383 |
BRCA | 59 | 159 | 678 | 896 |
CESC | 18 | 27 | 184 | 229 |
COAD | 11 | 55 | 184 | 250 |
ESCA | 44 | 0 | 104 | 148 |
GBM | 0 | 0 | 111 | 111 |
HNSC | 10 | 46 | 414 | 470 |
KIRC | 0 | 52 | 287 | 339 |
KIRP | 0 | 59 | 190 | 249 |
LGG | 0 | 21 | 466 | 487 |
LIHC | 150 | 16 | 171 | 337 |
LUAD | 0 | 52 | 376 | 428 |
LUSC | 0 | 26 | 325 | 351 |
OV | 0 | 18 | 146 | 164 |
PAAD | 11 | 0 | 132 | 143 |
PCPG | 0 | 19 | 131 | 150 |
PRAD | 0 | 0 | 143 | 143 |
SARC | 0 | 17 | 202 | 219 |
SKCM | 0 | 0 | 339 | 339 |
STAD | 75 | 11 | 245 | 331 |
TGCT | 0 | 0 | 112 | 112 |
THCA | 49 | 26 | 315 | 390 |
THYM | 12 | 0 | 98 | 110 |
UCEC | 20 | 101 | 341 | 462 |
Total | 501 (6.92%) | 727 (10.04%) | 6013 (83.04%) | 7241 (100%) |
Positive Correlation | Inverse Correlation |
---|---|
OV (R = 0.31) | COAD (R = −0.24) |
LUSC (R = 0.33) | UCEC (R = −0.32) |
BLCA (R = 0.38) | |
PAAD (R = 0.54) | |
LUAD (R = 0.49) | |
SARC (R = 0.5) | |
BRCA (R = 0.54) | |
THYM (R = 0.32) | |
KIRC (R = 0.25) | |
HNSC (R = 0.23) | |
PRAD (R = 0.39) | |
LGG (R = 0.34) | |
PCPG (R = 0.27) | |
Pan-cancer (R = 0.26) |
White | African American/Black | Asian | |
---|---|---|---|
BLCA | 18 | 51 | 11 |
BRCA | 135 | 97 | 56 |
CESC | 48 | 41 | 2 |
COAD | 200 | 9 | 160 |
ESCA | 52 | 0 | 52 |
HNSC | 13 | 20 | 14 |
KIRC | 27 | 27 | 0 |
KIRP | 9 | 9 | 0 |
LGG | 17 | 17 | 0 |
LIHC | 6 | 13 | 4 |
LUAD | 118 | 118 | 0 |
LUSC | 52 | 52 | 0 |
OV | 18 | 18 | 0 |
PAAD | 57 | 0 | 57 |
SARC | 25 | 25 | 0 |
STAD | 206 | 20 | 191 |
THCA | 10 | 3 | 7 |
THYM | 2 | 0 | 2 |
UCEC | 891 | 43 | 213 |
Cancer | Gene | Population | Previous Reports | Identified Variant (GRCh38) | REVEL Score 1 | Clinvar 2 | |
---|---|---|---|---|---|---|---|
Same Population | Other Population | ||||||
BRCA | BAP1 | White | Shahriyari et al. (2019) | 3:52442072-T/C | 0.829 | pathogenic | |
African American/Black | |||||||
BLM | White | Cybulski et al. (2019) | 15:91312388-C/T | 0.677 | uncertain significance | ||
African American/Black | |||||||
OV | ERCC5 | White | Doherty et al. (2011) | 3:103525633-G/T | 0.939 | pathogenic | |
African American/Black | Doherty et al. (2011) | ||||||
STAD | ATM | White | Helgason et al. (2015) | 11:108141997-C/T | 0.739 | uncertain significance | |
Asian | Cai et al. (2015) | ||||||
MSH6 | White | Karpińska-Kaczmarczyk et al. (2016) | 2:48028049-G/A | 0.857 | uncertain significance | ||
Asian | |||||||
PTEN | African American/Black | Nemtsova et al. (2020) | 10:89692905-G/A | 0.976 | likely pathogenic, pathogenic |
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Hsiao, Y.-W.; Lu, T.-P. Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers. J. Pers. Med. 2021, 11, 1287. https://doi.org/10.3390/jpm11121287
Hsiao Y-W, Lu T-P. Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers. Journal of Personalized Medicine. 2021; 11(12):1287. https://doi.org/10.3390/jpm11121287
Chicago/Turabian StyleHsiao, Yi-Wen, and Tzu-Pin Lu. 2021. "Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers" Journal of Personalized Medicine 11, no. 12: 1287. https://doi.org/10.3390/jpm11121287