Personal Genome Project

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The Personal Genome Project (PGP) is a long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personal genomics and personalized medicine. It was initiated by Harvard University's George M. Church in 2005. [1] [2] [3] As of November 2017, more than 10,000 volunteers had joined the project. Volunteers were accepted initially if they were permanent residents of the US and were able to submit tissue and/or genetic samples. Later the project was expanded to other countries.[ citation needed ]

Contents

The Study

The Project was initially launched in the US in 2005 [1] and later extended to Canada (2012), [4] United Kingdom (2013), [5] Austria (2014), [6] Korea (2015) [7] and China (2017). [8]

fMRI of the head of a 58 yr old male participant in the project. 100325 RS88UH 11 qc.gif
fMRI of the head of a 58 yr old male participant in the project.

The project allowed participants to publish the genotype (the full DNA sequence of all 46 chromosomes) of the volunteers, along with extensive information about their phenotype: medical records, various measurements, MRI images, etc. All data were placed within the public domain and made available over the Internet so that researchers could test various hypotheses about the relationships among genotype, environment and phenotype. Participants could decide what data they are comfortable to publish publicly and could choose to upload additional data or remove existing data at their own convenience.[ citation needed ]

An important part of the project was the exploration of the resulting risks to the participants, such as possible discrimination by insurers and employers if the genome shows a predisposition for certain diseases.[ citation needed ]

The PGP is establishing an international network of sites, including the United States (Harvard PGP), Canada (University of Toronto / Hospital for Sick Kids), and other countries that adhere to certain "conforming implementation" criteria such as no promise of anonymity and data return. [9] The Harvard Medical School Institutional Review Board requested that the first set of volunteers include the principal investigator George Church and other diverse stakeholders in the scientific, medical, and social implications of personal genomes, because they were well positioned to give highly informed consent. As sequencing technology becomes cheaper, and the societal issues mentioned above are worked out, it was hoped that a large number of volunteers from all walks of life would participate. The long-term goal was that every person have access to his or her genotype to be used for personalized medical decisions.[ citation needed ]

The first ten volunteers were referred to as the "PGP-10". These volunteers were:

  1. Misha Angrist, Duke Institute for Genome Sciences and Policy [10] Keith Batchelder, Genomic Healthcare Strategies, Esther Dyson, EDventure Holdings, Rosalynn Gill-Garrison, Sciona, John Halamka, Harvard Medical School, Stan Lapidus, Helicos BioSciences, Kirk Maxey, Cayman Chemical, James Sherley, Boston stem cell researcher, and Steven Pinker, Harvard

In order to enroll, each participant must pass a series of short online tests to ensure that they are providing informed consent. [11] By 2012, 2000 participants had enrolled [12] and by November 2017 10,000 had joined the project. [8]

In July 2014, at the 'Genetics, Genomics and Global Health—Inequalities, Identities and Insecurities' conference, Stephan Beck, the head of the UK arm of this project indicated that they had over 1000 volunteers, and had temporarily paused collection data due to lack of funding. As of November 2016, the pause was still in effect. [13]

Since 2016, participants of the PGP could choose to obtain their whole-genome sequenced performed for $999. [14] In the same year Complete Genomics contributed over 184 phased human genomes to the project. [15]

In February 2018, the results were published of the first 56 Canadian participants who had their whole genome analyzed. [16] Several DNA mutations that would have been expected by expert consensus to affect health of the participants had not done so, indicating that getting health data from the human genome was difficult. [17]

PGP Lumosity Project

On March 9, 2017, producers of the popular online brain-training program Lumosity announced they would collaborate with Harvard researchers to investigate the relationship between genetics and memory, attention, and reaction speed. [18] [19]

Scientists at the Wyss Institute for Biologically Inspired Engineering and the Harvard Medical School Personal Genome Project (PGP) planned to recruit 10,000 members from the PGP, to perform a set of cognitive tests from Lumos Labs’ NeuroCognitive Performance Test, a brief, repeatable, online assessment to evaluate participants’ memory functions, including object recall, object pattern memorization, and response times. The researchers would then correlate extremely high performance scores with naturally occurring variations in the participants’ genomes. To validate their findings, the team would sequence, edit, and visualize DNA, model neuronal development in 3-D brain organoids ex vivo, and finally test emerging hypotheses in experimental models of neurodegeneration.[ citation needed ]

See also

Related Research Articles

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The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements, DNA playing structural and replicatory roles, such as scaffolding regions, telomeres, centromeres, and origins of replication, plus large numbers of transposable elements, inserted viral DNA, non-functional pseudogenes and simple, highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA, such as pseudogenes, but there is no firm consensus on the total amount of junk DNA.

<span class="mw-page-title-main">Genomics</span> Discipline in genetics

Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

<span class="mw-page-title-main">Genetic testing</span> Medical test

Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, or through biochemical analysis to measure specific protein output. In a medical setting, genetic testing can be used to diagnose or rule out suspected genetic disorders, predict risks for specific conditions, or gain information that can be used to customize medical treatments based on an individual's genetic makeup. Genetic testing can also be used to determine biological relatives, such as a child's biological parentage through DNA paternity testing, or be used to broadly predict an individual's ancestry. Genetic testing of plants and animals can be used for similar reasons as in humans, to gain information used for selective breeding, or for efforts to boost genetic diversity in endangered populations.

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<span class="mw-page-title-main">George Church (geneticist)</span> American geneticist

George McDonald Church is an American geneticist, molecular engineer, chemist, serial entrepreneur, and pioneer in personal genomics and synthetic biology. He is the Robert Winthrop Professor of Genetics at Harvard Medical School, Professor of Health Sciences and Technology at Harvard University and Massachusetts Institute of Technology, and a founding member of the Wyss Institute for Biologically Inspired Engineering at Harvard. Through his Harvard lab Church has co-founded around 50 biotech companies pushing the boundaries of innovation in the world of life sciences and making his lab as a hotbed of biotech startup activity in Boston. In 2018, the Church lab at Harvard made a record by spinning off 16 biotech companies in one year. The Church lab works on research projects that are distributed in diverse areas of modern biology like developmental biology, neurobiology, info processing, medical genetics, genomics, gene therapy, diagnostics, chemistry & bioengineering, space biology & space genetics, and ecosystem. Research and technology developments at the Church lab have impacted or made direct contributions to nearly all "next-generation sequencing (NGS)" methods and companies. In 2017, Time magazine listed him in Time 100, the list of 100 most influential people in the world. In 2022, he was featured among the most influential people in biopharma by Fierce Pharma, and was listed among the top 8 famous geneticists of all time in human history. As of January 2023, Church serves as a member of the Bulletin of the Atomic Scientists' Board of Sponsors, established by Albert Einstein.

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<span class="mw-page-title-main">Whole genome sequencing</span> Determining nearly the entirety of the DNA sequence of an organisms genome at a single time

Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.

Complete Genomics is a life sciences company that has developed and commercialized a DNA sequencing platform for human genome sequencing and analysis. This solution combines the company's proprietary human genome sequencing technology with its informatics and data management software to provide finished variant reports and assemblies at Complete Genomics’ commercial genome center in Mountain View, California.

<span class="mw-page-title-main">Exome sequencing</span> Sequencing of all the exons of a genome

Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome. It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons—humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.

<span class="mw-page-title-main">$1,000 genome</span> Era of predictive and personalized medicine

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Personalized medicine involves medical treatments based on the characteristics of individual patients, including their medical history, family history, and genetics. Although personal genetic information is becoming increasingly important in healthcare, there is a lack of sufficient education in medical genetics among physicians and the general public. For example, pharmacogenomics is practiced worldwide by only a limited number of pharmacists, although most pharmacy colleges in the United States now include it in their curriculum. It is also increasingly common for genetic testing to be offered directly to consumers, who subsequently seek out educational materials and bring their results to their doctors. Issues involving genetic testing also invariably lead to ethical and legal concerns, such as the potential for inadvertent effects on family members, increased insurance rates, or increased psychological stress.

openSNP is an open source website where users can share their genetic information. Users upload their genes, including gender, age, eye color, medical history, Fitbit data. With a focus on user patient-led research (PLR), there is potential to redefine the way health research is conducted.

"It promises to be a vital supplement to standard research: it can focus on conditions that are neglected by standard research, such as rare diseases or side effects, and can draw on a broader range of data and deliver outcomes more rapidly. It can also be a way of realising valuable forms of social interaction and support in cases where members of a community conduct PLR together, for example, patients suffering from the same illness."

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Personalized genomics is the human genetics-derived study of analyzing and interpreting individualized genetic information by genome sequencing to identify genetic variations compared to the library of known sequences. International genetics communities have spared no effort from the past and have gradually cooperated to prosecute research projects to determine DNA sequences of the human genome using DNA sequencing techniques. The methods that are the most commonly used are whole exome sequencing and whole genome sequencing. Both approaches are used to identify genetic variations. Genome sequencing became more cost-effective over time, and made it applicable in the medical field, allowing scientists to understand which genes are attributed to specific diseases.

References

  1. 1 2 Church GM (2005). "The personal genome project". Molecular Systems Biology. 1 (1): 2005.0030. doi:10.1038/msb4100040. PMC   1681452 . PMID   16729065.
  2. ↑ Singer E (20 January 2006). "The Personal Genome Project. What would happen if genetic and medical records were freely available to anyone who wanted them". Technology Review.
  3. ↑ Duncan D (2010-06-07). "Scientist at Work: George M. Church - On a Mission to Sequence the Genomes of 100,000 People". The New York Times. Retrieved 2010-08-18.
  4. ↑ Abraham C (2012-12-07). "Would you make your DNA and health data public if it may help cure disease?". The Globe and Mail. Retrieved 2018-02-03.
  5. ↑ Sample I (2013-11-07). "Critics urge caution as UK genome project hunts for volunteers". the Guardian. Retrieved 2018-02-03.
  6. ↑ "Genom Austria launches as a new member of the Personal Genome Project". EurekAlert!. American Association for the Advancement of Science. 2014-11-25. Retrieved 2018-02-03.
  7. ↑ "Genome Korea in Ulsan Launched". Bio-IT World. 2015-11-25. Archived from the original on 2018-02-04. Retrieved 2018-02-03.
  8. 1 2 Addison F (2017-11-03). "Personal Genome Project Expands to China". Front Line Genomics. Retrieved 2018-02-03.
  9. ↑ "Personal Genome Project".
  10. ↑ Angrist M, Cook-Deegan RM (2006). "Who owns the genome?". New Atlantis. Washington, D.C. 11: 87–96. PMID   16789312. Archived from the original on 21 August 2007.
  11. ↑ Singer E (6 December 2007). "Your Personal Genome: George Church wants to sequence your genome". Technology Review. doi:10.2172/918689.
  12. ↑ Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, et al. (July 2012). "A public resource facilitating clinical use of genomes". Proceedings of the National Academy of Sciences of the United States of America. 109 (30): 11920–7. doi: 10.1073/pnas.1201904109 . PMC   3409785 . PMID   22797899.
  13. ↑ Kovalevskaya N (2016-11-16). "DNAdigest interviews Personal Genome Project: UK - DNAdigest.org". DNA digest. Retrieved 2018-02-03.
  14. ↑ "Veritas Genetics Launches $999 Whole Genome And Sets New Standard For Genetic Testing"
  15. ↑ Mao Q, Ciotlos S, Zhang RY, Ball MP, Chin R, Carnevali P, et al. (October 2016). "The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes". GigaScience. 5 (1): 42. doi: 10.1186/s13742-016-0148-z . PMC   5057367 . PMID   27724973.
  16. ↑ Reuter MS, Walker S, Thiruvahindrapuram B, Whitney J, Cohn I, Sondheimer N, et al. (February 2018). "The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants". CMAJ. 190 (5): E126–E136. doi:10.1503/cmaj.171151. PMC   5798982 . PMID   29431110.
  17. ↑ Abraham C (2018-02-03). "Cracks in the code: Why mapping your DNA may be less reliable than you think". The Globe and Mail. Retrieved 2018-02-03.
  18. ↑ "Personal Genome Project-Lumosity Study". Wyss Institute. Harvard University. 10 October 2017.
  19. ↑ Hysolli E (9 March 2017). "Brain-training app creators join in the genetics game". The Daily Gazette. Harvard University.
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