Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-8

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>and 50 K Xba via CNAT v2.0. The first three tracks are a trio (father, NA11839; mother, NA11840; daughter, NA10854). Note that for both of the first two tracks, the patterns observed on the X chromosome are atypical. The first two tracks show a unique and apparently abnormal pattern of red dots in the copy number range that is normal for females (1–3), with blue dots exposed in a lowered copy number range that is normal for males (1–2). The values (yellow area) for the first track are much higher than that of the second track, presumably because of the smaller number of heterozygous calls derived from the Hind array (see Table 3). Together, these observations suggest a pattern of SNPs that represents a combined male and female profile; our interpretation is that the labels were switched on two of the Hind datasets (see Table 3). The third track, showing data on an apparently normal female, has another pattern: many red and green dots mostly in the copy number range of 1 to 2.5, with values (yellow) intermediate between normal female and male values. This represents a female with a mosaic loss of the X chromosome. After the labeling error was corrected for the first two tracks, the results (NA11839 as male and NA11840 as female) were plotted in the last two tracks

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-2

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>ch can then be visualized on the UCSC Genome Browser. For case NA07055 (shown in Fig. 2), 50 K Xba SNP data from chromosome 2 are displayed. The three custom tracks, arranged in rows, are LOH value (color coded with more significant values having a darker color), copy number (in green), and copy number value (in blue). Note a region of deletion (dashed circle). The genome browser can be viewed for each chromosome at full scale or reduced to any region of interest. Additional tracks that are displayed in this example are chromosome band, gaps, known genes, Ensembl gene predictions, and SNPs. Dozens of additional tracks can be added or removed. Each WIG file that is generated can contain multiple SNP array data sets

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-4

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>op row; case L99-2287), 3 (second row; case L99-2297) and 2 (third row), and uniparental isodisomy of chromosome 14 (fourth row; case X_1054). The x-axis spans chromosomes 1–22 and X. B. Detailed view of microdeletions on chromosome 3 (top row) and 2 (bottom row). The x-axis spans chromosomes 2 and 3

Additional file 1 of Detecting antibody reactivities in Phage ImmunoPrecipitation Sequencing data

Additional file 1: Supplementary Materials

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-1

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>4). Each SNP array data set is organized in a row; options for types of input are 10 K, 50 K (Hind or Xba), or 100 K (combined Hind and Xba) arrays. The x-axis spans chromosomes 1–22 and X, with centromeres indicated (grey rectangles; see panel B for enlarged view). Note that a male case (bottom row) is easily distinguished from female cases by the profile of the hemizygous X chromosome, including many homozygous calls (blue dots), significant LOH -logvalues (grey background), and a significant -logvalue for copy number changes (yellow background). Also of note are a deletion on chromosome 2 (top row, dashed circle) and a region of UPD across chromosome 1 (bottom row, dashed circle). B. SNPscanPlot allows an expanded view of any chromosome(s); 22 and X are shown for the cases in panel A, highlighting the differences observed between male and female X chromosome SNP profiles

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-5

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>s. The y-axis indicates ratio of patient to control signal and (in a dye swap paradigm) control to patient signal. The x-axis indicates physical map position (units in Mb). Panel A: case L99-2287 (chromosome 7 microdeletion in facial dysgenesis). Panel B: case L99-2297 (chromosome 3p deletion syndrome). Panel C: case L99-2287 (deletion of chromosome 2 including CPS I deficiency). Arrows indicate region of deletion. The plots were generated using SpectralWare (Spectral Genomics) software

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-9

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>air, and produces a third track in the form of a ratio plot (in logscale) comparing the two samples. This feature is useful for any paired samples such as SNP profiles in normal versus cancer tissue. In this example the genotype changes from homozygous to heterozygous were indicated in red, while other optional color displays were suppressed. This highlighted a region of chromosomal amplification

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-7

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>16 of 23 cells revealed a deletion (an example is shown in A), while the remainder appeared euploid (B)

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-3

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>ing a description of SNPs in regions of consecutive homozygous calls (i.e. LOH) in table form (A) or with a plot (B). Both panels are screen shots; the labels in B have been redrawn for clarity

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan-0

<p><b>Copyright information:</b></p><p>Taken from "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan"</p><p>BMC Bioinformatics 2006;7():25-25.</p><p>Published online 18 Jan 2006</p><p>PMCID:PMC1382255.</p><p></p>g column headers with SNP identifiers and chromosomal position as well as SNP genotypes (AA, BB, AB, or NoCall), SNP copy number, and associated values. This text file is obtained as an output from the Affymetrix CNAT. The SNPscan website includes separate upload pages for additional SNP analysis tools