Supplementary Table 1 Comparison of Copy Numbers Detected in Analysis of Microarray Data

Supplementary Table 1 Comparison of copy numbers detected in analysis of microarray data and quantitative genomic PCR for Synexin 1 (SNX1)a,b

Patient Number / Synexin 1 Microarray / Synexin 1 qPCR
1 / 2 / 0.89
2 / 0 / 1
1 / 1
3 / 2 / 1.11
2 / 1.02
4 / 2 / 1.1
2 / 1.13
5 / 2
6 / 1

aPatient numbers are same as in Table 1. Synexin 1 microarray = copy numbers obtained in analysis of the microarray data where 0, 1, and 2 represent homozygous deletion, heterozygous deletion, and no change, respectively; Synexin 1 qPCR = absolute copy number in the affected tissue divided by the absolute copy number in the normal tissue as obtained using quantitative genomic PCR.

bResults from microarray analyses were not confirmed in patients 5 and 6 because the DNA sample was not of sufficient quantity to perform quantitative genomic PCR. We had more than one affected or normal sample from patients 2, 3, and 4, allowing us to perform two copy number analyses in these patients.

Supplementary Table 2 Primers used in quantitative genomic PCR to verify copy numbers obtained in analysis of microarray dataa

Geneb / Map Locus / Position / Size (bp) / CNC / Forward primer / Reverse primer
SYNX1 / 15q22.31 / 62195023 / 133 / 300 / CTTTTGTCATGTTGCCCAAG / TGCAGGTCCCACACAAATAA
AR / Xq12 / 66847971 / 155 / 300 / CGGAAGCTGAAGAAACTTGG / ATGGCTTCCAGGACATTCAG
ALB / 4q13.3 / 74503418 / 139 / 300 / GCTGTCATCTCTTGTGGGCTGT / ACTCATGGGAGCTGCTGGTTC

aPosition = physical position on the chromosome; CNC = optimum concentration of each primer used in quantitative genomic PCR (nM). Primers were designed to amplify a region as close to the SNP with CNV as possible, where applicable. Annealing temperature for all of the primers was 600C. Primers for ALB13 and AR14 were published previously.

bSYNX1 = synexin 1; AR = androgen receptor; ALB = albumin.