1. Next-Generation Sequencing–Based Detection of Germline Copy Number Variations in BRCA1/BRCA2 
Ane Y. Schmidt, Thomas v.O. Hansen, Lise B. Ahlborn, Lars Jønson, Christina W. Yde, Finn C. Nielsen 
The Journal of Molecular Diagnostics 
Volume 19, Issue 6, Pages (November 2017)
DOI: /j.jmoldx
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
Visualization of BRCA2 germline exon 17 to 20 duplication in JSI SeqPilot SeqNext software. The upper histogram shows the relative coverage of every target region of interest (ROI) of the patient sample in green and the average relative target coverage of control samples in blue. The lower histogram shows the ratio of the relative coverage of target ROIs calculated from patient versus controls. If the ratio exceeds the defined limits indicated by red lines, the bars change from light blue to dark blue, indicating a genomic change. A lower limit (lower red dotted line) of 70% (deletion) and an upper limit (upper red dotted line) of 135% (duplication) was used. Data are expressed as means ± SD of control samples.
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. Supplemental Figure S1
Visualization of BRCA1 germline copy number variations (CNVs) in JSI SeqPilot SeqNext software. Four BRCA1 CNVs [deletion (Del) of exons 1 to 3, 1 to 7, 1 to 14, and 3] detected from Illumina next-generation sequencing (NGS) data are shown in the JSI SeqPilot CNV mode. The upper histogram shows the relative coverage of every target region of interest (ROI) of the patient sample in green and the average relative target coverage of control samples in blue. The lower histogram shows the ratio of the relative coverage of target ROIs calculated from patient versus controls. If the ratio exceeds the defined limits indicated by the red lines, the bars change from light blue to dark blue, indicating a genomic change. We used a lower limit (lower dotted line) of 70% (deletion) and an upper limit (higher dotted line) of 135% (duplication). Data are expressed as means ± SD of control samples.
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. Supplemental Figure S2
Visualization of BRCA1 germline copy number variations (CNVs) in JSI SeqPilot SeqNext software. Four BRCA1 CNVs [deletion (Del) of exons 3 to 16, deletion of exons 5 to 7, duplication (Dup) of exon 13, and deletion of exons 13 to 15] detected from Illumina next-generation sequencing (NGS) data are shown in the JSI SeqPilot CNV mode. The upper histogram shows the relative coverage of every target region of interest (ROI) of the patient sample in green and the average relative target coverage of control samples in blue. The lower histogram shows the ratio of the relative coverage of target ROIs calculated from patient versus controls. If the ratio exceeds the defined limits indicated by red lines, the bars change from light blue to dark blue, indicating a genomic change. We used a lower limit (lower dotted line) of 70% (deletion) and an upper limit (higher dotted line) of 135% (duplication). Data are expressed as means ± SD of control samples.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

5. Supplemental Figure S3
Visualization of BRCA1 germline copy number variations (CNVs) in JSI SeqPilot SeqNext software. Four BRCA1 CNVs [deletion (Del) of exon 17, 17 to 18, 17 to 19, and 18 to 19] detected from Illumina next-generation sequencing (NGS) data are shown in the JSI SeqPilot CNV mode. The upper histogram shows the relative coverage of every target region of interest (ROI) of the patient sample in green and the average relative target coverage of control samples in blue. The lower histogram shows the ratio of the relative coverage of target ROIs calculated from patient versus controls. If the ratio exceeds the defined limits indicated by red lines, the bars change from light blue to dark blue, indicating a genomic change. We used a lower limit (lower dotted line) of 70% (deletion) and an upper limit (higher dotted line) of 135% (duplication). Data are expressed as means ± SD of control samples.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

6. Supplemental Figure S4
Visualization of BRCA1 germline copy number variations (CNVs) in JSI SeqPilot SeqNext software. Three BRCA1 CNVs [deletion (Del) of exon 19, 22, and 23 to 24] detected from Illumina next-generation sequencing (NGS) data are shown in the JSI SeqPilot CNV mode. The upper histogram shows the relative coverage of every target region of interest (ROI) of the patient sample in green and the average relative target coverage of control samples in blue. The lower histogram shows the ratio of the relative coverage of target ROIs calculated from patient versus controls. If the ratio exceeds the defined limits indicated by red lines, the bars change from light blue to dark blue, indicating a genomic change. We used a lower limit (lower dotted line) of 70% (deletion) and an upper limit (higher dotted line) of 135% (duplication). Data are expressed as means ± SD of control samples.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

7. Supplemental Figure S5
Visualization of BRCA2 germline copy number variations (CNVs) in JSI SeqPilot SeqNext software. Two BRCA2 CNVs [deletion (Del) of exons 12 to 16 and 20] detected from Illumina next-generation sequencing (NGS) data are shown in the JSI SeqPilot CNV mode. The upper histogram shows the relative coverage of every target region of interest (ROI) of the patient sample in green and the average relative target coverage of control samples in blue. The lower histogram shows the ratio of the relative coverage of target ROIs calculated from patient versus controls. If the ratio exceeds the defined limits indicated by red lines, the bars change from light blue to dark blue, indicating a genomic change. We used a lower limit (lower dotted line) of 70% (deletion) and an upper limit (higher dotted line) of 135% (duplication). Data are expressed as means ± SD of control samples.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

8. Supplemental Figure S6
Examination of the influence of identical duplications (Dups) in one batch on the copy number variation (CNV) calling. Visualization of a sample with a BRCA1 germline exon 13 duplication using one, two, or three samples containing the BRCA1 exon 13 duplication, respectively, in one batch of six samples. The data show that it is possible to call duplications if two identical duplications are present in a batch of six samples. However, if three identical duplications are present the CNV call does not exceed the upper limit of 135%. The lower dotted line represents 70% (deletion) and the higher dotted line represents 135% (duplication).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

9. Supplemental Figure S7
Examination of the influence of identical deletions (Dels) in one batch on the copy number variation (CNV) calling. Visualization of a sample with a BRCA1 germline exon 3 to 16 deletion using one, two, or three samples containing the BRCA1 exon 3 to 16 deletion, respectively, in one batch of six samples. The data show that it is possible to call deletions even if three identical deletions are present in a batch of six samples. The lower dotted line represents 70% (deletion) and the higher dotted line represents 135% (duplication).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

10. Supplemental Figure S8
Examination of the influence of identical deletions (Dels) in one batch on the copy number variation (CNV) calling. Visualization of a sample without rearrangement and inclusion of one, two, or three samples containing the BRCA1 exon 3 to 16 deletion, respectively, in one batch of six samples. The data show that it is possible to call samples without rearrangement even if two samples with identical deletions are present in a batch of six samples. However, if three identical deletions are present a false-positive duplication CNV call is detected. The lower dotted line represents 70% (deletion) and the higher dotted line represents 135% (duplication).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions