1. Strategy for Robust Detection of Insertions, Deletions, and Point Mutations in CEBPA, a GC-Rich Content Gene, Using 454 Next-Generation Deep-Sequencing Technology 
Vera Grossmann, Susanne Schnittger, Sonja Schindela, Hans-Ulrich Klein, Christiane Eder, Martin Dugas, Wolfgang Kern, Torsten Haferlach, Claudia Haferlach, Alexander Kohlmann 
The Journal of Molecular Diagnostics 
Volume 13, Issue 2, Pages (March 2011)
DOI: /j.jmoldx
Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
Next-generation sequencing of two AML cases. For both patients T13 and T15 mutations observed by next-generation amplicon sequencing are highlighted. A: Location of the mutations of sample T13 (open triangles) and T15 (filled triangles), corresponding to the functional protein domains. The CEBPA protein structure is given according to coding amino acids (lower part). Upper panel visualizes the overlapping amplicon design covering the complete coding sequence of CEBPA. B: Example of the Q83SfsX76 mutation in patient T15. As given on the right y axis for this amplicon, a 263-fold coverage was generated (blue line). The single-base deletion leading to the frameshift was detected in 139 (53%) of reads. C: Example of the A295V variant in patient T15. A substitution (884C>T) was observed in 412 (47%) of reads (left y axis). The overall coverage of 870 reads is highlighted by the blue line.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3. Figure 2
Sequencing coverage of the four CEBPA amplicons using standard GS FLX Titanium Sequencing emPCR conditions. For both patients T13 and T15, the number of obtained sequencing reads using the procedure as recommended by the manufacturer is given on the y axis (referred to as Condition 0). For each amplicon A1 to A4, the bar is colored according to the distribution of forward reads (dark area) and reverse reads (light area).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4. Figure 3
Sequencing coverage of the four CEBPA amplicons using various emPCR conditions. For both patients T13 and T15, four distinct GS FLX Titanium Sequencing emPCR conditions were tested (A–D). The number of obtained sequencing reads is given on the y axis. For each amplicon A1 to A4, the bar is colored according to the distribution of forward reads (dark area) and reverse reads (light area).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

5. Figure 4
Sequencing coverage of the four CEBPA amplicons using the optimized emPCR conditions B. For patients T13 and T15, two distinct variations of condition B (B.1 and B.2) were tested. The number of obtained sequencing reads is given on the y axis. For each amplicon A1 to A4, the bar is colored according to the distribution of forward reads (dark area) and reverse reads (light area).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

6. Figure 5
Independent testing cohort of 23 AML patients using the optimized emPCR condition B.1. The number of obtained sequencing reads is given on the y axis. A: Box-and-whisker plots depict the overall sequencing coverage of the four CEBPA amplicons A1 to A4. B: Box-and-whisker plots depict the overall sequencing coverage of the four CEBPA amplicons represented as forward and reverse reads.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions