Overlay of three mass spectra showing the ΔF508-specific mass signal changes generated in the T-specific cleavage reaction of the reverse strands

<p><b>Copyright information:</b></p><p>Taken from "Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS"</p><p>Nucleic Acids Research 2005;33(4):e38-e38.</p><p>Published online 24 Feb 2005</p><p>PMCID:PMC549577.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> The mass signal pattern is derived from a triplexed reaction encompassing exon 10, 21 and 24 of the CFTR gene. Three different individuals were analyzed, the upper mass spectrum representing a homozygous wild-type for ΔF508, a carrier of the ΔF508 mutation (middle) and an individual homoyzgous mutant ΔF508 (lower mass spectrum). Mass signals specific for the mutation are indicated with a line

Box plot graphic depicting the variability of repeated measurements for each step in the process (Step 1: bisulphite treatment; Step 2: PCR; Step 3: MassCLEAVE; Step 4: MALDI-TOF MS analysis)

<p><b>Copyright information:</b></p><p>Taken from "A new method for accurate assessment of DNA quality after bisulfite treatment"</p><p></p><p>Nucleic Acids Research 2007;35(5):e29-e29.</p><p>Published online 26 Jan 2007</p><p>PMCID:PMC1865059.</p><p>© 2007 The Author(s).</p> Boxes are centered on the median and range from the lower to the upper quartile. Whiskers indicate the interquartile range. Red whiskers indicate the standard deviation from the mean. Bisulfite treatment and PCR can be identified as the greatest source of process variability. The post-PCR processing (MassCLEAVE) and, in particular, the MALDI analysis show high precision in repeated measurements

Correlation between the results obtained from the quality control assays and PCR success from additional genomic targets of varying length

<p><b>Copyright information:</b></p><p>Taken from "A new method for accurate assessment of DNA quality after bisulfite treatment"</p><p></p><p>Nucleic Acids Research 2007;35(5):e29-e29.</p><p>Published online 26 Jan 2007</p><p>PMCID:PMC1865059.</p><p>© 2007 The Author(s).</p> The bar graphs in panel () and () show the results from the quality control assays similar to Figure 5. The QC assay indicates that incubation at 90°C limits amplification to only short amplicons

Gradient PAGE gel with CYBR Gold staining showing the DNA fragmentation of untreated genomic DNA (left) and after bisulfite treatment at varying temperatures (from left to right: 50, 70 and 80°C)

<p><b>Copyright information:</b></p><p>Taken from "A new method for accurate assessment of DNA quality after bisulfite treatment"</p><p></p><p>Nucleic Acids Research 2007;35(5):e29-e29.</p><p>Published online 26 Jan 2007</p><p>PMCID:PMC1865059.</p><p>© 2007 The Author(s).</p> The figure indicates that an increase of the incubation temperature during bisulfite treatment results in increased DNA fragmentation

Panel () shows the probability distributions for observed methylation ratios based on the binomial distribution and different amounts of starting molecules

<p><b>Copyright information:</b></p><p>Taken from "A new method for accurate assessment of DNA quality after bisulfite treatment"</p><p></p><p>Nucleic Acids Research 2007;35(5):e29-e29.</p><p>Published online 26 Jan 2007</p><p>PMCID:PMC1865059.</p><p>© 2007 The Author(s).</p> Shown are examples for 10, 25, 50 75 and 90% methylated molecules in the starting template. With a sample size of 3000 molecules, 95% of all randomly sampled probes will contain between 48 and 52% methylated DNA when the DNA sample contains 50% methylated DNA (red colored distribution). However, when the DNA sample contains only 300 molecules, this range is expanded from 43 to 57% (blue colored distribution). Panel () shows the 95% confidence intervals for sampling-means as a function of the number of the sampled molecules. Shown are results for 10 (blue), 25 (red) and 50% (black) methylated molecules in the starting template

Summary of analysis results for each of the studies performed. Sens = sensitivity.

<p>Spec = specificity; NA = Not applicable.</p

Summary of sample types utilized for each of the studies performed.

<p>Summary of sample types utilized for each of the studies performed.</p

Paired comparison of z-scores.

<p>Z-scores were calculated for paired samples with previously described GC normalized, repeat masked z-scores on the x-axis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057381#pone.0057381-Palomaki1" target="_blank">[7]</a> and z-scores from the same libraries sequenced in 12-plex on the y-axis. Samples classified by karyotype analysis as trisomies for A) Chromosome 21, B) Chromosome 13, or C) Chromosome 18 are shown in blue; unaffected samples for each aneuploidy condition are shown in gray. Red horizontal and vertical lines in each plot represent the respective classification cutoff for that chromosome (z = 3 for chromosome 21, z = 3.95 for chromosomes 13 and 18).</p

Paired comparison of z-scores.

<p>Z-scores were calculated for 1269 paired samples with previously described GC normalized, repeat masked z-scores on the x-axis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057381#pone.0057381-Palomaki1" target="_blank">[7]</a> and z-scores from the high-throughput assay on the y-axis. Samples classified by karyotype analysis as trisomies for A) Chromsome 21, B) Chromosome 13, or C) Chromosome 18 are shown in blue; unaffected samples for each aneuploidy condition are shown in gray. Red horizontal and vertical lines in each plot represent the respective classification cutoff for that chromosome (z = 3 for chromosome 21, z = 3.95 for chromosomes 13 and 18). Black line in plot represents y = x.</p