Supplementary Material

Transcription

1 The Open Biology Journal, 2009, Volume 2 i Table 1. Sequences of qpcr Primers and Probes Position SNP/Gene Forward primer [5' to 3'] Reverse Primer [5' to 3'] TaqMan probe [FAM5' to 3'BHQ] Left SNP_A GCTCATGTCTAGAGCTCCAGCAT AACCCTGAGTTTCCCTCTGATTC ATGACGCGCCAAGCTTCAAGACCA CNV 19 Middle SNP_A GCCACTGCATCAATAAAACTTCTTC CCTACAATGGTTGCAAACAGAATAAAT CTCACATGACCTGCATTTCACTGGTTTCC Right SNP_A CATCCTAGAAGGTGGTCCTGAAA AGACTCAGCTCAGAGCACAGCAT CCAAAGCACCCTGTTACCTCCTCTATGACA Left SNP_A GGATGAAAGGGAAAGGCATTTT TCTCAGACCAGATTGATGAAATGTG CCCAAAGCCTTGACGCTGCCCT CNV 57 Middle SNP_A ACAAAGCATCTAGAGTGCCAACAC CACCGTCCACTTACACAAATGAA CAGCCTCACCTACATTTTATCCCTTGGCA Right SNP_A AAATCAAAGCCAGCTGCCTTAT CTCACCATCCCAGCTCAAGAA CCTCAGGCAGGCCACCCTTCTCAC Left SNP_A TCTTAGCGTTCTCAGATATTTTGCA GACCAGTCATGGGACTTCTCACA TGAGTCCTGTCTCCAGTCCATCTCAATGTG CNV 77 CNV 114 CNV 119 CNV Others CNV 1 Others CNV 2 Middle SNP_A TTCCAAAAATAGACACGGAAGGA AAAAGCAGTTGAGGTAATGAATACTGTAGT CCTTCCAAGCCCCAATAGTGGGCA Right SNP_A TCAGCCTCAAATTATGATACAGTACGT TGTCCAAGTGAGAGGTCCTTCTCT TACTACAGCAGAGCTGAACACAGCATGCC Left SNP_A CTGGGAAACCTCTTGATAGTGGTAA GCTCAGGCATAGGTCAATGAAAG CCCATGCTCACCTGCTCCAATCTCCTAT Middle Gene_OR4M1_exon CCCTCATCTGACTTCTCCTATGTATTT GGGCTGTAATGGAAGAGTACCAAA CTGTTGGCTAATCTGGCCCTCCTTGA Right SNP_A GAGCCATGATCACATAGTTGCACTA TCTATCTAAGGATGTCTACCTGGTCACT AGCCTGAGTGACAGCGCAAGACCC Left SNP_A TGTTCTCCATTCACAGAAGCATTT GGTGATATTTTAGGAAGAGCTGTGTCA TGTGCAGTAAACAGCAAAAGCCAACAAGC Middle Gene_BC066981_exon CAGCCACCATCTGCTTTTAACAG AGGGTTTCCTGCTAGTTGGTGAA AGCGAACAGATCGCGTCTACCAACCAG Right SNP_A ATGCTTTGCAGAAGTGAGCTCAT TCTCAGGACACCATTTTTCAAGTG TAGAAGAGGCCTGCCCACCAAGAAGTCA Left SNP_A ATCAGGGTTAGCTGCAAAAGGTA GATAAGAGGTAGGTCTCTGTCAAGTAGTTG CTCTATGCCCAGCAAAAGATACGTGCTCA Middle SNP_A TCACAGACCTTGCTTCCTCTTTC GCTGGACGATTTGGTTCCTTAGT CATCCACCAGCCAGGAAGAGAGCCTT Right SNP_A AGACCCAACTCCTTCTTCAGTCA TGGGACTCCTCATTGAAAGATGT TGTGCTGCCCCCACAGCTAGTTTG Left SNP_A CCATCAGCTAATGCTCTCATTCTG GAGTGTGACTCTGCAGCCTTTAAAG TTCATACCCACCCAGCTTCTCCACTGAA Middle SNP_A CCACATAGATTCAGGTGCTTTCAC GGGCCAATTTGCAGCTATAAGTA TTCCTCAAACTGCAGGGCCCATG Right SNP_A CCCTTGTCTTCTCGGTTCTTAGAT AGGGTCCAAGGTTATGGCATTAA CTTCCTCAAATCCAACCTCATTCATCCATG Middle SNP_A SNP_A CCTTACTCACTAGCAACCCCTCTT AGATTCCTGCTTCTTTGAGTTCAGA CCACCCAAGCCACTCAGCTGTCC GAPDH GCACCGTCAAGGCTGAGAA CAAAGCACATTTCTTCCATTCTGT AAATCCCATCACCATCTTCCAGGAGTGA

2 ii The Open Biology Journal, 2009, Volume 2 Table 2. Unique CNVs identified in this study. Highlighted entries indicate where overlapping CNVs from different subjects were broken up into non-overlapping ones. The Status column indicates whether the CNV reflects copy number gain (Gain), copy number loss (Loss), or Gain in some individuals and Loss in others (Both). The column indicates the source of other CNVs that our CNV is concordant with: 1. Sebat et al [5]; 2. Iafrate et al [6]; 3. McCarroll et al [7]; 4. Redon et al [9] SNPs 1 1p NA Loss 2 1p NA Loss 3 1p NA Gain 4 4 1p NA Gain 5 1p NA Gain 6 1p NA Loss 1,4 7 1p NA Gain 8 1q NA Loss 3 9 1q NA Gain 10 1q NA Loss q NA Gain 12 2p NA Gain p NA Gain 14 2p NA Loss 15 2q12.2-2q NA Gain 16 2q NA Loss 17 2q NA Loss 18 2q NA Loss 19 2q14.3-2q NA17200, NA Loss 1,4 20 2q21.1-q NA Loss q21.3-2q NA Loss 22 2q NA Loss 23 2q24.3-2q NA Loss 24 2q NA Gain 25 3p22.2-3p NA Gain

3 The Open Biology Journal, 2009, Volume 2 iii SNPs 26 3q NA Loss 27 3q NA Gain 28 3q NA Loss q NA Loss 30 3q q NA Loss 31 3q NA Gain 32 4p NA Loss 33 4q NA Loss 34 4q NA17107, NA17156, NA Loss 35 4q NA Loss 36 4q NA Loss 37 4q NA Loss 38 4q NA Loss 39 4q NA Gain 40 5q NA Loss 41 5q NA Gain q NA Loss 43 5q NA Loss 44 5q NA Loss 45 6p NA Loss 46 6p24.1-6p NA Loss 47 6q NA Gain 48 6q NA Loss 49 6q NA Loss 50 6q NA Loss 51 7p NA Loss 52 7p NA Gain

4 iv The Open Biology Journal, 2009, Volume 2 SNPs 53 7p NA Gain 54 7p NA Loss 55 7q q NA Gain 56 7q NA17115, NA Both q NA Gain 58 7q NA Loss 59 7q NA Loss q NA Gain p NA Gain 1,4 62 8p NA17059, NA Both 63 8p NA Gain 1,4 64 8p NA17059, NA Both 65 8p NA Gain 66 8p23.2-8p NA Loss p NA17160, NA Both 68 8p NA Loss 69 8p NA17013, NA Loss p NA Gain 71 8p NA Loss 72 8q NA Loss 73 8q NA17106, NA Gain 74 8q NA Loss 75 8q NA17011, NA Loss

5 The Open Biology Journal, 2009, Volume 2 v SNPs 76 8q NA Loss 77 8q NA17253, NA17251, NA17208, NA17125, NA Loss 78 9p NA Loss 79 9p NA17112, NA Loss p NA Loss 81 9p NA Loss 82 9p NA Loss 83 9p NA Gain 84 9p NA Loss 85 9q NA Loss 86 9q q NA Loss q NA Gain 88 10q NA Loss 89 10q NA Loss 90 10q NA Loss 91 10q NA Gain 92 10q NA Gain 93 10q NA Gain 94 10q NA17216, NA17208, NA17134, NA17125, NA Gain 95 11p NA Loss 96 11p NA Loss 97 11p NA Gain

6 vi The Open Biology Journal, 2009, Volume 2 SNPs 98 11q q NA Loss 99 11q NA Gain q NA Loss q23.2-q NA Gain q NA17206, NA Both q23.3-q NA Gain p NA Gain q NA Loss q NA Loss q NA Loss q NA Loss q NA Gain q NA Loss q NA Loss q NA Loss q NA Loss q NA17278, NA Gain 1, q NA Loss q NA Gain q NA Gain q NA Loss q NA17104, NA Gain q NA Loss q q NA Gain q NA Loss p NA Gain p NA Loss

7 The Open Biology Journal, 2009, Volume 2 vii SNPs q NA Loss q NA17011, NA Both q NA Loss q NA Gain q NA Loss q NA Loss q NA Loss q NA Gain q NA Loss q NA Gain q NA Gain q NA Gain q NA Loss q q NA17207, NA17156, NA17160 NA17207, NA17156, NA17160, NA Loss Loss 1, q NA Loss 141 Xp NA X Gain Xp NA X Gain 143 Xq NA X Loss 4

8 viii The Open Biology Journal, 2009, Volume 2 Table 3. Significantly enriched GO categories among genes that are encompassed by CNVs. There are a total of 8775 genes that are represented on the 50K Xba SNP array of which 364 are encompassed by the CNVs identified in this study. The enrichment score indicates the ratio between the actual number of interesting genes and the expected number of interesting genes from each GO category, with the P-value calculated based on a hypergeometric distribution Gene category # of ref. genes in category # of genes Expected # of genes Enrichment P-value olfactory receptor activity E-19 sensory perception of smell E-18 sensory perception of chemical stimulus E-18 rhodopsin-like receptor activity E-14 G-protein coupled receptor activity E-12 G-protein coupled receptor protein signaling pathway E-11 sensory perception E-11 transmembrane receptor activity E-10 neurophysiological process E-10 receptor activity E-07 physiological response to stimulus E-07 chemoattractant activity E-07 organismal physiological process E-06 cell surface receptor linked signal transduction E-06 chemokine activity E-06 response to stimulus E-06 intrinsic to membrane E-06 chemokine receptor binding E-06 integral to membrane E-06 glutathione transferase activity E-06 signal transducer activity E-05 G-protein-coupled receptor binding E-05 membrane part E-05 membrane E-05 chylomicron E-05 T cell receptor complex E-05 transferase activity\, transferring alkyl or aryl [other than methyl] groups E-05

9 The Open Biology Journal, 2009, Volume 2 ix Gene category # of ref. genes in category # of genes Expected # of genes Enrichment P-value lipoprotein metabolism E-04 immunological synapse E-04 NAD[P]+-protein-arginine ADP-ribosyltransferase activity E-04 glycoprotein metabolism E-03 protein amino acid glycosylation E-03 biopolymer glycosylation E-03 glycoprotein biosynthesis E-03 T cell receptor binding E-03 Golgi to plasma membrane transport E-03 sterol transport E-03 cholesterol transport E-03 lipid transport E-03 taxis E-03 chemotaxis E-03 T cell activation E-03 external side of plasma membrane E-03 locomotory behavior E-03 protein amino acid N-linked glycosylation E-03 voltage-gated sodium channel activity E-03 cell recognition E-03 lymphocyte activation E-03 protein biosynthesis E-03 transferase activity\, transferring glycosyl groups E-03