I: What Is the Genome Project?
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Mapping the Genome exons, and noncoding regions, or introns. I: 71/)iatLi the We’re making progress, but the problems are still unsolved. On the other hand, most participants at the 1986 meeting e !13t9ject? agreed that a major effort in genetic and !2m physical mapping was appropriate, That conclusion was confirmed by the report, published in 1987, of the DOE’s Health Bob Moyzis: This discussion is meant to Now many of us, including me, thought and Environment Research Advisory address scientists. particularly physical the straight sequencing approach was Committee. Many individuals with scientists, who know very little about crazy because it ignores biology. Yes, a physical-science background do not the Human Genome Project and may we can read the sequence, pick out understand that a DNA sequence with our have many misconceptions about it. a gene, and use the genetic code to a genetic map is nearly useless. Let’s share our perceptions of how this translate the coding regions of the gene project got started. Why are we doing into the sequence of amino acids that David Botstein: Most of us were it, and why did the idea of taking on composes the protein. But then we run unaware of the DOE workshop and the entire human genome gain support into a big problem: How do we know report, but the idea of understanding in the scientific community? what the protein does? At present we the human genome stirred LLpso much have no way to determine the function of interest that the National Research David Botstein: The answers are a protein from its amino-acid sequence Council organized its own comtnittee complicated because the human genome alone. Wally Gilbert likes to say that to assess the feasibility of the Project. is largely unexplored territory. It’s if we had a catalog of all the protein Some members of that committee are tremendously information-rich, and amino-acid sequences, we would be here—Maynard Olson, Lee Hood, and differenl people have had different able to deduce protein functions. Some I. We independently recommended ideas about the best way to go about day we may get there, but right now that the Human Genome Project go finding out what’s there. The initial that’s science fiction, not science. ahead—but, as Bob pointed out, in an proponents of the Genome Project, entirely different manner than originally especially Charles DeLisi in the De- Bob Moyzis: Interpreting protein func- proposed. We said, “Let’s postpone partment of Energy [DOE], said, “The tion is a problem. But the straight se- sequencing the genome until we develop human genome is the blueprint for the quencing approach, as initially proposed, better sequencing technology and focus development of a single fertilized egg, presented other serious difficulties. on developing the tools, the genetic and into a complex organism of more than First and foremost, the technology to physical maps, needed to interpret the 10[3 cells. The blueprint is written in a sequence the whole genome was just not sequence once we have it. Let’s build coded message given by the sequence of available. That was the conclusion of some biology into this effort. ” nucleotide bases—the As, Cs, Gs, and Ts the human genome workshop sponsored that are strung along the DNA molecules by the DOE in 1986 in Santa Fe, New Bob Moyzis: But we still have a in the genome. So let’s read the entire Mexico, and it is true today. We’re problem of perception in the scientific sequence from one end to the other, not too bad at reading stretches of DNA community. The conclusion of every put the whole thing in a computer, and 10,000 bases long—the average length of meeting and report on the Human give it to the theoreticians and computer a gene—but present technologies are still Genome Project has been that the goal is analysts to decode the instructions. ” too labor-intensive and too expensive notto immediately sequence the entire And what instructions does the human to think of sequencing the 6 billion human genome. That idea died an early genome contain’? Everyone who has bases in the human genome. However, death. But every negative report about taken high-school biology knows that the technology is changing rapidly, a the Project says that we are going to be DNA contains genes, that genes are the point we’ll return to later. We’re also doing this mindless sequencing. coded messages for making proteins, not certain how to pick out the genes and that proteins carry out all of the from all the other DNA sequences in Maynard Olson: Critics often do not functions of an organism. So why not the genome or how to sepamte the gene take the time to understand what they begin by reading the sequence’? sequences into protein-coding regions, or are criticizing. 71 Mapping the Genome Norton Zinder: I’d like to go back to genetic traits, which are the unseen an earlier point, that different people messages in the genetic material, In the are interested in different aspects of the case of humans, looking for Mendelian genome. The most ambitious interest patterns of inheritance is often the is a very long-term goal-to understand only method we have for connecting the whole blueprint. But there’s a large phenotype with genotype. group of people, and maybe they ‘re in the majority, who are more practical. Bob Moyzis: Mendel’s laws apply only They are interested in understanding to discrete variable traits-for example human disease, and they support the having or not having unusually short Genome Project because the maps that fingers, a trait called brachydactyly. will be developed are just tbe tools Because those traits [normal or short needed to find the genes responsible digits] are inherited according to the for inherited diseases, Victor McKusick ratios predicted by Mendel, geneticists has compiled a catalog of over 4000 can infer a number of things. First, thaf such diseases and many of them are digit length is determined by a single pair *vo/.toll”Zill[[cl Mendelian, which means that they of genes, one inherited from each parent, Until recently people are each caused by a single mutant and second that the brachydactyly gene gene. People are very excited about the has two versions, or alleles, say A and tried to guess which prospect of finding those genes. a, where A is the rare dominant allele protein from among the that causes the anomalous digit length. Bob Moyzis: It’s ironic that the genetic- tens of thousands of mapping community had little to do, I Most variable traits are not Mendelian. human proteins was feel, with initiating the Human Genome They result from the complex interaction Project, recent books documenting the of many genes. On the other hand, many produced by the mutant history of this project notwithstanding. inherited diseases are the result of a sin gene . the new Once the Project gained momentum, gle mutant gene. How do we determine however, it was clear that the human that? We can ‘t do contro[leci-breed ing approach is to avoid genetic-mapping community would be experiments and analyze thousands of playing around with lots a primary user of the maps, particularly offspring as Mendel did. But if we trace in the search for the genes causing the disease through the generations of of proteins and instead the Mendelian diseases that Norton fdmilies affected by the disease, we can to find the responsible just mentioned. Our audience may use statistical analysis to infer from a be surprised to learn that the method relatively small sample whether a single gene in the DNA. used to infer that a single gene is the gene-pair is involved, and if so, whether cause of an inherited disease goes all the mutant gene, the allele that causes the way back to Mendel. Despite all the disease, is dominant or recessive, the advances we’ve made in molecular [For a discussion of Mendel’s laws, see genetics, Mendel’s laws and his indirect “Understanding Inheritance.”] methods of inference still provide the basic methods for much of what is done Norton Zinder: Yes, but how do we in genetics. go further toward understanding the disease? Until recently people tried to David Botstein: Mendel identified the guess which protein from among the basic unit, the quantum, of heredity, tens of thousands of human proteins was which is the gene. Mendel’s laws are produced by the mutant gene. They the quantum mechanics of genetics. would use various biochemical and They provide a quantitative link between cytological methods to compare normal physical traits, the traits we see, and and disease-affected tissues, but often LOs Almrw.j Scicncr h-uimher 20 I99.2 Mapping the Genome the dise~se gives no clue as to what the combinations of the two tmits in proteins might be involved. The new the offspring tell us whether or not approach is to avoid playing around the two gene pairs are on the same with lots of’ proteins and instead to chromosome pair. [See “Classical find the responsible gene in the DNA, Linkage Mapping,”] sequence the gene, determine its protein product, and then try to determine what The interesting thing is that some frac- the protein does. tion of the time the alleles—particular forms of the two genes-on a given How do we find the gene responsible chromosome are nor co-inherited. How for a Wndelian trait? Until 1980 we do they break apart? During the forma- had no practical method.