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In CNAG, the tumor samples were compared in silico to the 6 best matched control samples (lowest standard deviation) available among a set of non-matched healthy individuals.
Four experiments were performed: (1) the study samples were compared with matched control samples; (2) the study samples were compared with nonmatched control samples; (3) the study samples were compared with themselves; and (4) the matched and nonmatched control samples were compared.
Study Design: Eleven serum and six amniotic fluid samples previously collected and stored at −20°C from gravid women carrying a 47,XY,+21 fetus were each paired with five matched control samples of identical specimen type from gravid women carrying a presumed euploid male fetus.
For ΔT2 calculation, T2 differences were calculated between magnetically labeled and cell-number matched control samples.
We assumed that expression fell down if it was at least 2-fold lower than in matched control samples.
Of the 113 samples, 10 breast cancer samples and 10 matched control samples were used for the discovery phase.
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Sex and age-matched control samples were from normal volunteers.
Sex and age-matched control samples were from normal volunteers (n = 15).
Two independent sets of ethnicity-matched control samples (CG1 [N = 917]), and CG2 [N = 616]) were used for comparison.
The minor allele frequency for 16/47 SNPs was less than 5% in all MDS or race-matched control samples, leaving 31 SNPs that could be analyzed with this sample size (Table S3).
This study was powered to detect changes in minor allele frequencies that occurred in at least 10% of MDS cases, therefore, race-matched control samples were not genotyped for the 12 novel SNPs identified in our 46 MDS samples because they occurred at such low frequencies (1.4 4.7%).
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