Skip to main content

Table 2 High confidence, non-synonymous variants identified in the diagnostic prostate biopsy sample containing conventional adenocarcinoma (Dx [PR-259]) and subsequent liver metastasis with small cell/neuroendocrine carcinoma (NePC [PR-258])

From: Comprehensive serial molecular profiling of an “N of 1” exceptional non-responder with metastatic prostate cancer progressing to small cell carcinoma on treatment

     

Dx (PR-259)

NePC (PR-258)

  

Location

Gene

Ref

Alt

AA change

Var. allele frequency (FAO/FDP)

Read depth (FDP)

Var. allele frequency (FAO/FDP)

Read depth (FDP)

AV_TX

AV_NUC

chr17:7577094

TP53

G

A

p.R282W

1.6 %

755

69 %

217

NM_000546

c.C844T

chr18:48604783

SMAD4

C

p.L535fs

36 %

227

67 %

196

NM_005359

c.1605delC

chr12:49449077

KMT2D

T

C

p.K11E

18 %

22

37 %

180

NM_003482

c.A31G

chr5:7878077

MTRR

C

G

p.P141R

15 %

89

55 %

142

NM_002454

c.C422G

chr19:17953318

JAK3

C

T

p.R223H

54 %

76

60 %

70

NM_000215

c.G668A

chr6:32166327

NOTCH4

T

C

p.T1543A

42 %

608

35 %

231

NM_004557

c.A4627G

  1. High confidence, non-synonymous variants identified in the diagnostic prostate biopsy sample containing conventional adenocarcinoma (Dx [PR-259]) and paired subsequent liver metastasis with small cell/neuroendocrine carcinoma (NePC [PR-258]) are shown. For each variant, the location (hg19), gene, reference (Ref.) and variant (Alt.) alleles, and amino acid (AA) change info is given. The variant (Var.) allele frequency is the flow-corrected variant containing read count (FAO) divided by flow-corrected read depth (FDP). For the KMT2D and TP53 variants in PR-259, the Var allele frequency was calculated using non-flow-corrected read counts (AO/DP) due to those variants not passing filtering in that sample. The reference sequence (Refseq) and nucleotide (Nuc) change used to derive the AA change are also given. Variants identified as SNPs by exome sequencing of germline DNA are indicated in gray. Prioritized somatic variants are bolded