1. Utilization of Whole-Exome Next-Generation Sequencing Variant Read Frequency for Detection of Lesion-Specific, Somatic Loss of Heterozygosity in a Neurofibromatosis Type 1 Cohort with Tibial Pseudarthrosis 
Rebecca L. Margraf, Chad VanSant-Webb, David Sant, John Carey, Heather Hanson, Jacques D'Astous, Dave Viskochil, David A. Stevenson, Rong Mao 
The Journal of Molecular Diagnostics 
Volume 19, Issue 3, Pages (May 2017)
DOI: /j.jmoldx
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
A–C: Allelic imbalance analysis generated from the exome next-generation sequencing (NGS) data are plotted for individual 1; % variant read frequency versus chromosome 17 positions. The blood (germline) sample data are the red dots, the pseudarthrosis (somatic) sample data are the blue dots. Arrows indicate the LOH area (B and C). A: Blood only. B: Pseudarthrosis sample overlay on the blood sample. C: Pseudarthrosis data only. D and E: Microarray data for individual 1 pseudarthrosis sample, blue dots. D: Allele peaks data. E: Copy number log2 ratio data. Arrow indicates the deletion area, which includes the NF1 gene. F: NGS read depth data analysis using Contra (black circles).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3. Figure 2
A–C: Allelic imbalance data generated from the exome next-generation sequencing data are plotted for individual 4; % variant read frequency versus chromosome 17 positions. The blood (germline) sample data are the red dots, the pseudarthrosis (somatic) sample data are the blue dots. Arrows indicate the LOH area (B and C). A: Blood only. B: Pseudarthrosis sample overlay on the blood data. C: Pseudarthrosis data only. D and E: Microarray data for individual 4, the allele peaks data. Arrow indicates the start of the LOH area, which includes NF1 (E). D: Blood sample. E: Pseudarthrosis sample.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4. Figure 3
A: Microarray copy number data for individual 4, log2 ratio plot. Arrow indicates location of NF1. B: Next-generation sequencing read depth data analysis using Contra.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions