Simultaneous detection of copy number changes and CpG methylation of genes in the Chromosome 15q11 imprinted region with a novel method; Methylation-specific MLPA (MS-MLPA)

TUBGCP1-D02-154-M 1.200 1.050 0.560 1.000 1.070 0.510 1.170 1.160 1.040 1.150 0.980 1.000 CYFIP1-D01-136-M 1.040 1.000 0.540 0.950 0.970 0.460 1.110 1.130 1.010 1.060 1.000 0.940 MKRN3-D02-172-M 1.190 1.080 0.540 0.560 0.500 0.570 1.130 1.230 1.110 0.620 0.520 0.560 MAGEL2-D02-178-M 1.060 1.070 0.530 0.520 0.440 0.510 1.060 1.060 0.990 0.530 0.510 0.530 MAGEL2-D01-193-M 1.070 0.990 0.590 0.580 0.420 0.480 1.110 1.080 1.180 0.640 0.520 0.490 NDN-D02-319-M 1.040 0.990 0.560 0.520 0.520 0.540 0.990 1.020 1.000 0.530 0.560 0.550 NDN-D01-418-M 1.000 1.020 0.480 0.550 0.430 0.540 0.900 0.880 0.980 0.500 0.540 0.470 SNRPN-M09-142-M 1.050 1.100 0.600 0.500 0.540 0.530 1.110 1.100 0.620 0.610 0.530 0.520 SNRPN-D06-166-M 1.00 1.04 0.64 0.47 0.54 0.53 1.13 1.11 0.58 0.60 0.53 0.48 SNRPN-M08-190-M 1.05 1.06 0.62 0.54 0.61 0.53 1.07 1.13 0.58 0.60 0.51 0.53 SNRPN-D05-229-M 1.110 1.030 0.630 0.550 0.550 0.510 1.120 1.110 0.590 0.570 0.530 0.510 SNRPN-D04-247-M 1.100 1.110 0.630 0.560 0.530 0.570 1.050 1.070 0.580 0.580 0.510 0.520 SNRPN-D02-256-M 1.02 0.97 0.50 0.50 0.61 0.49 0.99 1.09 0.48 0.57 0.56 0.55 SNRPN-D01-292-M 0.950 1.040 0.540 0.490 0.440 0.510 1.050 1.150 0.490 0.500 0.530 0.510 UBE3A-D01-160-M 1.040 1.030 0.640 0.490 0.550 0.580 1.140 1.120 0.540 0.570 0.540 0.520 UBE3A-M01-184-M 1.01 1.13 0.56 0.49 0.51 0.58 1.10 1.16 0.49 0.58 0.58 0.58 UBE3A-D02-355-M 1.030 1.130 0.570 0.590 0.550 0.590 1.060 1.010 0.510 0.540 0.510 0.530 UBE3A-M02-400-M 1.120 0.940 0.510 0.590 0.530 0.510 0.890 0.830 0.620 0.570 0.490 0.490 ATP10A-D01-364-M 1.050 1.060 0.520 0.520 0.540 0.530 1.020 1.000 1.150 0.480 0.560 0.540 ATP10A-D02-382-M 0.92 0.92 0.43 0.44 0.52 0.54 0.94 0.91 0.92 0.47 0.45 0.47 GABRB3-D01-220-M 1.040 0.990 0.600 0.540 0.550 0.510 1.130 1.040 1.070 0.540 0.490 0.530 GABRB3-D02-409-M 0.940 0.930 0.460 0.540 0.530 0.540 0.860 0.920 1.050 0.540 0.560 0.520 OCA2-D01-436-M 1.140 1.030 0.450 0.610 0.520 0.640 1.030 0.930 1.180 0.580 0.540 0.520 OCA2-D02-445-M 0.950 0.890 0.500 0.500 0.520 0.500 0.900 0.860 0.990 0.520 0.480 0.440 APBA2-D01-202-M 0.970 0.930 1.030 0.950 0.920 0.940 1.050 1.090 1.030 1.140 0.960 1.000 BLM-M01-346-M 0.990 0.990 1.000 1.030 0.960 1.030 0.960 1.080 1.030 0.910 1.050 1.020 IGF1R-D01-454-M 1.030 0.970 1.000 1.130 1.000 1.030 0.910 0.970 1.110 1.040 1.050 0.990 Control Chr 17p13 1.04 1.07 0.93 1.06 1.15 1.20 0.97 1.11 0.89 0.94 1.09 1.13 Control Chr 17q21 1.00 0.91 0.84 1.00 0.97 1.01 1.00 1.00 0.86 0.98 0.99 1.00 Control Chr 22q11 0.870 0.960 0.920 0.980 1.060 0.990 0.950 0.980 0.930 0.930 1.020 0.920 Control Chr 22q12 1.050 0.990 1.060 1.010 1.020 1.000 1.010 1.090 1.040 1.000 1.000 0.970 Control Chr 5q31 1.05 1.12 1.18 1.20 1.01 1.20 1.05 1.09 1.22 1.10 1.21 1.12 Control Chr 2p16 0.970 1.000 0.940 0.950 1.000 1.000 1.000 0.980 0.920 0.990 0.990 0.960 Control Chr 3p25 0.980 1.090 1.010 1.160 1.120 1.150 0.870 0.970 1.110 0.930 1.160 1.110 Control Chr 3p22 1.06 1.01 1.11 0.97 0.99 0.96 1.12 1.14 1.04 1.11 0.97 0.98 Control Chr 6q26 0.84 1.00 1.05 0.98 0.96 0.99 1.00 0.92 1.01 1.06 0.94 1.01 Control Chr 10p15 1.030 1.030 0.640 0.990 0.880 0.970 1.040 1.000 0.990 1.060 0.980 0.940 Control Chr 13q12 1.030 0.960 1.150 1.000 0.870 0.950 1.090 0.980 1.000 1.110 0.960 1.020 Control Chr 13q14 a 0.970 1.020 1.060 0.990 1.000 0.960 0.990 0.950 0.990 0.980 0.970 0.970 Control Chr 13q14 b 0.980 1.030 0.960 0.970 1.010 1.040 1.040 1.090 0.930 1.000 1.060 1.060 Control Chr 14q13 1.010 1.170 1.030 1.090 1.130 1.120 1.040 1.100 1.030 1.050 1.100 1.110 Methylation status 0% 0% 0% 0% 0% 0% 100% 100% 100% 100% 100% 100% Syndrome AS AS AS AS AS AS PWS PWS PWS PWS PWS PWS Cause PAT UPD PAT UPD MAT DEL MAT DEL MAT DEL MAT DEL MAT UPD MAT UPD PAT DEL PAT DEL PAT DEL PAT DEL Table 1 . Summary of the deletions detected using MS-MLPA with the P028 probe mix. Relative copy numbers were obtained by comparing the sample peak ratio with the average peak ratio from four control DNA samples. Deletions are highlighted in gray . a b c d