Post HGP projects Flashcards
What is the HapMap project? Outline the procedure.
The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap was used to find genetic variants (SNPs) affecting health, disease and responses to drugs and environmental factors.
The project collaborated among researchers at academic centers, non-profit biomedical research groups and private companies in Canada, China, Japan, Nigeria, the United Kingdom, and the United States.
Sampling:
- A total of 270 people of African, Asian and European origin.
- Yoruba people from Ibadan, Nigeria: 30 sets of samples from two parents and an adult child (trios).
- Japanese samples: 45 unrelated people from Tokyo.
- Chinese samples: 45 unrelated people from Bejing.
- Thirty US trios with European ancestry.
The blood samples were converted into cell lines (B lymphocytes infected eith EBV indefinitely divide- transformed lymphoblasts) for DNA isolation. The aim was to identify all SNPs, of which they found to be 11 million.
What is a haplotype?
A set of closely linked alleles/DNA sequences/SNPs that are inherited as a unit. Haplotypes are produced as a product of recombination mechanisms.
What are tagged SNPs?
One SNP can be representative of other SNPs which are inherited as a unit through recombination. These are known as tagged SNPs.
How are SNPs analysed?
Through genotyping and genome wide association studies (GWAS).
What is a GWAS?
In genetics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an examination of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait.
What were the findings of the ENCODE project?
- The human genome is pervasively transcribed
- Many new non-protein-coding transcripts identified
- Previously unrecognized transcription start sites identified
- Chromatin accessibility and histone modification pattern predictive of transcriptional activity
- Distal DNaseI hypersensitive sites have characteristic histone modification patterns distinct from promoters
- DNA replication timing correlates with chromatin structure
- Approx. 5% of the sequence under evolutionary constraint
- Many functional elements unconstrained by evolution
What is a CNV?
Copy Number Variation (CNV) – a variation in which a segment of DNA (at least 500 bp long) is found in different copy numbers among different individuals.
What is the CNV Project?
The Copy Number Variation (CNV) Project investigates the impact on human health of CNVs - gains and losses of large chunks of DNA sequence. An international consortium between the Sanger Institute (UK), Charles Lee (Harvard Medical School) and Steve Scherer (Hospital for Sick Kids, Toronto) worked on this projct.
What was the procedure for the CNV Project?
They designed an array to measure copy number for the majority of a recently-compiled inventory of CNVs from an extensive discovery experiment, and several other sources. They then used the array to type 3,000 common controls and 2,000 cases of each of the diseases: bipolar disorder (BD), breast cancer (BC), coronary artery disease (CAD), Crohn’s disease (CD), hypertension (HT), rheumatoid arthritis (RA), type 1 diabetes (T1D), and type 2 diabetes (T2D).
Based on the pilot data, they chose the Agilent Comparative Genomic Hybridisation (CGH) platform, and aimed to target each CNV with 10 distinct probes
A total of 19,050 case-control samples were sent for assaying: ~2,000 for each of the eight diseases and ~3000 common controls. These were augmented by 270 HapMap samples and 610 duplicate samples for QC purposes.
They performed association testing at each of the CNVs which passed QC, in two parallel approaches. First, we applied a frequentist likelihood ratio association test that combines calling (using CNVtools) and testing into a single procedure. Second, we undertook Bayesian association analyses to calculate a Bayes Factor to measure strength of association with the disease phenotypes. Careful analysis of ttheir association testing revealed several sophisticated biological artefacts which can lead to false positive associations. Simultaneously studying eight diseases helped greatly in identifying these artefacts and stringent QC was invaluable in eliminating false positive associations.
What were the findings of the CNV Project?
- Crohn’s disease: two distinct CNVs 22kb apart upstream of the IRGM gene, one of which was novel.
What is HapMap useful for?
When all SNPs are identified it can be used for the identification of genes responsible for many common diseases using GWAS.
What is ENCODE useful for?
Characterisation of the genome function, which will refine our knowledge of many human diseases, e.g. diseases caused by alteration in chromatin structure (e.g. Sotos syndrome).
What is the CNV Project useful for?
Find the proportion of genetic diseases caused by CNVs, which is currently unknown. Find the contribution of CNVs to common complex diseases such as diabetes. Some CNVs protect against malaria and HIV, so are of particular interest.
