1. Evaluation of Second-Generation Sequencing of 19 Dilated Cardiomyopathy Genes for Clinical Applications 
Sivakumar Gowrisankar, Jordan P. Lerner-Ellis, Stephanie Cox, Emily T. White, Megan Manion, Kevin LeVan, Jonathan Liu, Lisa M. Farwell, Oleg Iartchouk, Heidi L. Rehm, Birgit H. Funke 
The Journal of Molecular Diagnostics 
Volume 12, Issue 6, Pages (November 2010)
DOI: /jmoldx
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

2. Figure 1
Flow chart of experimental design and analytical pipeline. Pooled, positive controls were amplified by PCR as described in Materials and Methods. The number of mutations is indicated for each positive control sample. Each positive control sample was sequenced on one lane of one flow cell on the Illumina GAII instrument. The Illumina GAII pipeline uses three software packages for image analysis (Firecrest), base calling (Bustard), and analysis (Gerald). Variant detection was carried out using the NextGENe software package (SoftGenetics, LLC). The number of false positives (FP), false negatives (FN), and true positives (TP) identified by NextGENe are indicated for the given parameters and thresholds described in Materials and Methods.
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

3. Figure 2
Illumina GAII sequence data. A: Average condensed coverage for each amplicon within the region of interest (ROI) for each sample. Amplicons are arranged by concatenation of the ROI in alphabetical order of gene names and by sequential order of exons (see Supplemental Table 2 at B: Distribution of the fraction of bases within the ROI with a given condensed coverage in intervals of 10 (see Supplemental Table 3 at C: Graphical representation of the distribution of condensed coverage within and surrounding the ROI. Dotted lines demarcate the boundaries of the ROI. The read depths of all bases within a given bin is averaged over all amplicons and plotted as a point in the graph. To do this, we divided each amplicon's region of interest into 10 bins and calculated the average read depth within each bin by taking the mean of the coverage of all of the bases. The flanking regions are obtained from a 200-bp window divided into four bins.
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

4. Figure 3
Comparative analysis of array-based resequencing and Illumina GAII sequencing workflows with regard to cost and turnaround time. Laboratory workflows for the DCM array (left) and DCM SGS test (right) are shown. Steps that lead to increased test cost or turnaround time are highlighted in gray. The estimated relative impact of transitioning the DCM test from the array-based technology to SGS-based technology is shown on the right by arrows as well as the level of expected increase.
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions