SNPtrio

Schema

SNPtrio searches informative SNPs based on the following schema. Please refer to this table to understand what information is plotted (on various tracks, in various colors) on a typical SNPtrio output.

Since copy number information is not always available for SNP data, SNPtrio users only need genotype calls in order to use it. Hence, the basis of this schema is biallelic calls (copy number equal to two) for each individual in a trios. Therefore, chromosome X of the son or other deleted regions on the child will be flagged by SNPtrio as a uniparental inheritance (UPI) region. SNPtrio users can use copy number information, when it is available, to assess whether a UPI region identified by SNPtrio is a deletion or a true uniparental disomy (UPD) or autozygosity. The 'X' in this schema marks possible inheritance for each trio SNP calls. While "no calls" or miscalls are possible for each trio, this schema does not include them.

SNPtrio plots SNPs belong to the highlighted boxes in this schema, with the colors indicated by the 'X' inside each box, respectively. The gray X marks in white boxes are considered uninformative from SNPtrio's point of view. Abbreviations: iUPD-P, uniparental isodisomy - paternal (plotted brown or green); hUPD-P, uniparental heterodisomy - paternal (plotted brown); BPD, biparental disomy (plotted black); hUPD-M, uniparental heterodisomy - maternal (plotted blue); iUPD-M, uniparental heterodisomy - maternal (colored yellow or blue); MI-S, Mendelian inconsistency - single allele (plotted red); MS-D, Mendelian inconsistency - double alleles (plotted pink).

SNPtrio Heredity Table and Color Schema

Pedigrees of SNPtrio's Schema

Trio relationships in the above heredity table can be presented in the pedigree form. Here, some alleles are shown in white color in order to show which alleles the child has inhereted.

The sequence of the five tracks on SNPtrio's plot (see sample patterns below) are based on the order as shown in this pedigree table, with the iUPI-P and hUPI-P combed into one UPI-P track, and the hUPI-M and iUPI-M combined into one UPI-M track.