1000 Genomes Project
This article needs to be updated.(October 2023) |
The 1000 Genomes Project (1KGP), taken place from January 2008 to 2015, was an international research effort to establish the most detailed catalogue of human genetic variation at the time. Scientists planned to sequence the genomes of at least one thousand anonymous healthy participants from a number of different ethnic groups within the following three years, using advancements in newly developed technologies. In 2010, the project finished its pilot phase, which was described in detail in a publication in the journal Nature.[1] In 2012, the sequencing of 1092 genomes was announced in a Nature publication.[2] In 2015, two papers in Nature reported results and the completion of the project and opportunities for future research.[3][4]
Many rare variations, restricted to closely related groups, were identified, and eight structural-variation classes were analyzed.[5]
The project united multidisciplinary research teams from institutes around the world, including China, Italy, Japan, Kenya, Nigeria, Peru, the United Kingdom, and the United States contributing to the sequence dataset and to a refined human genome map freely accessible through public databases to the scientific community and the general public alike.[2]
The International Genome Sample Resource was created to host and expand on the data set after the project's end.[6]
Background
Since the completion of the
The diversity of
Natural selection
It also aimed to provide evidence that can be used to explore the impact of Natural selection on population differences. Patterns of DNA polymorphisms can be used to reliably detect signatures of selection and may help to identify genes that might underlie variation in disease resistance or drug metabolism.[12][13] Such insights could improve understanding of phenotypic variations, genetic disorders and Mendelian inheritance and their effects on survival and/or reproduction of different human populations.
Project description
This section needs to be updated.(April 2021) |
Goals
The 1000 Genomes Project was designed to bridge the gap of knowledge between rare genetic variants that have a severe effect predominantly on simple traits (e.g.
The primary goal of this project was to create a complete and detailed catalogue of
Secondary goals included the support of better SNP and probe selection for genotyping platforms in future studies and the improvement of the human reference sequence. The completed database was expected be a useful tool for studying regions under selection, variation in multiple populations and understanding the underlying processes of mutation and recombination.[15]
Outline
The
Over the course of the next three years,[
Almost 10 billion bases were to be sequenced per day over a period of the two year production phase, equating to more than two human genomes every 24 hours. The intended sequence dataset was to comprise 6 trillion DNA bases, 60-fold more sequence data than what has been published in DNA databases at the time.[14]
To determine the final design of the full project three pilot studies were to be carried out within the first year of the project. The first pilot intends to genotype 180 people of 3 major geographic groups at low coverage (2×). For the second pilot study, the genomes of two nuclear families (both parents and an adult child) are going to be sequenced with deep coverage (20× per genome). The third pilot study involves sequencing the coding regions (exons) of 1,000 genes in 1,000 people with deep coverage (20×).[14][15]
It was estimated that the project would likely cost more than $500 million if standard DNA sequencing technologies were used. Several newer technologies (e.g.
In keeping with Fort Lauderdale principles Archived 2013-12-28 at the Wayback Machine, all genome sequence data (including variant calls) is freely available as the project progresses and can be downloaded via ftp from the 1000 genomes project webpage.
Human genome samples
Based on the overall goals for the project, the samples will be chosen to provide power in populations where
For the pilot studies human genome samples from the
Complying with extensive ethical procedures, the 1000 Genomes Project will then use samples from volunteer donors. The following populations will be included in the study:
* Population that was collected in diaspora
Community meeting
Data generated by the 1000 Genomes Project is widely used by the genetics community, making the first 1000 Genomes Project one of the most cited papers in biology.[17] To support this user community, the project held a community analysis meeting in July 2012 that included talks highlighting key project discoveries, their impact on population genetics and human disease studies, and summaries of other large-scale sequencing studies.[18]
Project findings
Pilot phase
The pilot phase consisted of three projects:
- low-coverage whole-genome sequencing of 179 individuals from 4 populations
- high-coverage sequencing of 2 trios (mother-father-child)
- exon-targeted sequencing of 697 individuals from 7 populations
It was found that on average, each person carries around 250–300 loss-of-function variants in annotated genes and 50-100 variants previously implicated in inherited disorders. Based on the two trios, it is estimated that the rate of de novo germline mutation is approximately 10−8 per base per generation.[1]
See also
- Human Genome Project
- HapMap Project
- Personal genomics
- Population groups in biomedicine
- 1000 Plant Genomes Project
- List of biological databases
References
- ^ PMID 20981092.
- ^ PMID 23128226.
- PMID 26432245.
- PMID 26432246.
- ^ "Variety of life". Nature News & Comment. 2015-09-30. Retrieved 2015-10-15.
- Mount Sinai School of Medicine. 2020-07-07. Retrieved 2023-10-01.
- PMID 20981085.
- ^ JC Long, Human Genetic Variation: The mechanisms and results of microevolution, American Anthropological Association (2004)
- PMID 12799463.
- PMID 17122850.
- S2CID 205357396.
- ^ EE Harris et al., The molecular signature of selection underlying human adaptations, Yearbook of Physical Anthropology 49: 89-130 (2006)
- S2CID 13722452.
- ^ a b c d e f G Spencer, International Consortium Announces the 1000 Genomes Project, EMBARGOED (2008) http://www.nih.gov/news/health/jan2008/nhgri-22.htm
- ^ a b c d e f Meeting Report: A Workshop to Plan a Deep Catalog of Human Genetic Variation, (2007) http://www.1000genomes.org/sites/1000genomes.org/files/docs/1000Genomes-MeetingReport.pdf
- PMID 26568821.
- ^ C. King (2012) The Hottest Research of 2011. Science Watch http://archive.sciencewatch.com/newsletter/2012/201203/hottest_research_2012/
- ^ 1000 Genomes Project Community Analysis Meeting http://1000gconference.sph.umich.edu/
External links
- 1000 Genomes - A Deep Catalog of Human Genetic Variation - official web page
- International HapMap Project Archived 2014-04-16 at the Wayback Machine - official web page
- Human Genome Project Information