Genome Projects Flashcards
What are the two main approaches used to assemble fragments, give examples
Map-based sequencing (HGP) and whole genome shotgun sequencing (Celera Genomics)
Outline the HGP, what was the focus/aim and time of launch.
The HGP (1990) focused on developing new automated methods for sequencing, cloning etc to create genetic maps
Who are the IHGSC?
They consist of 20 research groups, large research centers (e.g. Sanger Institute, MIT).
Outline the timeline of Celera genomics and the process of developing its genome
In 1998-99 Craig V. Annuounced his plan to sequence the human genome within 2 years. This meant he would implement the use of whole genome shotgun sequencing where small fragment clones from genomic DNA are sequenced which is easy to manipulate because of its size. However, it was suspected to not work due to the size of the human genome.
Beyond HGP what was the major effort about? Timeline?
The major effort was directed to identifying all human genes and regulatory elements.
2004 - >21,000 human genes validated.
2005-7 - the HapMap consortium reports increasingly detailed SNP maps.
2008 - launch of the 1000 genome project.
What are some challenges of data sharing?
Issue of how to protect the privacy of human participants, computational and logistics problems, etc..
What was the issue of data analysis in the HGP?
The computational needs of HGP was considered last minute, and had little planning. Therefore, thousands of individually assembled sequence segments had to be joined together. Data analysis had proper planning in future projects (e.g. 1000 genomes project)
Outline the aim and time of ENCODE project.
(2003) Aimed to produce an encyclopedia of DNA elements including: transcribed and regulatory regions, etc..
What did the pilot of the ENCODE project outline?
Demonstrated that the Genome is much more extensively transcribed than previously thought. (63% of transcripts don’t encode proteins)
Outline the aim and time of earth biogenome project, UK involvement?
(2018) this is a 10 year project to sequence genomes of all 1.5 million known plants, animals, and fungi. In the UK, the Wellcome Sanger IN. Is the leading effort to sequence all 60k eukaryote species in British isles.
Outline the aim and time of 1000 genomes project, UK involvement?
(2008) aim to sequencing at least 2,500 genomes from across the world. - Aim was to capture rare genetic variations that occur in <5% of people (hence 1000 genomes). Focus on SNPs, indels, and large structural changes.
- 2008 – major portions of genomes from 180 people sequenced and genomes of two 3-member families.
- 2009 – sequences of a thousand gene-rich regions from genomes of 900 individuals obtained.
- 2009-10 – main project underway to sequence 2,500 genomes from total of 22 different populations.
Outline the aim and time of cancer genome atlas?
(2006-2017) aim was to enhance the ability to diagnose, treat, and prevent cancers.
Outline the aim and time of UK10K project?
(2010) aims to better understand the link between low frequency, rare genetic variants and human disease.
The UK 10K project proved the value of reading the genomes of several thousand people for some diseases. Despite this complex disease need larger numbers, so…
This led to initiatives in the UK such as the 100,000 Genomes Project & in the US the Million Veteran Program.
Outline the aim and time of 100,000 genomes project?
(2012) was enabled by the PM of England. Aimed to sequence 100,000 genomes from NHS patients: focused on patients with rare disease and their families and patients with cancer.
