Type an arr result, see the plot
ISCN microarray nomenclature in, a simulated array out, with every mistake explained in plain language. The plot is a simulation of what the written result describes; it is not the data behind any report.
Mosaic calculator
Read the upper heterozygous band off a BAF plot (0.5 for no mosaicism, up to 1 for every cell abnormal) and get the fraction of abnormal cells under each model. The BAF alone cannot choose the model; the copy number track does.
| Model in the abnormal cells | Upper band | Solve for f | Estimate | Log R (theory) |
|---|
Every valid estimate gives the same upper band. Only the log R and copy number track can pick one; low-level mosaicism also hides in the noise, so an estimate below about 10 to 15 percent is uncertain on real data.
About ArrayDraw
ArrayDraw is a free, browser-based simulator for learning to read SNP microarray results. You pick or build a genetic scenario (a deletion, a duplication, a mosaic, uniparental disomy, contamination, triploidy, consanguinity) and the page draws the copy number and allele tracks a real array would produce, with the arithmetic behind every band spelled out. It is the microarray sibling of KaryoDraw, which draws karyotypes from ISCN notation.
Who it is for
Genetic counseling students, ABGC and ABMGG board candidates, genetics residents and fellows, and laboratory trainees. Anyone who has stared at a B allele frequency plot and wanted to know why the bands sit where they sit.
How the plots are made
Each simulated person has up to four haplotypes per chromosome: the two the proband received (M and P) and the two the parents did not pass on (M2 and P2). Every SNP draws an allele on each haplotype at a random population frequency. A case lists cell populations and the haplotype copies each one carries, genome-wide or in a region, and the signal at each SNP is the weighted count of A and B alleles across those cells: B allele frequency is B over A plus B, allele difference is A minus B scaled to one copy, and log R is log2 of the total over the sample median. Realistic mode adds what real platforms do: normalization to the sample median, signal compression, noise, waves and outliers. Theoretical mode shows the bare arithmetic. The genotypes are drawn once per seed, so a slider moves the signal without reshuffling the points.
Band coordinates come from the UCSC cytoBandIdeo tables for GRCh38 and GRCh37. The pseudoautosomal boundaries are the assembly definitions for each build. Probe-free regions (centromeres, heterochromatin, the acrocentric short arms) are left empty, as on a real array.
Not a clinical tool
ArrayDraw generates simulated data for education. It is not for interpreting patient results. Every plot, export and shared link is labeled as simulated. Nothing you type is sent anywhere: the whole simulation runs in your browser.
Credits
- Fee T. SNP Microarray Interpretation Guide, Version 1. Greenwood Genetic Center; 2021. The inspiration for this project: a simulated-data guide to the same patterns. ArrayDraw reuses none of its text, figures or layout.
- Conlin LK, Thiel BD, Bonnemann CG, et al. Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum Mol Genet. 2010;19(7):1263-1275. doi:10.1093/hmg/ddq003
- Rehder CW, David KL, Hirsch B, Toriello HV, Wilson CM, Kearney HM. American College of Medical Genetics and Genomics: standards and guidelines for documenting suspected consanguinity as an incidental finding of genomic testing. Genet Med. 2013;15(2):150-152. doi:10.1038/gim.2012.169
- ISCN 2024: An International System for Human Cytogenomic Nomenclature. Karger; 2024.
- Peiffer DA, Le JM, Steemers FJ, et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 2006;16(9):1136-1148.
Free to use
No account, no paywall. Use it in class, in a lecture, on a handout; export a plot and keep the label. The code is free software under the AGPL-3.0 and the teaching text is also under CC BY-SA 4.0; credit ArrayDraw and link to it.
Who makes it
ArrayDraw is developed and maintained by StudyRare. Something wrong or missing? Email feedback@arraydraw.com.