Table 2 Clinicopathological features, variant allele frequencies (VAFs), associated somatic loss of heterozygosity (LOH) and/or second gene hit of prostate cancer (PCa) patients by ancestry presenting with potentially pathogenic (PP) SVs and cautionary PP-SVs as defined by this study

From: Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men

Gene name

Pathogenicity

SV (impact) type

Patient No.

Patient ID2

Expression1

VAF3

Ancestry

Age

PSA

ISUP GG

Tumour LOH4

Tumour 2nd hit5

SLC3A1

PP-SV (LP)

DUP (IED)

1

N0001

ND

0.33

African

75

22.9

4

LOH-neg

No

–

–

 

2

SMU094

ND

0.30

African

64

15

4

LOH-CNG

CNL

OCA2

PP-SV (LP)

DEL (pLoF)

1

N0059

ND

0.45

African

79

153

5

LOH-neg

CNG

PIGN

PP-SV (P)

DEL (pLoF)

1

SMU083

ND

0.51

African

86

40.5

3

LOH-CNL

No

SLC7A2

PP-SV

DEL (pLoF)

1

UP2035

ND

0.48

African

70

680

5

LOH-neg

CNL

–

–

 

2

KAL0054

ND

0.49

African

64

42.9

5

LOH-CNG

No

DNAJC15

PP-SV

DEL (pLoF)

1

17135

ND

0.48

European

63

7.8

5

LOH-neg

No

BCL2L11

PP-SV

DEL (pLoF)

1

KAL0101

Low

0.45

African

71

32.3

5

LOH-CNN

No

BARD1

PP-SV

DEL (pLoF)

1

N0073

ND

0.49

African

62

unk

unk

LOH-CNN

No

COL4A2/COL4A1

PP-SV

DUP (CG)

1

UP2039

High/NE

0.35

African

71

319

4

LOH-neg

No

SLC2A5

PP-SV

DUP (IED)

1

11099

ND

0.33

European

70

9.9

5

LOH-neg

No

FOXP1

PP-SV

INV (pLoF)

1

UP2101

Low

0.41

African

57

75

5

LOH-neg

CNG

–

–

–

2

N0084

ND

0.41

African

65

591

4

LOH-neg

No

WASF1

PP-SV

INV (pLoF)

1

N0048

ND

0.32

African

70

83.3

5

LOH-neg

CNG

MLH1

PP-SV

INV (pLoF)

1

SMU080

Low

0.43

African

64

23.3

4

LOH-neg

No

RB1

PP-SV

INV (pLoF)

1

SMU064

ND

0.37

African

70

13.7

3

LOH-neg

No

CTNNA1

PP-SV

TRA (pLoF)

1

13179

ND

0.50

European

59

8.4

5

LOH-neg

No

AK8-DST

PP-SV

TRA (pLoF)

1

11452

ND

0.47

European

67

11

1

LOH-neg

No

LTBP1/BIRC6

Cautionary PP-SV

DUP (CG)

1

5287

ND

0.39

European

54

4.3

5

LOH-neg

CNG

PHC3-PRKACA

Cautionary PP-SV

TRA (pLoF)

1

SMU061

Avg./Avg.

0.49

African

65

12.1

3

LOH-neg

CNL

KCTD3-DST

Cautionary PP-SV

TRA (pLoF)

1

UP2039

ND

0.40

African

71

319

4

LOH-neg

CNL

–

–

–

2

SMU101

ND

0.42

African

70

4.3

3

LOH-neg

No

PKHD1

Cautionary PP-SV

TRA (pLoF)

1

N0056

ND

0.36

African

70

153

5

LOH-neg

CNG

   

2

SMU196

ND

0.39

African

47

9.5

1

LOH-neg

No

  1. CG copy gain, CNG copy-number gain, CNL copy-number loss, CNN copy-number neutral, DEL deletion, DUP duplication, IED intragenic exon duplication, INV inversion, ISUP GG International Society of Urological Pathology Group Grading, TRA translocation, LOH loss of heterozygosity, LP likely pathogenic, ND not determined, NE no expression, neg negative, P pathogenic, pLoF potentially loss-of-function, SV structural variant, unk unknown, VAF variant allele frequency. Note, all gene names are in italic; age is in years and PSA in ng/mL. Pathogenic (P) and Likely pathogenic (LP) are ClinVar defined.
  2. 1Gene expression derived from blood-matched RNAseq analysis. 2While no known family history of prostate, breast or ovarian cancer was reported for these patients, SMU080 reported a sister with cervical cancer and SMU061 a mother with stomach cancer. 3Variant allele frequency (Supplementary Table 8). 4Loss of heterozygosity status was inferred from TITAN. 5The details of the second somatic hit locations were shown in Supplementary Table 9.
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