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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 chipcandidate regionLocusaverage space selectedboundaries selected (kb)# of probesreason for selectingareferences
selectedRET10q11.2300 nt100 kb813linkage, mutation, association[1]
9q319q312.5 kb0 kb1824linkage[3]
9p24.19p24.13.5 kb0 kb142preliminary dataunpublished
PHOX2B4p13500 nt10 kb49association, transcriptional, HSCR increased prevalence[1, 20, 21]
NRG18p12500 nt10 kb473association[9, 22]
SEMA3A/3D7q21.112.5 kb10 kb508association[10, 11, 22]
6q25.16q25.13.5 kb0 kb714preliminary dataunpublished
21q2221q2250 kb0 kb202HSCR increased prevalence[1]
3p213p213.5 kb0 kb1141linkage[4]
19q1219q123.5 kb0 kb1085linkage[4]
NRTN19p13.3800 nt5 kb18mutation[1]
16q23.316q23.33.5 kb0 kb714linkage[23]
NKX2–114q13800 nt5 kb17transcriptional, mutation[24]
SOX1022q13800 nt5 kb27transcriptional[1]
22q11.222q11.250 kb0 kb162HSCR increased prevalence[25]
ECE11p36.1800 nt5 kb103mutation[1]
ZEB22q22.3800 nt0 kb165mutation[1]
EDNRB13q22800 nt5 kb112linkage, mutation[1]
GDNF5p13.1-p12800 nt5 kb42mutation[1]
EDN320q13.2-q13.3800 nt5 kb44mutation[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