Journal: Journal of Assisted Reproduction and Genetics

Article Title: A randomized and blinded comparison of qPCR and NGS-based detection of aneuploidy in a cell line mixture model of blastocyst biopsy mosaicism

doi: 10.1007/s10815-016-0784-3

Figure Lengend Snippet: a Sensitivity across three sets of analyses for each mixture level: qPCR default settings, VeriSeq default settings, and VeriSeq with criteria defined by Vera-Rodriguez, et al. (custom VeriSeq). Sensitivity is based on detecting trisomy of 13, 15, and 18, and monosomy of X ( n = 24 at each mixture level for each platform). Asterisks indicate statistically significant differences. b Specificity across all samples for the same three analysis methods based on the frequency of detecting a normal copy number for each of the remaining chromosomes known to be uniformly normal. Asterisks indicate statistically significant differences. c Example plots of samples which were given false-positive predictions of mosaic aneuploidy using previously published custom settings for VeriSeq PGS data analysis. FP false positive, TP true positive, FN false negative

Article Snippet: Blinded computational prediction of aneuploidy was made with either (i) previously established criteria for qPCR [ ], termed “default qPCR,” (ii) as recommended by the supplier utilizing the automatic aneuploidy calls made by Bluefuse Multi software (BlueFuse, Illumina Inc., version 4.2(20289)), termed “default VeriSeq,” or (iii) using previously defined [ ] customized criteria for VeriSeq PGS (which examine changes in the median copy numbers and override automated calls made by Bluefuse Multi software), termed “custom VeriSeq”.

Techniques:

Journal: Journal of Assisted Reproduction and Genetics

Article Title: A randomized and blinded comparison of qPCR and NGS-based detection of aneuploidy in a cell line mixture model of blastocyst biopsy mosaicism

doi: 10.1007/s10815-016-0784-3

Figure Lengend Snippet: Example plots from qPCR CCS and VeriSeq PGS analyses of the trisomy 18 male and euploid female ( a and c ), and trisomy 13 and trisomy 15 ( b and d ) six-cell mixture sets. Vertical boxes outline chromosomes of interest in each set. As the level of aneuploidy increases in the sample, there is a concomitant change in the copy number values of the chromosomes of interest

Article Snippet: Blinded computational prediction of aneuploidy was made with either (i) previously established criteria for qPCR [ ], termed “default qPCR,” (ii) as recommended by the supplier utilizing the automatic aneuploidy calls made by Bluefuse Multi software (BlueFuse, Illumina Inc., version 4.2(20289)), termed “default VeriSeq,” or (iii) using previously defined [ ] customized criteria for VeriSeq PGS (which examine changes in the median copy numbers and override automated calls made by Bluefuse Multi software), termed “custom VeriSeq”.

Techniques:

Journal: Journal of Assisted Reproduction and Genetics

Article Title: A randomized and blinded comparison of qPCR and NGS-based detection of aneuploidy in a cell line mixture model of blastocyst biopsy mosaicism

doi: 10.1007/s10815-016-0784-3

Figure Lengend Snippet: Box and whisker plots showing the distribution and variance of copy number assignments for target mosaic chromosomes as the percent of spike-in aneuploidy increases in the sample with each respective platform (qPCR and VeriSeq NGS). As the level of aneuploidy increases in the sample, there in an overall increase in the copy number of the chromosomes of interest (13, 15, and 18) and a decrease in the copy number of X as the percentage of female cells decreases in the sample

Article Snippet: Blinded computational prediction of aneuploidy was made with either (i) previously established criteria for qPCR [ ], termed “default qPCR,” (ii) as recommended by the supplier utilizing the automatic aneuploidy calls made by Bluefuse Multi software (BlueFuse, Illumina Inc., version 4.2(20289)), termed “default VeriSeq,” or (iii) using previously defined [ ] customized criteria for VeriSeq PGS (which examine changes in the median copy numbers and override automated calls made by Bluefuse Multi software), termed “custom VeriSeq”.

Techniques: Whisker Assay