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Table 1 Custom array-CGH design: regions mapped and probe density

From: Copy number variations in candidate genomic regions confirm genetic heterogeneity and parental bias in Hirschsprung disease

probes on the chip

candidate region

Locus

average space selected

boundaries selected (kb)

# of probes

reason for selectinga

references

selected

RET

10q11.2

300 nt

100 kb

813

linkage, mutation, association

[1]

9q31

9q31

2.5 kb

0 kb

1824

linkage

[3]

9p24.1

9p24.1

3.5 kb

0 kb

142

preliminary data

unpublished

PHOX2B

4p13

500 nt

10 kb

49

association, transcriptional, HSCR increased prevalence

[1, 20, 21]

NRG1

8p12

500 nt

10 kb

473

association

[9, 22]

SEMA3A/3D

7q21.11

2.5 kb

10 kb

508

association

[10, 11, 22]

6q25.1

6q25.1

3.5 kb

0 kb

714

preliminary data

unpublished

21q22

21q22

50 kb

0 kb

202

HSCR increased prevalence

[1]

3p21

3p21

3.5 kb

0 kb

1141

linkage

[4]

19q12

19q12

3.5 kb

0 kb

1085

linkage

[4]

NRTN

19p13.3

800 nt

5 kb

18

mutation

[1]

16q23.3

16q23.3

3.5 kb

0 kb

714

linkage

[23]

NKX2–1

14q13

800 nt

5 kb

17

transcriptional, mutation

[24]

SOX10

22q13

800 nt

5 kb

27

transcriptional

[1]

22q11.2

22q11.2

50 kb

0 kb

162

HSCR increased prevalence

[25]

ECE1

1p36.1

800 nt

5 kb

103

mutation

[1]

ZEB2

2q22.3

800 nt

0 kb

165

mutation

[1]

EDNRB

13q22

800 nt

5 kb

112

linkage, mutation

[1]

GDNF

5p13.1-p12

800 nt

5 kb

42

mutation

[1]

EDN3

20q13.2-q13.3

800 nt

5 kb

44

mutation

[1]

genome

    

3130

  

replicated

    

301 (×5)

  

normalization

    

1262

  

Agilent controls

    

1482

  
  1. a linkage = reported in linkage with HSCR; mutation = reported as mutated in isolated HSCR; association = found associated with HSCR; transcriptional = suggested as involved in HSCR due to transcriptional evidences; preliminary data = suggested as deleted or amplified by preliminary results, later not confirmed; HSCR increased prevalence = increased prevalence of HSCR among patients with disorders caused by these genes/loci