Table 3 Results of next generation sequencing.

From: Variant morphology and random chromosomal integration of BK polyomavirus in posttransplant urothelial carcinomas

Case No

Material

BKPyV genome

Tumor genome

Reads (n)

Genotype

Additional variant

Break point

BKPyV-DNA copies/cell

BKPyV integration site

Pathogenic/likely pathogenic variant

1

FFPE

191

Ib2

8 bp + 10 bp deletion NCCR

LTag

0.77

11p14; LGR4: Promotor?, 4 kb upstream of LGR4

None

2

FFPE

143

IV

nd

nd

0.3

nd

TTN (p.Arg28364*), PCLO (p.Arg3542*), PANK2 (p.Thr237Met), KMT2D (p.Pro4914Leu)

3

FFPE

1.606

IV

7 bp + 23 bp deletion NCCR

VP2

4.3

6p22; DEK/RNF144B intergenic

ATM (p.Lys1965fs), RYR1 (p.Arg4825Cys)

4

FFPE

176

Ib2

nd

VP3

0.61

2p21; THADA: intron 23 or 24

FLG (p.Ser1906*)

5

Fresh frozen tissue

1.946

Ia

nd

VP2 + VP3

2.87

9q21; SMC5/KLF9 intergenic + 3p21/5p15; PRKAR2A/SLC6A1 possible translocation?

None

  1. FFPE formalin-fixed paraffin-embedded tissue, NCCR noncoding control region, nd not detected.
  2. *Nonsense mutation introducing a stop codon.
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