PMC:2948432 / 12937-14220 JSONTXT

{"project":"2_test","denotations":[{"id":"20140953-15714058-43951738","span":{"begin":1064,"end":1068},"obj":"15714058"},{"id":"20140953-18370098-43951739","span":{"begin":1077,"end":1081},"obj":"18370098"},{"id":"20140953-19697059-43951740","span":{"begin":1098,"end":1102},"obj":"19697059"}],"text":"MLPA Data Analysis\nGene dosage analysis was automated using the MLPA analysis program included with GeneMarker software version 1.6 (Softgenetics, Pennsylvania, USA) according to the manufacturer's instructions. Data were normalized using the “population normalization” mode (as recommended by the MLPA kit manufacturers for analysis of tumor DNA). Peak heights were normalized according to the median height of all test and control peak heights of similar fragment size. Normalized peak heights were then compared to a synthetic control sample (average of peak heights from four human genomic DNA samples with normal gene dosage at 9p) with default analysis parameters to determine gene dosage ratios where the median point within the data set is considered to be 1, and a gene dosage ratio for each probe region was calculated with reference to the synthetic control (Fig. 1B). In previous publications using MLPA on FFPE-derived DNA, gene dosage cut-offs of 0.7 for loss and 1.3 for gain have been used according to manufacturer's instructions (van Dijk et al.,2005; Takata,2008; Buffart et al.,2009) (and author correspondence with MRC-Holland). In our analysis, gene dosage was treated as a continuous variable to account for the effect of any possible contaminating normal DNA."}

{"project":"0_colil","denotations":[{"id":"20140953-15714058-957390","span":{"begin":1064,"end":1068},"obj":"15714058"},{"id":"20140953-18370098-957391","span":{"begin":1077,"end":1081},"obj":"18370098"},{"id":"20140953-19697059-957392","span":{"begin":1098,"end":1102},"obj":"19697059"}],"text":"MLPA Data Analysis\nGene dosage analysis was automated using the MLPA analysis program included with GeneMarker software version 1.6 (Softgenetics, Pennsylvania, USA) according to the manufacturer's instructions. Data were normalized using the “population normalization” mode (as recommended by the MLPA kit manufacturers for analysis of tumor DNA). Peak heights were normalized according to the median height of all test and control peak heights of similar fragment size. Normalized peak heights were then compared to a synthetic control sample (average of peak heights from four human genomic DNA samples with normal gene dosage at 9p) with default analysis parameters to determine gene dosage ratios where the median point within the data set is considered to be 1, and a gene dosage ratio for each probe region was calculated with reference to the synthetic control (Fig. 1B). In previous publications using MLPA on FFPE-derived DNA, gene dosage cut-offs of 0.7 for loss and 1.3 for gain have been used according to manufacturer's instructions (van Dijk et al.,2005; Takata,2008; Buffart et al.,2009) (and author correspondence with MRC-Holland). In our analysis, gene dosage was treated as a continuous variable to account for the effect of any possible contaminating normal DNA."}