1
Supplementary Table 1 Comparison of copy numbers detected in analysis of microarray data and
2
quantitative genomic PCR for Synexin 1 (SNX1)a,b
3
Patient
Synexin 1
Synexin 1
Number
Microarray
qPCR
1
2
0.89
2
0
1
1
1
2
1.11
2
1.02
2
1.1
2
1.13
3
4
5
2
6
1
4
5
6
a
7
analysis of the microarray data where 0, 1, and 2 represent homozygous deletion, heterozygous
8
deletion, and no change, respectively; Synexin 1 qPCR = absolute copy number in the affected
9
tissue divided by the absolute copy number in the normal tissue as obtained using quantitative
Patient numbers are same as in Table 1. Synexin 1 microarray = copy numbers obtained in
10
genomic PCR.
11
b
12
sample was not of sufficient quantity to perform quantitative genomic PCR. We had more than one
13
affected or normal sample from patients 2, 3, and 4, allowing us to perform two copy number
14
analyses in these patients.
Results from microarray analyses were not confirmed in patients 5 and 6 because the DNA
15
Supplementary Table 2 Primers used in quantitative genomic PCR to verify copy numbers obtained in analysis of microarray dataa
16
Geneb
SYNX1
AR
ALB
Map Locus
15q22.31
Xq12
4q13.3
Position
62195023
66847971
74503418
Size (bp)
133
155
139
CNC
300
300
300
Forward primer
Reverse primer
CTTTTGTCATGTTGCCCAAG
TGCAGGTCCCACACAAATAA
CGGAAGCTGAAGAAACTTGG
ATGGCTTCCAGGACATTCAG
GCTGTCATCTCTTGTGGGCTGT ACTCATGGGAGCTGCTGGTTC
17
18
a
19
(nM). Primers were designed to amplify a region as close to the SNP with CNV as possible, where applicable. Annealing temperature
20
for all of the primers was 600C. Primers for ALB13 and AR14 were published previously.
21
bSYNX1
22
23
24
25
26
27
28
29
Position = physical position on the chromosome; CNC = optimum concentration of each primer used in quantitative genomic PCR
= synexin 1; AR = androgen receptor; ALB = albumin.