Pathogenic variants reveal candidate genes for prostate cancer germline testing for men of African ancestry

Abstract

Prostate cancer (PCa) germline testing, while gaining momentum, is ancestry restrictive and African exclusive. Through whole genome sequencing for 217 African ancestral cases (186 southern African, 31 Pan representative), we identify 172 potentially pathogenic variants in 78 DNA damage repair or PCa related genes. Prevalence for reported (13/217, 5.99%) and cumulative predicted (24/217, 11.06%) variants of significance (11 genes) falls below that reported for non-Africans. Conversely, BRCA1, HOXB13, CDK12, MLH1, MSH2, and BRIP1 remain unimpacted. Through pathogenic ranking based on variant frequency and functionality, clinical presentation and tumour-matched biallelic inactivation, top-ranked candidates include PREX2, POLE, FAT1, BRCA2, POLQ, LRP1B and ATM. Besides notable impact of DNA polymerases, including POLG, Fanconi anaemia genes include FANCD2, FANCA, FANCG, ERCC4, FANCE and FANCI, while DNA mismatch repair genes MSH3 and PMS1 outranked known namesakes MSH6 and PMS2. This study provides insights into the spectrum of African-relevant potentially pathogenic PCa variants, highlighting much-needed gene candidates for ancestry-inclusive germline testing.

Fig. 1. Population genetic ancestral substructure for 217 African prostate cancer (PCa) cases.

Admixture plot for the study cohort including 186 South African (SAPCS) and 31 PPCG African ancestral patients using k-means clustering for k = 3 (A, cross-validation error = 0.252, Supplementary Data 1) and k = 4 (B, cross-validation error = 0.255, Supplementary Data 1). Population fractions have been determined against reference controls defined as; European (CEU, n = 20), Asian (CHB, n = 20), west African or Yoruba (YRI, n = 20), African American (ASW, n = 20), San (KSGP, n = 20) and east African or Luhya (LWK, n = 20).

Fig. 2. Study workflow for the identification of African-relevant prostate cancer (PCa) Potentially Pathogenic Variants (PPVs) and Potentially Oncogenic Variants (POVs), including population-specific low-frequency (PSLF) PPVs/POVs and candidate genes.

Step 1. From genome-wide small variants (SNVs, single nucleotide variants; indels, insertions or deletions <50 bases) derived from 217 African PCa cases (blue) 45 rare DNA Damage Repair (DDR) or PCa related PPVs in 34 genes (Table 1) and a single PSLF-PPV (Table 3) were identified. Step 2. Rare and low-frequency PPV candidate genes (n = 223) were further filtered for non-African representative PPVs using European-biased PCa (PPCG, orange) and healthy (MGRB, red) datasets, provided multi-ethnic validation for 22 gene candidates, genetic conservation for five genes and no further PPV candidate exclusion. Step 3. Prioritizing African-derived variants of unknown significance (VUS) for classification as POVs, as per exclusion and inclusion criteria (grey), yielded 138 rare DDR/PCa related POVs in 61 genes (Table 2) and 16 PSLF-POVs in 11 genes (10 overlapping with POV candidates, Table 3). Minor allele frequency (MAF) filtering (steps 1 and 3) was based on all population and African restricted gnomAD v4.0 data. Step 4. All class potential pathogenic variants were further filtered using population control MAFs >2% (SAC, southern African controls; EAC, east African controls) and variant allele frequency (VAF) < 30% for a total of 172 variants of pathogenic potential across 78 candidate genes.

Fig. 3. Ranking for potentially pathogenic or oncogenic variants (PPV/POVs) and associated candidate genes for African-inclusive prostate cancer (PCa) germline testing (GT).

A Ranking system overview based on variant, clinical and tumour features. B Ranking for 24 rare PPV/POVs identified in known PCa GT genes, including previously reported (known) and not reported (unknown) variants. C The 11 known PCa GT genes ranked by weight (total ranked score), prevalence and total number of variants. D Ranking for 142 reported (known) and not reported (unknown) rare PPV/POVs impacting 66 candidate genes not included in PCa GT panels. E Ranking by weight (ranked score) for all 78 known and unknown PCa GT gene candidates, with population-specific low-frequency (PSLF) candidates assessed independently and represented as gene duplicates (stars), while providing an additional gene candidate CREBBP.