20.04.19 Whole genome sequencing projects e.g. 100,000 genomes Flashcards
What will 100,000 project sequence
- 25,000 cancer patients (blood and tumour)
- 17,000 people with rare diseases (plus 2 additional blood relatives)
Who runs 100,000 project
Genomics health England. Part of Department of Health.
Aims of 100,000 project
- Create new genomic medicine service for NHS.
- Enable new medical research.
- Bring benefit to patients
- Create ethical and transparent programme based on consent
- Enable new scientific discovery and medical insights
- Kick start the development of the UK genomics industry
Key dates for 100,000 project
- Announced by PM in Dec 2012
- Genomics England launched 2013
- Project live 2015
- Deadline for labs to have 85% cases reported= April 2020.
What is a GeCIP
- Genomics England Clinical Interpretation Partnership.
- Researchers from NHS and University involved in the analysis of sequence data.
What is the approximate cost of 100,000 project
£206 million
Where does sequencing take place for the 100,000 project
Hinxton. Provided by Illumina
What is a GMC
- Genomic Medicine Centre
- 13
- Identify, enroll and register suitable patients. Obtain consent and detailed phenotypic information. Validate findings.
What information is fed back to patients (100,000 project)
- Pertinent findings regarding their main condition.
- Patients can opt for feedback on high probability pathogenic findings (will develop as project progresses)
- Information on 12 serious actionable conditions, e.g. cancer predisposition (BRCA, FAP)
- Carrier status (CF, sickle cell, DMD, SMA type 1)
WGS as part of NHS genomic medicine service in future
- January 2020, Genomics England announced that 300,000 genomes would be delivered over the next 5 years.
- Done through 7 Genomic Laboratory Hubs (GLH).
- Certain cancers and rare diseases will be eligible
- Aim to support diagnosis, inform and improve treatment pathways and thus outcomes.
- Due to go live in 2020
What is the Scottish Genome Partnership (SGP)
- £15 million investment by University of Edinburgh and Glasgow in Jan 2015.
- Sequencing of 3,000 Scottish genomes.
- Started March 2016.
What is the ENCODE project
- ENCODE= Encyclopedia of DNA elements
- Public research consortium launched by US National Human Genome Research Institute (NHGRI) in 2003.
- Aims to build a comprehensive catalog of candidate functional elements in the human genome.
- Includes data sets from ChIP-seq, RNAseq, DNA methylation etc
What is the BiLEVE project
- UK Biobank Lung Exome Variant Evaluation
- One of the first studies using samples and data from UK biobank (resource from 500k volunteers).
- Study into the genetics of lung disease, particularly chronic obstructive pulmonary disease.
- Associations between SNPs and lung function, chance of developing disease in smokers vs non-smokers. Smoking addiction.
- Genome wide genotyping using Affymetrix array
What is the PAGE study (not prenatal genome project)
- PAGE= Population Architecture using Genomics and Epidemiology
- US study initiated in 2008 by NHGRI.
- Investigates the epidemiologic architecture of well-replicated genetic variants associated with complex disease in large, ethnically diverse population-based studies.
- 270,000 participants.
What is the DDD study
- DDD= Deciphering Developmental Delay
- Funded by Wellcome Trust, Department of Health and NIHR
- Patients with severe undiagnosed developmental disorders and their parents using a combination of exome sequencing and array-based detection of chromosomal re-arrangements.
- 14k families recruited.
- Diagnostic yield is 35%
- 10% trios have an affected parent.
- 12 new genes identified
