Supplementary Table Bed Track 2p23.5 Supplementary Table
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Supplementary Table Bed Track 2p23.5 browser position chr2:1,278,152-2,285,559 track name=dups_COS_cases description=COS_case_duplications visibility=4 color="0,0,250" itemRgb="on" db=hg18 chr2 1618945 1835426 COS-NSB1358 chr2 1713636 1857129 COS-NSB534 track name=dups_GROUP_cases description=GROUP_case_duplications visibility=4 color="0,0,250" itemRgb="on" db=hg18 chr2 859616 1826716 GROUP-Pt1 chr2 1400000 4500000 GROUP-Pt5 track name=dups_Cardiff_cases description=Cardiff_case_duplications visibility=4 color="0,0,250" itemRgb="on" db=hg18 chr2 1785886 2269413 WTCCC01-20577D2 track name=dups_ISC_cases description=ISC_case_duplications visibility=4 color="0,0,250" itemRgb="on" db=hg18 chr2 1712998 1815909 ISC-SZ1-3083 chr2 1712998 1922382 ISC-SZ2-3176 chr2 1716437 1826717 ISC-SZ3-2121 track name=dups_Japan_cases description=Japanese_case_duplications visibility=4 color="0,0,250" itemRgb="on" db=hg18 chr2 987335 1842013 1079-p829.CEL track name=dups_ISC_controls description=ISC_control_duplications visibility=4 color="0,0,128" itemRgb="on" db=hg18 chr2 1589517 1827407 ISC-CT1-4962 Supplementary Table Quantitative RT-PCR Results Sample Name COS534 CTRL680 CTRL1816 COS1358 CTRL1357 CTRL1360 CTRL1359 Detector Name MYT1L_21-22 MYT1L_21-22 MYT1L_21-22 MYT1L_21-22 MYT1L_21-22 MYT1L_21-22 MYT1L_21-22 avg ctrl Ct avg expt Ct 20.56 20.44 21.07 20.54 20.98 20.92 20.54 delta Ct 6.56 16.23 14.72 15.98 15.79 15.79 15.87 Sex female female female male male female male Race AA AA AA W W W W Pedigree expt-proband ctrl-mother ctrl-unrelated expt-proband ctrl-father ctrl-mother ctrl-brother CNV by microarray present absent absent present absent present absent COS534 CTRL680 CTRL1816 COS1358 CTRL1357 CTRL1360 CTRL1359 MYT1L_22-23 MYT1L_22-23 MYT1L_22-23 MYT1L_22-23 MYT1L_22-23 MYT1L_22-23 MYT1L_22-23 20.63 20.55 21.18 20.07 20.59 20.97 19.95 No Amplification No Amplification No Amplification No Amplification No Amplification No Amplification No Amplification NA NA NA NA NA NA NA female female female male male female male AA AA AA W W W W expt-proband ctrl-mother ctrl-unrelated expt-proband ctrl-father ctrl-mother ctrl-brother present absent absent present absent present absent COS534 CTRL680 CTRL1816 COS1358 CTRL1357 CTRL1360 CTRL1359 MYT1L_22-24 MYT1L_22-24 MYT1L_22-24 MYT1L_22-24 MYT1L_22-24 MYT1L_22-24 MYT1L_22-24 20.58 20.49 21.09 20.01 20.51 20.92 19.97 No Amplification No Amplification No Amplification No Amplification No Amplification No Amplification No Amplification NA NA NA NA NA NA NA female female female male male female male AA AA AA W W W W expt-proband ctrl-mother ctrl-unrelated expt-proband ctrl-father ctrl-mother ctrl-brother present absent absent present absent present absent COS534 CTRL680 CTRL1816 COS1358 CTRL1357 CTRL1360 CTRL1359 PXDN_1 PXDN_1 PXDN_1 PXDN_1 PXDN_1 PXDN_1 PXDN_1 20.58 20.54 21.09 20.03 20.52 20.92 20.08 No Amplification No Amplification No Amplification No Amplification No Amplification No Amplification No Amplification NA NA NA NA NA NA NA female female female male male female male AA AA AA W W W W expt-proband ctrl-mother ctrl-unrelated expt-proband ctrl-father ctrl-mother ctrl-brother present absent absent present absent present absent 27.12 36.67 35.79 36.52 36.77 36.72 36.40 Quantitative RT-PCR Description Briefly, total RNA was purified from cultured lymphoblastoid cell lines using the RNeasy Mini kit (Qiagen, Germantown, MD). cDNA was reverse transcribed with the High Capacity RNA-tocDNA kit (ABI, Foster City, CA) to generate >4ug of cDNA for each individual sample. 200ng of cDNA were input for each duplexed 20uL reaction performed in quadruplicate for optimized QPCR gene expression analysis. Each individual was assayed in duplex with GAPDH as an endogenous control (NM_002046; Hs.PT.45.1164609) and an inventoried PrimeTime qPCR assay from IDT as the target exon. The catalog numbers are listed(IDT DNA, Iowa City, IA): PXDN exon 1/3 (NM_012293; Hs.PT.45.1199300), MYT1L exon 21/22 (NM_015025; Hs.PT.45.1254527), MYT1L exon 22/24 (NM_015025; Hs.PT.45.5033403), and MYT1L exon 23/24 (NM_015025; Hs.PT.45.3839659). Singleplex assays for the endogenous control GAPDH and each target exon was performed to ensure the absence of competition for amplification efficiency. Simplex results concurred with duplex results for amplification detection. Taqman Gene Expression Master Mix (ABI, Foster City, CA) was utilized and reactions were optimized for each amplicon on the StepOne Real Time system for 40 cycles using the full cycling protocol. Samples were compared with unaffected family members (where available) or an sex/age/ethnicity matched control with and without the CNV in question was used. Relative quantitation for the absence and presence for each transcript junction was calculated for each sample. The following conditions and variables were applied: delta C(t) = (quadruplicate C(t) value of target exon - quadruplicate C(t) value of endogenous control GAPDH), delta C(t) average = value of the average delta C(t) of the matched control DNA. Samples were performed in quadruplicate with a technical replicate standard deviation threshold <= 0.16. Acceptable cycles for the detected presence of an exon junction were between 20-27.
