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numbering of the regions and the location in region 21q in which marker D17S74 is located. The terminology of the marker is that of section 74 of chromosome 17. This marker correlated to the position of the BRCA1 gene.
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early onset breast cancer is segregating. At the bottom of the gure is a gel of the various bands produced, showing the alleles of D17S74, marked A E in decreasing size of fragment probed. The individuals in the pedigree are shown directly over their lanes in the gel. The original parents were dead (diagonal line) and thus were not typed. The mother, two of her daughters, and two of her granddaughters were diagnosed with breast cancer in ages ranging from twenty-three to forty ve years of age (yellow). Note that in every case of breast cancer, the woman has the B allele of marker D17S74. It is this correlation that localized the breast cancer gene to that region of the chromosome. D17S74 was the 183rd marker M. King and her colleagues studied; the other markers showed no correlation with breast cancer. (Reprinted with permission from J. M.
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Hall et al., Linkage of Early-Onset Familial Breast Cancer to Chromosome 17q21, Science, 250:1684 89, 1990. Copyright 1990 American Association for the Advancement of Science.)
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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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13. Genomics, Biotechnology, and Recombinant DNA
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Mapping and Sequencing the Human Genome
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Figure 13.41 The physical location of a gene or marker can
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be found by probing chromosomes with a complementary DNA sequence that has a speci c uorescent compound bound to it. When activated, the probe is seen (bright yellow spots) in a laser scanning confocal microscope. The chromosomes are counterstained with propidium iodide, which makes them uoresce red. In this case, the probe has located a sequence on human chromosome 11. ( Peter Menzel/Photographed at Yale
University Medical School.)
to sequencing, bacterial arti cial chromosomes (BACs) were used. The bacterial arti cial chromosomes are derivatives of the fertility factor (F factor, see chapter 7). They have properties of stability and homogeneity that make them more compatible with automated sequence techniques. To begin sequencing, each individual chromosome is broken up into overlapping segments of about 150,000 bp in a BAC library. Each BAC is then digested into smaller pieces that are cloned in cosmids or P1 phages digested into smaller pieces for sequencing.
Before we de ne the techniques further, we should mention that we are not dealing with just one map of the genome, but several different kinds of maps. Although the ultimate goal was the complete DNA sequence of the genome, yielding the exact location of every gene, we needed to go through several stages to get there remember, we are trying to keep track of 3.3 billion bases. We are familiar with the genetic linkage map of chromosomes described in chapter 6. These maps are called classical linkage maps; they de ne distances in recombination frequencies. A modern linkage map is one that uses RFLP markers along its length instead of genes. There is also a physical map, in which distances are in physical units of base pairs. These maps can be of microsatellite markers or of sequence-tagged sites (STSs). Sequence-tagged sites are DNA lengths of 100500 base pairs that are unique in the genome. They are created by polymerase chain reaction ampli cation of primers obtained by sequencing segments of the genome. The primers are then tested to be sure the sequence is unique. About 50% of attempts yield sequencetagged sites. The physical map can also be marked off in differences among individuals that amount to changes in single base pairs. These differences are called singlenucleotide polymorphisms (SNPs pronounced snips ). These are located about every one thousand bases along the human genome. These single-nucleotide polymorphisms are expected to be especially useful in keeping track of differences among individuals in genes responsible for diseases. RFLPs, microsatellite markers, STSs, and SNPs allow us to keep track of BACs and cloned pieces in cosmids and P1 phages. However, as we locate various DNA pieces, we will be building up continuous regions of a chromosome by overlapping these pieces. These overlapping, contiguous clones are referred to as contigs. This process is repeated chromosome by chromosome. In other words, we are creating a library of overlapping clones that cover the complete length of each chromosome. In essence, we are putting together a linear jigsaw puzzle. Contigs are created by comparing the segments that clones have in common, if any ( g. 13.42). From shared segments, we can infer which parts of the clones overlap. Through this process, contigs of parts of the chromosome can be built up ( g. 13.43). Later, contigs comprising part of a chromosome can be ordered by taking an end clone of a completed contig and using it as a probe to begin chromosome walking to nd an end clone of a nearby contig ( g. 13.44). For example, let s begin with a BAC from chromosome 7 of 150,000 base pairs long with three sequencetagged sites located along its length. We can determine neighboring BACs by shared sequence-tagged sites. The BAC is then digested and cloned into cosmids. The
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