NGS methods

Question 1

What is a targeted gene panel and what are benefits of this method?

Answer 1

Sequencing assay of a number of specific genes linked to a particular genetic condition Targets exons of ~20-100 genes. Selection of genes to be included is usually determined by using PanelApp.

Benefits- Low cost and reduced liklihood of IF

Question 2

What is exome sequencing and what are the benefits of this method?

Answer 2

Sequencing assay which involves sequencing all exon (~180,000). Can be used to reach a diagnosis for patients with complex phenotypes and for those patients where a variant has not been detected previously in a targeted approach.

Benefits- Higher diagnostic yield, higher likelihood of IF, but can control with sub-panel

Question 3

What is whole genome sequencing and what are the benefits of this method?

Answer 3

Sequencing assay which involves sequencing the whole genome of patient samples (introns and exons)

Question 4

What are the challenges associated with short read alignment?

Answer 4

1. Human genome is very large! 3 billion bases

2. Reads will not always match exactly due to SNPs