1. SNPitty The Journal of Molecular Diagnostics
Job van Riet, Niels M.G. Krol, Peggy N. Atmodimedjo, Erwin Brosens, Wilfred. F.J. van IJcken, Maurice P.H.M. Jansen, John W.M. Martens, Leendert H. Looijenga, Guido Jenster, Hendrikus J. Dubbink, Winand N.M. Dinjens, Harmen J.G. van de Werken 
The Journal of Molecular Diagnostics 
Volume 20, Issue 2, Pages (March 2018)
DOI: /j.jmoldx
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
Overview of the web interface of SNPitty. BAF visualization is shown using artificial data for three samples with a selection for human chromosomes 1, 2, and 19. Chromosomes or regions are indicated with alternating gray and white backgrounds; regional names are displayed on top. Black dashed lines show the homozygous BAF ranges (0,1), whereas the red dash-dot lines reflect the putative borders of balanced heterozygosity or homozygosity BAF values 0.05, 0.45, 0.55, 0.95, respectively.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3. Figure 2
Validation of SNPitty by serial dilution of glioma tumor tissue with matched normal. Glioma tumor tissue was serially diluted with an increasing amount of near-adjacent normal tissue, 0% (purple circles), 10% (blue circles), 20% (red rhombi), 40% (green squares), 60% (blue triangles), to 100% (orange triangles), respectively. The dilution series show an increasing BAF deviation for heterozygous markers on 1p and 19q, with respect to a higher tumor cell percentage. Black dashed lines show the homozygous BAF ranges (0,1), whereas the red dash-dot lines reflect the putative borders of balanced heterozygosity or homozygosity BAF values 0.05, 0.45, 0.55, 0.95, respectively. Markers that retained homozygous state in all six samples are filtered. ∗IDH1 c.395G>A (p.R132H) somatic mutation.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4. Figure 3
Detection of EGFR amplification and heterozygous PTEN deletion in glioblastoma using SNPitty. A: BAF visualization of heterozygous markers (blue circles), accompanied with respective read coverage (blue bars) and log2 copy number ratio (dashed blue line with blue squares), on the EGFR and PTEN regions for a single glioblastoma sample. Black dashed lines show the homozygous BAF ranges (0,1), whereas the red dash-dot lines reflect the putative borders of balanced heterozygosity or homozygosity BAF values 0.05, 0.45, 0.55, 0.95, respectively. B: EGFR gene amplification by fluorescence in situ hybridization (FISH) in respective sample. FISH analysis was performed using EGFR, Her-1 (7p11) probe (red), and SE 7 control probe (green). Original magnification, ×63 (B).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

5. Figure 4
Detection of homozygous deletions using SNPitty. BAF visualization of heterozygous markers (blue circles), accompanied with respective read coverage (blue bars), on the chromosome arm 9p and CDKN2A region for a single glioblastoma sample. LOH on 9p is accompanied by a homozygous deletion of CDKN2A. The remaining heterozygous state of CDKN2A is a reflection of the nonmalignant tissue present in the sample. Read coverage is shown in transparent blue bars. Black dashed lines show the homozygous BAF ranges (0,1), whereas the red dash-dot lines reflect the putative borders of balanced heterozygosity or homozygosity BAF values 0.05, 0.45, 0.55, 0.95, respectively.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

6. Figure 5
Discovering a two-hit model of TP53 in mediastinal squamous cell carcinoma using SNPitty. A: BAF visualization of heterozygous markers, accompanied with respective read coverage, on the flanking and coding regions of TP53 for mediastinal squamous cell carcinoma (SCC) (blue circles and blue bars) and near-adjacent prostate tissue samples (matched normal, red rhombi and red bars). ∗Additional homozygous nucleotide positions to display genomic read coverage in TP53 region. ∗∗c.536A>G (p.H179R) somatic missense mutation. Black dashed lines show the homozygous BAF ranges (0,1), whereas the red dash-dot lines reflect the putative borders of balanced heterozygosity or homozygosity BAF values 0.05, 0.45, 0.55, 0.95, respectively. B: Immunohistochemistry of p53 shows an overexpression of p53 in malignant tissue of the respective mediastinal squamous cell carcinoma sample. Original magnification, ×63 (B).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

7. Figure 6
Detection of distinct LOH in multiple tumor samples using SNPitty. BAF visualization of heterozygous markers on chromosomes 1, 3, 5, 8, 10, 11, 13, and 18 for squamous cell carcinomas, originating from lung (red rhombi) and vertebrae tumors (green squares), and single matched normal prostate sample (blue circles). Black dashed lines show the homozygous BAF ranges (0,1), whereas the red dash-dot lines reflect the putative borders of balanced heterozygosity or homozygosity BAF values 0.05, 0.45, 0.55, 0.95, respectively.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

8. Figure 7
Detection of chromosomal abnormality in whole-exome sequenced peripheral blood from a Down syndrome patient using SNPitty. BAF visualization of informative heterozygous markers (covered with >175 reads) from whole-exome sequenced peripheral blood (blue circles) on chromosome 5 and chromosome 21. Black dashed lines show the homozygous BAF ranges (0,1), whereas the red dash-dot lines reflect the putative borders of balanced heterozygosity or homozygosity BAF values 0.05, 0.45, 0.55, 0.95, respectively. n = 954 (chromosome 5); n = 554 (chromosome 21).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions