1. Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients 
Mary Alikian, Peter Ellery, Martin Forbes, Gareth Gerrard, Dalia Kasperaviciute, Alona Sosinsky, Michael Mueller, Alexandra S. Whale, Dragana Milojkovic, Jane Apperley, Jim F. Huggett, Letizia Foroni, Alistair G. Reid 
The Journal of Molecular Diagnostics 
Volume 18, Issue 2, Pages (March 2016)
DOI: /j.jmoldx
Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
Pictorial representation of breakpoint mapping read types obtained by next-generation sequencing of ABL1 and BCR sequences in a patient with chronic myeloid leukemia. A: An example of split reads. These single reads are composed of material from two noncontiguous regions on the reference genome that map directly across the fusion junction and are thus capable of identifying breakpoints to base pair resolution. Based on the sequence information obtained from these reads, sequencing primers (gray arrows) are designed for confirmation by Sanger sequencing. B: An example of discordant pairs of reads in which individual reads in a pair map to different genes. Clusters of discordant read pairs allow indirect estimation of the position of the fusion site to within up to 1 Kbp. C: The effect of an inversion at the fusion site on read orientation. BCR and ABL1 components of the split read run in opposite genomic directions.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3. Figure 2
Comparison of the sensitivity of four methods of disease quantification in 46 samples from six chronic myeloid leukemia (CML) patients. Quantification results are shown for the follow-up samples of six patients with CML according to substrate type and platform used. The four techniques are listed. Samples are represented by circles on a linear timeline (not to scale), with the earliest sample on the far left. The vertical dotted lines represent the point of achievement of molecular remission (MR)4 or lower [based on quantitative RT-PCR (RT-qPCR) analysis of the proceeding sample]. Digital PCR (dPCR) and RT-dPCR values are after preamplification. LoD, limit of detection; LoQ, limit of quantification.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4. Figure 3
Comparison of the DNA-based digital PCR (dPCR) and digital RT-PCR (RT-dPCR) readings in 46 samples from six chronic myeloid leukemia patients. DNA dPCR results are shown with blue bars and RT-dPCR results with green bars. The vertical red dashed lines represent the point of achievement of molecular remission (MR)4 or lower [based on quantitative RT-PCR (RT-qPCR) analysis of the proceeding sample]. Precise readings are provided in Table 4 and Supplemental Tables S7 and S8. Plotted dPCR and RT-dPCR values are after preamplification. The bar charts depict five scenarios: i) DNA is detected while RNA is not; ii) RNA is detected while DNA is not; iii) both DNA and RNA are detected, but DNA quantity is higher than that of RNA; iv) both DNA and RNA are detected with higher RNA quantity compared to DNA; and v) neither DNA nor RNA is detected.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions