Table 1.

Clinical presentation, patient ancestry, sequencing statistics, and genomic variation

UP2003UP2039UP2099UP2113UP2116UP2133
EthnicitySA ColouredSA ColouredZuluPediSwatiZulu
Clinical presentation at diagnosis
 Age (years)767176889958
 PSA levels (ng/mL)3,45931910012365100
 Gleason score9888109
 Family history prostate cancerYesNoNoNoNoNo
Ancestral fractionsa
 African: Bantu/KhoeSan0.421/0.4170.622/0.3780.868/0.1320.944/0.0560.975/0.0250.868/0.132
 Non-African: Eur/Asian0.138/0.02400000
WGS statistics
 Blood/Tumor coverage43X/86X40X/75X42X/82X58X/86X41X/87X43X/81X
 Tumor purity0.420.680.780.410.440.43
Germline variations (total number)
 SNVs4,447,9824,463,2454,459,4924,361,4914,398,8764,465,481
 Ins535,378547,399539,284568,665533,522569,188
 Del569,071580,344572,637600,646565,696605,795
Somatic variants (total number)b
 SNVs11,4638,0177,939138,9906,94611,463
 Ins1,0068441,0777,4011,0031,471
 Del1,7601,1821,36223,1511,3261,448
 Nonsynonymous9552421,5075679
 TMB per Mbp4.63.33.45534.7
 SV-DEL (bases impacted)124 (296,889,562)7 (31,812,041)46 (198,385,225)27 (7,785,288)56 (125,131,631)54 (315,444,459)
 SV-DUP (bases impacted)16 (310,358,766)2 (50,355)9 (134,176,076)7 (13,696,461)6 (98,051,676)234 (320,826,012)
 SV-INV (bases impacted)12 (262,977,083)1 (287,931)6 (500,592,107)0 (0)2 (79,698,508)4 (3,017,735)
 SV-CTX191171220
 Chained eventc000001 (4)
 SCNA-Gains/Losses2,325/3,9793,466/6,1846,759/4,7841,863/2,5243,009/5,13011,593/13,848
TCGA molecular subtyped
 Classification (mutation)SPOP (F133I)UCUCFOXA1 (D226G)UCUC
Oncogenic driver mutations
 SNV: TransFIC/CanDrAe28/21(8)18/11(2)15/11(5)613/237(113)8/20(4)25/14(6)
 SV-DEL: High Impactf21(9)2(0)16(7)1(1)12(8)16(6)
SCNA recurrent focal amplifications
CCND1 (11q13.3)High gainHet lossSome gainHigh gainSome gainHigh gain
MYC (8q24.21)High gainSome gainHigh gainDiploidHigh gainHigh gain
SCNA recurrent focal deletions
PTEN (10q23.31)DiploidHet lossSome gainDiploidSome gainHet loss
TP53 (17p13.1)Het lossHet lossSome gainDiploidSome gainHom del
FANCD2 (3p25.3)Het lossHet lossDiploidDiploidDiploidHom del
SPOPL (2q22.1)Hom delHet lossSome gainHigh gainHet lossDiploid
MAP3K7 (6q15)Het lossSome gainHet lossDiploidHom delHet loss
CHD1 (5q15)Hom delHet lossSome gainDiploidSome gainHet loss
  • Abbreviations: CTX, interchromosomal translocation; del, deletion <50 bp; DEL, deletion >50 bp; DUP, duplication; Eur, European; Het loss, heterozygous loss; Hom del, homozygous deletion; ins, insertion < 50 bp; INV, inversion; SA Coloured, South African Coloured; UC, unclassified.

  • aAncestral fractions based on STRUCTURE analysis.

  • bNumber of SNVs/indels detected using MuTect and that of SVs (hg38) from high-confidence results of somatic callers.

  • cIn brackets is the number of interchromosomal translocations involved.

  • dA total of seven TCGA subtypes.

  • eOverlapping results in brackets.

  • fOncogenic potentials reported in MalaCard in brackets.