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Table 4 Fluorescence signal intensity ratios obtained by genotyping six SNPs in RNA (cDNA) and genomic DNA from the HUVEC and HAEC cells using the two microarray-based minisequencing methods and two reference methods.

From: Detecting imbalanced expression of SNP alleles by minisequencing on microarrays

 

Fluorescence signal ratio

Difference in cDNA and gDNA ratios

(p-value)

cDNA/gDNAc

SNPa

Methodb

cDNA

gDNA

  

rs4331 ACE

I

4.1

1.7

0.00095

2.4 (1.9–2.8)

 

II

0.94

0.33

0.0060

2.8 (1.8–4.0)

rs1042719 ADRB2

I

0.50

0.95

0.000025

0.54 (0.47–0.69)

 

II

0.33

0.47

0.0070

0.71 (0.67–0.75)

 

TM

0.086

0.19

<0.0001

0.47 (0.31–0.56)

 

MS

0.48

0.99

<0.0001

0.48 (0.34–0.62)

rs5351 EDNRB

I

6.3

3.5

0.00014

1.8 (1.6–2.0)

 

II

8.7

5.6

0.0030

1.6 (1.4–1.8)

rs5925 LDLR

I

0.87

1.0

0.33

0.85 (0.63–1.1)

 

II

0.37

0.27

0.029

1.4 (1.1–1.5)

 

TM

3.3

1.4

0.15

2.4 (1.4–5.6)

 

MS

0.36

0.28

0.027

1.3 (0.98–1.5)

rs5930 LDLR

I

1.1

0.78

0.035

1.5 (1.1–1.9)

 

II

0.54

0.29

0.0030

1.8 (1.5–2.3)

rs1433099 LDLR

I

2.0

2.0

0.66

0.96 (0.84–1.1)

 

II

0.57

0.46

0.33

1.2 (0.65–1.5)

 

TM

1.0

0.49

<0.0001

2.0 (1.9–2.1)

 

MS

0.47

0.32

0.060

1.5 (1.0–2.0)

  1. a rs4331 ACE, rs1042719 ADRB2 and rs5351 EDNRB were analysed in HUVEC and rs5925 LDLR, rs5930 LDLR and rs1433099 LDLR were analysed in HAEC.
  2. b Minisequencing using (I) immobilised primers; (II) cyclic primer extension and "tag-arrays", TaqMan (TM) and solid-phase minisequencing (MS). TM-assays were not possible to design using the Assay-by-Design and Assay-on-Demand service at ABI for the remaining three SNPs, MS was performed for the SNPs with working TM-assays.
  3. c Mean and range is given for five parallel reactions.