Assignment Task

Introduction

In the practical you will be given two lists, one comprising 23 gene names and the other 21 DNA sequence variants (see table at the end of the document) - the selected genes and sequence variants are part of a genetic study.

Tasks

1. Establish the correct genevariant pairs using a genome browser; variants may also be located outside a gene typically, the nearest gene(s) to this variant will be included in the list. Obtain a reference sequence for all variants.

2. Use database resources to explore what is known about the function of each gene and the protein it encodes as well as its tissue expression profile. Prepare a table with each gene’s potential implication to disease.

3. Establish the functional impact of each sequence variant; for example, is a variant located in a coding region of the genome and if yes, does it alter an amino acid or is it overlapping a regulatory element.

4. For those genes you have established an association to a human trait(s) report the number of known rare variants and how many of these rare variants are Loss of Function.

5. Based on all the information assembled, assess whether the genes found in question 1 could be divided in to subgroups underlying a specific trait or combination of traits.