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Term Paper on the Human Genome Project (HGP)

INTRODUCTION:

Human Genome project (HGP) is an international project which is coordinated by United States Department of Energy (DOE) and National Institute of Health (NIH). The main aim of this project is to determine the sequence of every nucleotide in the human genome and to identify all the genes contained with in the genome. It was formally started in 1990 and was intended to finish the working reference genome by 2005 but due to the technical advancements, it was finished 2 years earlier i.e. in 2003. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner; additional contributions came from Japan, France, Germany, China, and others.

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The initial approach of HGP was to break the genome into pieces as it was too long (6 billion nucleotides) to sequence as a whole, determine the order of nucleotides and then to determine the nucleotide sequence for each piece. But a private company split from the public project and began to sequence the nucleotides with a view to patent them. This made HGP to change their approach and to provide the nucleotide sequence for each piece even before knowing their order.

HGP’s most significant aspect is that it reverses the way in which science is normally done today. Generally researchers take a specific problem and then try to find the cause for it like the DNA sequence of a gene or genes. But HGP will give the order of the nucleotides in the human genome, identify putative genes but will not identify their functions. In fact it may take decades to identify the gene products and to understand how they interact with each other.

HGP is also involved in determination of nucleotide sequence for the genomes of other organisms, mostly lab animals. Because their genomes have many similarities to the human genome and knowing their sequences will help researchers to identify genes and their functions in human.

(Tim Williams, ‘Human Genome Project and its ethical, legal and social implications).

AIMS OF HGP:

Human DNA sequencing was completed in the spring of 2003. In June 2000, rough draft of human genome was completed. Human genome Project Goals and completion dates are shown in table 1.

Human Genome Project Goals and Completion Dates

Area	HGP Goal	Standard Achieved	Date Achieved
Genetic Map	2- to 5-cM resolution map (600 – 1,500 markers)	1-cM resolution map (3,000 markers)	September 1994
Physical Map	30,000 STSs	52,000 STSs	October 1998
DNA Sequence	95% of gene-containing part of human sequence finished to 99.99% accuracy	99% of gene-containing part of human sequence finished to 99.99% accuracy	April 2003
Capacity and Cost of Finished Sequence	Sequence 500 Mb/year at < $0.25 per finished base	Sequence >1,400 Mb/year at <$0.09 per finished base	November 2002
Human Sequence Variation	100,000 mapped human SNPs	3.7 million mapped human SNPs	February 2003
Gene Identification	Full-length human cDNAs	15,000 full-length human cDNAs	March 2003
Model Organisms	Complete genome sequences of E. coli, S. cerevisiae, C. elegans, D. melanogaster	Finished genome sequences of E. coli, S. cerevisiae, C. elegans, D. melanogaster, plus whole-genome drafts of several others, including C. briggsae, D. pseudoobscura, mouse and rat	April 2003

Functional Analysis

Develop genomic-scale technologies

High-throughput oligonucleotide synthesis 1994 DNA microarrays 1996 Eukaryotic, whole-genome knockouts (yeast) 1999 Scale-up of two-hybrid system for protein-protein interaction 2002

Table 1

(Ref: Francis.S.Collins, Michael Morgan, Arisitdes Patrinos)

The main aims of this project were,

1. Mapping and Sequencing the Human Genome:

- To generate a working draft of 90%of the human genome, Obtain a complete, high quality genomic sequence and to make all this data available to the public for free.

- By developing highly efficient new sequencing technologies which is 2-3% more efficient than current technology, HGP aims to create a long-term and more sustainable sequencing capacity.

2. Mapping and Sequencing the Genomes of Model Organisms:

- To obtain a complete genomic sequencing of C.elegans by 1998, Drosophila by 2002 and mouse by 2008.

Researchers noticed that clues can be obtained to identify and understand the human genes by studying the sequence of genes in nonhuman genomes. Complete genomic sequences have already been obtained for bacteria E.coli and yeast S. cerevisiae. The work has been extended to sequencing of genomes of the roundworm, fruit fly, and mouse.

3. Data Collection and Distribution:

- To improve the current databases and to develop new databases and better tools for data generation, capture and for comprehensive functional studies.

-To expand the support for the current approaches and innovative technologies

Researchers found more investments in current and new databases are important for the success of HGP and also to the future usefulness of the data. The data collection tools are to be designed analogous to the model organism databases with links to phenotypic information.

4. Ethical, Legal, and Social Considerations:

Rapid advances in the filed of genetics and its applications in normal life pose a new problem for ethical and policy issues for individuals and society. HGP aims to identify and address these implications through ELSI programs.

- To analyse and to address the implications of determining DNA sequence information to the society.

- To facilitate safe and effective integration of genetic technologies and also to educate society about genomics in non-clinical and research settings.

5. Research Training:

Planners found that future genomics researchers need training in interdisciplinary areas that include biology, computer science, engineering, mathematics, physics, and chemistry. In addition scientists also need some management skills for leading large data-production efforts. To cater all these needs HGP aims to nurture the genomic scientists and to establish their career paths and increase the number of scholars who has knowledge in genomics, ethics, law or the social sciences.

6. Technology development:

HGP aims to develop methods to detect different type of variations that occur in genomes especially single nucleotide polymorphisms (SNP’s) that occur about once every 1000 bases as researchers believe SNP maps help them to identify genes complex diseases such as cancer, diabetes, vascular disease, and some forms of mental illness. These associations are very hard to make using the conventional method of hunting the genes as a single gene may contribute very less to disease risk. This project aims to develop technologies which can rapidly identify the DNA sequence variants.

7. Technology Transfer:

Many new private firms have already been established in order to develop applications to

genome research and also collaborations between government funded agencies and private firms have increased. HGP aims to encourage and enhance technology transfer both into and out of centers of genome research.

(Ref: Human Genome Project Goals

http://www.ornl.gov/sci/techresources/Human_Genome/hg5yp/hlight.shtml) 

OUTCOMES OF HGP:

Courtesy: U.S. Department of Energy Human Genome Project.

The current and most potential outcomes of the HGP are in the fields of

Molecular Medicine:

HGP is starting to show its profound impacts on biomedical research. Because of the detailed availability of the genome maps researchers are able to associate genes with dozens of genetic conditions, including myotonic dystrophy, fragile X syndrome, neurofibromatosis types 1 and 2, inherited colon cancer, Alzheimer's disease, and familial breast cancer. New era of molecular medicine is characterized less by treating for the symptoms and to concentrate more on the root cause of the disease. Microbial genomics help pharmaceutical researchers to gain a thorough understanding of how pathogenic microbes cause disease. Sequencing these pathogenic microbes’ help to reveal the vulnerabilities for the disease and identify new drug targets.

Implications of HGP on molecular medicine are mainly focused on

• Improved diagnosis of disease

• Earlier detection of genetic predispositions to disease

• Rational drug design

• Gene therapy and control systems for drugs

Energy and Environmental Applications:

In 1994, DOE initiated the Microbial Genome Program to sequence the genomes of bacteria useful in energy production, environmental remediation, toxic waste reduction, and industrial processing. Information obtained from the characterization of complete microbial genomes will lead to development of energy related biotechnologies such as photosynthetic systems, microbial systems that can work in extreme environments and can readily metabolize on available renewable sources and waste materials. The expected benefits also include development of diverse new products, processes, and test methods that will open the door to a cleaner environment. Microbial genome sequencing will help lay a foundation for knowledge that will ultimately benefit human health and the environment. Using microbial genomics new energy sources (biofuels) can be created, environmental monitoring techniques to detect pollutants can be carried out,

Risk Assessment:

Researchers know that genetic differences make some people more susceptible to radiation and others resistant to such agents. Understanding the genome sequence will have an enormous effect how risks are posed to individuals by exposure to toxic agents.

HGP helps to assess the health damage and risks caused by radiation exposure, including low dose exposures and exposure to mutagenic agents and cancer causing toxins. HGP may reduce the likelihood of heritable mutations.

DNA Forensics (Identification):

DNA sequencing enables to identify the organism as the sequences are unique to that species. To identify the individuals, DNA fingerprints are used which uses the genetic material of the individual. HGP allows to

• Know the potential suspects whose DNA matches with that of the evidence left at crime scenes and to exonerate the wrongly accused person

• Establish paternity and other family relationships by comparing the child DNA with that of the parents.

• Can be a big help to wild life officials as it can identify endangered wild species.

Agriculture, Livestock Breeding, and Bio-processing:

Knowing plant and animal genome helps researchers to make plants and animals which are drought resistant, high yielder and disease resistant. This will help the producers to reduce cost on agriculture and farming and provide consumers more nutritious and pesticide free food. Biopesticides are manufactured which does not use any harmful chemicals.

Ref: Potential Benefits of Human Genome Project Research 

Ethical, Legal, Social, Implications OF HGP:

The U.S. Department of Energy (DOE) and the National Institutes of Health (NIH) devoted 3% to 5% of their annual Human Genome Project (HGP) budgets toward studying the ethical, legal, and social issues (ELSI) surrounding availability of genetic information. This has become the world’s largest bioethical program and has become a model for many such programs around the world.

Some of the Ethical issues surrounding the HGP are:

Genetic manipulation for non-medical reasons can be an ethical dilemma.

Use of genetic manipulation to alter the somatic cells to treat disease is generally considered as ethical because risks are localized to a single person. Alterations in germline involve more significant issues since risks are carried across next generations.

Ethical permissibility of genetic manipulation reflects mainly around two situations

1. Distinction between somatic cell and germline intervention, and

2. Distinction between therapeutic and enhancement engineering

(Ref: Marion L. Carroll and Jay Ciaffa)

Future generations may feel limited by choices made regarding their genetic traits.

Future generations may not feel happy with the choices made by their parents regarding their physical, cognitive or emotional traits. There is a danger posing their social-historical trends and biases which could leave genetic limitations on future generations.

(Ref: Marion L. Carroll and Jay Ciaffa)

Should mandatory genetic screening be rejected in all situations?

Mandatory genetic screening of the adult population may pose a serious ethical issue about the person’s privacy and their liberty. In the justice system longstanding practices of DNA fingerprinting and other testing are already in practice. People may not be ready for more calls for mandatory genetic testing.

(Ref: Marion L. Carroll and Jay Ciaffa)

Some Social concerns of HGP:

Fairness in the use of genetic information:

Issues like who should have access to genetic material and its use may arise.

Once genetic basis for disease and other phenotypic traits were pinpointed what parameters are to be set for the acquisition and use fair use of genetic material? Genetic screening can be taken as key with the consent of a patient and it is considered ethical. Sometimes even this may cause some ethical challenges like knowledge of the serious disease with which one or more can be affected can create difficult situations for both patients and their families.

(Ref: Marion L. Carroll and Jay Ciaffa)

Privacy and confidentialityof genetic information:

Issues like who should own genetic material and control it, issues like who has the authority to know genetic material

An example of how ELSI research has helped to inform public policy can be known through a fact that more than 40 states in U.S. have passed genetic nondiscrimination bills (Ref: Francis.S.Collins, Michael Morgan, Arisitdes Patrinos)

REFERENCES:

1. Tim Williams, ‘Human Genome Project and its ethical, legal and social implications’.

http://dsp-psd.pwgsc.gc.ca/Collection-R/LoPBdP/BP/prb0008-e.htm viewed on April 8, 2008.

2. Francis.S.Collins, Michael Morgan, Arisitdes Patrinos, The Human Genome Project-Lessons from Large scale Biology, Science300, pg286 (2003).

3. Human Genome Project Goals

http://www.ornl.gov/sci/techresources/Human_Genome/hg5yp/hlight.shtml viewed on April 8, 2008.

4. Potential Benefits of Human Genome Project Research

http://www.ornl.gov/sci/techresources/Human_Genome/project/benefits.shtml viewed on April 9, 2008.

5. Marion L. Carroll and Jay Ciaffa, The Human Genome Project: A Scientific and Ethical Overview

http://www.actionbioscience.org/genomic/carroll_ciaffa.html viewed on April 9, 2008 

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