Gene sharing: Unrelated samples

Description   Prerequisites   Dialog   Practical tips   Algorithm

Description

Identification and statistical evaluation of genes where all the affected have variants compatible with the disease model. Unaffected samples are used as an additional filter.

Prerequisites

The analysis can be applied to any variant files loadable in Filtus, as long as the genotype format is correctly given in the input settings. In particular, samples from different variant files can be analyzed together, even if the files have different formats.

For recessive analyses, all involved samples must have a well defined gene column (specified in the input settings).

Dialog

Gene sharing dialog
Model
The genetic disease model, either Dominant, Recessive c/h (which includes both compound heterozygous and homozygous models) or Recessive homoz (homozygous only).

Affected
The affected samples, separated by comma. Samples can be specified in various ways:

Healthy
The unaffected/control samples. Notational options are as for the Affected field.

Practical tips

Tip 1: The identified genes are displayed in the main window, sorted on the p-value. You can sort on any column by right clicking on the column header.

Tip 2: Right click on a gene to view the relevant variants in that gene. You can also view the variants in all identified genes simultaneously, or in the genes on top of the list.

The algorithm

The p-values are computed according to the statistical model described in Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic mendelian diseases by exome sequencing by Zhi and Chen (2012).