Chapter 13

NextGENe Online Help : The NextGENe Sensitive Aneuploidy Detection Tool

The NextGENe Sensitive Aneuploidy Detection Tool

The NextGENe Sensitive Aneuploidy Detection tool (the NextGENe SAD tool) is designed for the detection of whole chromosome aneuploidies in low coverage whole genome sequencing samples. You can use the tool to test for aneuploidy even samples where the fetal fraction is low (~8-10%), such as the case with non-invasive prenatal testing (NIPT). This chapter details the NextGENe SAD tool, including how to open the tool, how to set the preferences for working in the tool, how to set up a model for training the tool, how to run an analysis with the tool, and how to view and work with the analysis results that the tool produces.

What are you interested in?

• Introduction to the NextGENe Sensitive Aneuploidy Detection Tool

• Opening the NextGENe SAD Tool

• The NextGENe SAD Tool Main Window

• Specifying Preferences for the NextGENe SAD Tool

• Adding a Model in the NextGENe SAD Tool

• Viewing and Working with Model Results

• Viewing Information for and Re-running an Existing Model

• Analyzing Samples with the NextGENe SAD Tool

• Viewing and Working with Analysis Results

• Viewing Information for and Re-running an Existing Analysis

All other NextGENe tools, with the exception of the NextGENe Format Conversion tool and the NextGENe AutoRun tool, are discussed in detail in NextGENe Tools. The NextGENe Format Conversion tool is discussed in The NextGENe Format Conversion Tool. The NextGENe AutoRun tool SAD tool is discussed in The NextGENe AutoRun Tool.