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Back To Vidyya Twenty Questions About DNA Sequencing

(And The Answers)

1. Q: What is DNA?

A: The hereditary substance found in all living cells is deoxyribonucleic acid, or DNA. It is composed of four different chemical subunits, called bases, that are represented by the letters A, T, C, and G. The order of the bases provides coded instructions for everything a cell does. Determining the order of the bases along the DNA strand is called sequencing.
2. Q: Whatís a genome? A: Genome refers to the complete set of genetic instructions carried within a single cell of an organism. In most cases, the DNA in each cell is the same. Every living thing has a genome, though they can vary from quite small (a few thousand bases for some viruses) to quite large. 3. Q: How many bases, or letters, are in the human genome? A: About three billion. If all the letters were printed out, it would fill a stack of books as high as the Washington Monument. The mouse genome also has 3 billion bases. A worm has 100 million, a fruit fly has 160 million, and the yeast used in making bread has 12.5 million. 4. Q: Why do scientists want to sequence the human genome? A: DNA sequence contains the instructions for everything a cell does, from the moment of conception until death. Changes in DNA spellings can increase your chances of developing an illness, protect you from getting sick, or predict the way your body will handle medicines. Once scientists can read the DNA instruction book, they will be able to better understand and treat diseases. 5. Q: What is the Human Genome Projectís plan for human DNA sequencing?
A: The Human Genome Project began sequencing the DNA of laboratory organisms to help refine the technology needed to begin the larger, more complex human genome. In addition, we hope to understand human genes by comparing human DNA with DNA from mice, flies, roundworms, and yeast. These comparisons make the human sequence much easier to understand. Two years ago, the first funds were awarded to begin sequencing human DNA. Sequencing goals of the Human Genome Project 1998-2003 plan include increasing capacity to deliver a complete human genome sequence by the end of the year 2003, two years earlier than originally planned.
6. Q: How much human sequence has been produced so far?
A: A working draft of the complete Genome was finished in June, 2000. Scientists expect to have a completely finished sequence of the human genome by the end of 2001. All sequence produced by Human Genome Project scientists is in a freely accessible database. Celera Genomics, a privately held company, is responsible for a portion of the genomic mapping. Information from this company is not in the public domain.
7. Q: How much has it cost?
A: In 1990, when the Human Genome Project began, DNA sequencing cost $10 per base. The process has been streamlined and automated and better machines read the sequence fragments quickly and more cheaply. These advances, together with sophisticated computer programs that help interpret the data, have dramatically reduced the cost to roughly 50 cents per base for high-quality "finished" sequence. This figure covers the cost of shotgun sequencing, as well as the cost of closing the gaps and finishing the sequence. Altogether, the NIH genome project has spent about $84 million on human DNA sequencing as of June 1998.
8. Q: What does "shotgun" sequencing mean?
A: Shotgun sequencing refers to a method that uses enzymes to cut DNA into hundreds (or thousands) of random bits. That's necessary because today's automated sequencing machines, though faster and cheaper than older "by-hand" methods, still decipher only relatively short DNA fragments about 500 bases long. Scientists then have to piece the sequenced fragments back together, bit by bit, so it looks like the original genome. Computers usually perform that step. The Human Genome Project shotgun approach is applied to cloned DNA fragments that already have been mapped so that it is known exactly where they are located on the genome, making assembly easier and much less prone to error.
9. Q: How much has the federal government spent on the Human Genome Project so far?
A: Almost $1.5 billion since it began in 1990. That includes funding for both the Department of Energy and the National Institutes of Health programs, which have used those funds to develop detailed genome maps, identify and map half of the 80,000 or so human genes, sequence the genomes of several laboratory organisms, develop new technologies, and fund social impact studies.
10. Q: What else does the Human Genome Project do?
A: The project has developed maps of the human genome, that is, a set of closely spaced molecular landmarks to guide gene hunters. Project scientists also are mapping the genome of the laboratory mouse. Genome researchers have identified almost half of the 80,000 or so human genes, and completed the DNA sequence of two important microbial genomes, the bacteria E. coli and baker's yeast. By the end of the year, the first genome sequence of a multi-celled animal (the roundworm) will be completed.

As new human sequence is deposited, scientists are using this information to understand how genes function, how genetic material varies between people, and how certain genetic variations can predispose to disease. Just as important, the public Human Genome Project spends 5 percent of its research budget on studies of the ethical, legal, and social implications of new genetic technologies. Funding also is provided to improve current sequencing technology.


11. Q: How will scientists benefit from the sequence provided by the Human Genome Project?

A: First, the Human Genome Project will provide a truly complete and highly accurate reference genome sequence. That level of completeness is necessary to provide researchers with the best possible tool for understanding the function of genes and their role in human health and disease. Second, the public effort will sequence mapped DNA fragments derived from known locations in the genome, so scientists can be certain which region they are studying. Finally, the public project will post its sequence in a freely accessible database within one day of obtaining the data, allowing all scientists immediate access to the data.
12. Q: Whose genome is being sequenced?
A: The Human Genome Project is sequencing DNA collected from a number of volunteers whose identity will remain secret to protect their privacy.


13. Q: Who has access to the human DNA sequence?

A: Scientists around the world participating in the public sequencing effort have agreed to submit their data to public databases within one day of verification. That means any scientist, whether at a university, corporation, or government lab, can log on by computer and have full access to the sequence data.


14. Q: What does "finishing" the sequence mean?

A: Some parts of the human genome are easier to sequence than others. One strategy is to sequence the easy parts and leave the rest. Though that would provide some useful data, it will leave gaps in areas that are likely to contain important biological information. The Human Genome Project has promised to fill in the gaps, or "finish" the complete human DNA sequence. 15. Q: If only part of the genome contains genes, why sequence the whole thing? A: The more we study DNA, the more we understand how it carries out its amazing work. Besides the part that codes for protein, genes are made up of several parts that control their activity. Sometimes all the parts are clustered in the same DNA neighborhood, but other times, they may be scattered far from each other. Some parts are very easy to spot and some aren't. So, having a complete genome sequence that includes all of a gene's parts is the best way to study how they work. Already we have learned that critical clues to cancer, diabetes, and osteoporosis lie in the areas of the genome that do not code for proteins. 16. Q: What areas of the sequence will be finished first? A: Efforts to produce a high-quality, accurate, finished sequence will focus initially on those areas in the genome that contain the most genes. The sooner the gene-rich areas are sequenced, the faster researchers around the world can use that important information to study disease. 17. Q: What is "quality" sequence? A: High-quality sequence is complete, with all the difficult areas "finished." Further, the international community of Human Genome Project researchers has adopted a "4A" standard for quality sequence:
    The sequence must be accurate, that is, the DNA spellings must be correct. The publicly funded genome project will ensure accuracy of 99.99 percent or better.
    The sequence must be assembled. Large-scale DNA sequencing relies on the accurate assembly of smaller lengths of sequenced DNA into much longer regions so it reflects the original piece of genomic DNA.
    Because human DNA sequence must also be affordable, a portion of the genome project research budget funds technology development to reduce costs as much as possible.
    Finally, high-quality, finished DNA sequence must be accessible. Human Genome Project sequence data is deposited in public databases on a daily basis.
Other measures of quality reflect how useful the sequence is to researchers performing experiments. 18. Q: Why did they decide to speed up the public sequencing project? A: The sooner the public effort to sequence the human genome is complete and deposited in a publicly accessible database, the sooner it will benefit all scientists working to understand and treat disease at a molecular level. Sequencing technology has improved dramatically in recent years and pilot sequencing projects have been a tremendous success. The time is ripe to accelerate full-scale sequencing of the human genome. 19. Q: What happens after the genome is sequenced? A: Completing the DNA sequence of the human genome will provide scientists with a tool for genetics akin to the Periodic Table of the Elements. Instead of 100 chemical elements, though, the genome contains about 80,000 elements, the human genes. Once you have the table of the elements, you can begin to figure out how the genes function, how genes interact, and how they contribute to common disorders. 20. Q: Can information about my own DNA be used to harm me in any way? A: Studies have shown that people have lost jobs and health insurance and suffered other types of discrimination based on their genetic makeup. A very important goal of the Human Genome Project is to ensure that new abilities to read and interpret genetic information are used to benefit people not to harm them. That's why the project has set aside 5 percent of its research budget to study and address the ethical, legal, and social implications (ELSI) of genome research. While those studies have provided policy makers with valuable knowledge for developing laws to prohibit genetic discrimination in health insurance and employment, and to protect the privacy of personal genetic information, much still needs to be done in both the legislative and research arenas to ensure that genetic information is used safely and appropriately.
 
 

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Editor: Susan K. Boyer, RN
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