The 100,000 Genomes Project; Cardiovascular GeCIP

Question 1

How is library preparation pursued to facilitate WGS?

Answer 1

1. DNA sample first retrieved, extract Extract nucleic acids from blood, tissue, saliva, etc.
2. Shear dsDNA into fragments
3. Attach adapters to fragments

Question 2

How is the library sequenced?

Answer 2

Library taken and loaded onto a flowcell: similar to a microscope slide

HTS machine processes a flowcell containing lanes

Each lane may contain multiple samples (indexed with a DNA barcode)

Read group (RG) specifies a combination of sample and flowcell

DNA libraries deposited on flowcell
-> amplified to form clusters

Used method to amplify fragments to clusters which is a variation of pcr- called bridge amplification because we are performing this process on the surface of the flow cell

Once flowcell and clusters prepared, loaded onto sequencing machine and sequencing by synthesis performed, fragments sequenced and different coloured reversible terminators used to determine base pair sequence of each of the fragments on flow cell

Results in enormous amount of short read sequences representative of all our library or genomic DNA sample

Question 3

How is NGS data analysis facilitated?

Answer 3

1. Sequence read alignment: Taking reads and aligning against reference genome in our case human reference genome and identifying all the mapping locations of these reads, along that reference genome
2. Once process complete, can perform quality control of that data look at coverage, how well is the genome covered?
3. Once pleased with data, variant calling pursued. Looking for variants in data relative to reference genome

Question 4

Typically, we will detect 3 Million variants in any given human genome

True of false

Answer 4

True

Question 5

What does all this genetic variation mean?

Answer 5

We need extensive annotation tools to make informed decisions about variants

Question 6

What is the order of importance of functional consequences?

Answer 6

1. NonSense
2. Frameshift causing indels
3. Splice site
4. NonSynonmous
5. Non frameshift causing indels
6. Synonymous
7. NonCoding

Question 7

The function of non genetic variants is more difficult to elucidate

What can be used?

Answer 7

Functional predictions programs

• SIFT (protein altering)
• PolyPhen

Question 8

What is the 100,000 genomes project

Answer 8

100,000 genomes project

Bring direct benefit to patients

Enable new scientific discovery and medical insights

Create an ethical and transparent programme based on consent and engagement

To kick-start the development of a UK genomics industry

England- wide collection

GMCs (genomic medicine centres)

Question 9

What is the NHS?

Answer 9

NHS was established in 1948
Worlds largest publically funded health service
One of the largest employers in the world (1.5 Million)
100k doctors, 300k nurses
1.4 million patients treated every 24 hours
116 Billion annual budget

Question 10

Who/what is being sequenced in by Genomics Health England?

Answer 10

Rare diseases - families

Cancers – germline and tumour samples

Question 11

What is the role of technology in Genomics health england?

Answer 11

Illumina have been commissioned to sequence the DNA of participants

Whole genome sequences returned to
Genomics England ready for analysis

Dedicated team of bioinformaticians for clinical interpretation.

Question 12

How does genomics health england use data?

Answer 12

The data is analysed within secure infrastructure (information governance)

Participant privacy and confidentiality

Anonymised data

Scientists and clinicians will access the data for research

Improve diagnosis rate of rare diseases

Understand how genomics impacts health and healthcare

Suggest possible new treatments (precision medicine)

Understand the causes of disease

Question 13

How are we interpreting the mutations ?

Answer 13

This is the most difficult part

We can recruit patients and generate genetic data faster than we can interpret it

Genetic findings can be actionable

Question 14

What is used to aid variant interpretation, apart from ACMG?

Answer 14

Genomics England Panel App

Community driven genetic interpretation

Crowdfunding research

‘Experts’ develop lists of possible genes than can cause a disease panels are reviewed by the community

Diseases have specific sets of virtual gene panels as a first port-of-call to look for pathogenic mutations

Question 15

What is is the classification of variants by genomics England designed to do?

Answer 15

Maximise diagnostic efficiency
Balance sensitivity and specificity

Variants within virtual panel divided into three tiers-

Tier 1 variants
Known pathogenic
Protein truncating

Tier 2 variants 
Protein altering (missense)
Intronic (splice site)

Tier 3 variants
Loss-of-function variants in genes not on the disease gene panel

Expert review is required

Question 16

What are the objectives of Cardiovascular GeCIP?

Answer 16

To provide the genetic diagnosis to patients with cardiovascular diseases

To identify new causative genes for phenotypes included within the project

To functionally characterise causative genetic variants and mechanisms of disease

To examine genotype/phenotype relationships and identify factors relevant to prognosis and response to treatment
If possible, to identify potential for orphan drug or novel therapeutic strategies

To equip trainees with the necessary genomic medicine knowledge and skills for the genomics era

Question 17

The range of diseases covered by the Cardiovascular GECIP is…

Therefore Cardiovascular GeCIP is divided into what?

Answer 17

broad, involving conditions of the myocardium, blood vessels, lymphatics, and also lipid metabolism leading to premature atherosclerosis

‘sub-domains’

• Cardiomyopathy
• Arrhythmias
• Familial thoracic aortic aneurysms and dissection
• Congenital heart disease
• Primary lymphoedema
• Familial hypercholesterolaemia
• CADASIL negative small vessel cerebral disease

Question 18

What three main arrythmia syndrome phenotypes eligible for WGS?

Answer 18

Long QT Syndrome (LQTS)
Brugada Syndrome (BrS)
Catecholaminergic polymorphic ventricular tachycardia (CPVT)

Question 19

What does the data access include?

Answer 19

The dataset includes de-identified, linked information for each participant:

• Genome sequence data
• Variant call files
• Phenotype/clinical data
• Hospital Episode Statistics (HES)

GeCIP members need to belong to a participating institution e.g. St Georges

Access to the 100,000 Genomes dataset is via a remote desktop hosted by the Genomics England datacentre – the Research Environment

After logging on, a virtual desktop will open in a window of your internet browser

No sequencing or clinical data is available for download

On board high-performance computer (HPC) for genome analysis