The Functional Genome

Question 1

What is meant by Next generation sequencing?

Answer 1

A number a rapid modern technologies for high throughput DNA sequencing

Question 2

What is Whole Exome Sequencing? (WES)

Answer 2

Whole Exome Sequencing is used to capture the sequence of the coding region of the genome

Question 3

What is Whole Genome Sequencing? (WGS)

Answer 3

Whole Genome Sequencing captures the whole thing

Question 4

What are the purposes of both WES and WGS?

Answer 4

Aim to identify potential diseases causing genetic variants

Question 5

What are the filtering steps using WES? (VD)

Answer 5

3 Million SNPs -> 15,000-20,000 coding SNPs -> 7,000-10,000 non synonymous coding SNPs -> 200-500 novel non synonymous coding SNPs -> One of several putative genes

Question 6

What happens between step 1 and step 2?

Answer 6

Target sequencing of exons

Question 7

What happens between step 2 and step 3?

Answer 7

Remove synonymous variants

Question 8

What happens between step 3 and step 4?

Answer 8

Remove previously identified variants

Question 9

What happens between step 4 and step 5?

Answer 9

Restrict to variants fitting dominant/recessive model of inheritance

Question 10

Briefly describe what happens in WES

Answer 10

• WES data is subjected to a prioritisation filtering protocol
• 15-20,000 coding SNPs reduced to one or several candidate genes
• Checked for co-segregation (family members) and validated by Sanger sequencing