Table 3 The proportion of alternative splicing variants calculated from ddPCR-based and NGS-based data in selected paired tumour and non-tumour tissues (with raw data overview).

From: Comprehensive quantitative analysis of alternative splicing variants reveals the HNF1B mRNA splicing pattern in various tumour and non-tumour tissues

 

3p

Δ7

Δ7–8

Δ8

ddPCR

NGS

ddPCR (%)

NGS (%)

ddPCR (%)

NGS (%)

ddPCR (%)

NGS (%)

ddPCR (%)

NGS (%)

tmp/µl

cov

Pancreas T

29.9

27.5

2.8

1.5

2.6

3.2

10.4

5.7

385

3766

Pancreas NT

30.2

30.5

3.9

1.7

2.8

4.2

11.4

5.2

165

1409

Large intestine T

33.2

32.8

3.9

3.7

5.1

5.6

15.1

6.9

214

2572

Large intestine NT

32.7

32.5

1.8

0.7

1.2

1.2

6.0

3.9

281

2775

Prostate T

24.4

21.2

4.4

1.8

2.2

2.5

4.8

2.5

66

663

Prostate NT

29.7

27.2

1.2

1.8

0.5

0.4

2.7

1.0

158

2490

Kidney T

30.1

23.8

4.7

0.8

2.7

1.5

6.9

1.1

916

3897

Kidney NT

28.4

25.2

1.2

1.1

0.6

1.0

2.3

1.9

981

11,619

Endometrium T

27.4

25.9

0.4

0.1

0.8

0.7

1.5

0.3

170

2301

Endometrium NT

31.5

24.4

1.6

0.8

0.8

0.9

2.7

2.3

203

1786

Ovary T

19.8

16.4

1.8

2.4

2.1

2.0

9.1

3.3

137

866

Ovary NT

30.0

24.3

2.0

1.2

1.1

2.0

5.2

3.5

113

1082

  1. Numbers represent the percentage of each individual variant related to the overall HNF1B mRNA expression (calculated as the sum of canonical exon 3 and 3p variants in both approaches). Each line represents data from one representative sample; ddPCR tmp/µl represents number of HNF1B templates per 1 µl of cDNA detected by ddPCR; NGS cov. represents peak coverage of HNF1B exon 3. T tumour tissue, NT non-tumour tissue.
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