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The Human Genome

• There are approximately 20,000 genes in the human genome.
  
• The human genome possesses about 3 x 10⁹ nucleotides.
  
• Genes are 1-200,000 kb in size (average 10 kb).
  
• Genes have exons (coding sequences) and introns (noncoding sequence found between exons).
  
• It includes 22 autosomes plus X and Y (sex) chromosomes.
  
• Genes are arranged linearly on chromosomes.
  

Table I Perspectives on the Number of Genes and the Genetic Distance in the Human Genome

 

Figure 15.1

Genetic and physical map of the X chromosome. Association of a trait with a position on a given chromosome is a critical step in gene identification. The relationship between genetic loci is measured on a genetic map as the frequency of recombination events between the loci. On physical maps relationships between loci are measured in nucleotides. The genetic and physical maps have the same linear sequence although the distances are not correlated. After narrowing the chromosomal localization, a candidate gene can be localized on a genetic map that contains marker genes known to map to that chromosomal region. Subsequently, the gene can be localized on a physical map that allows delineation of its position with a higher degree of resolution.

 

 

 

Table II Gene Identification Enables Therapeutic and Diagnostic Possibilities by Increased Understanding of Protein Function, Mutation Identification, and Expression Patterns

There are Four Major Routes to Gene Identification

1. Functional Cloning - know the function of the gene, purify protein, clone
   
2. Candidate Gene - identify a potential candidate gene based on mechanism of the primary pathology
   
3. Positional Cloning - identify gene without prior knowledge of gene function, solely based on mapping
   
4. Positional Candidate - identify Expressed Sequence Tag (EST) or cDNA and compare its chromosomal localization with a disease locus map
   

Table III Examples of Gene Identification
	Functional Cloning	Candidate Gene	Positional Cloning	Positional Candidate
	Identification of the target gene based on knowledge of its function.	Survey of previously identified genes that seem to perform the function altered in the disease.	Identification of the gene based on its map position in the genome.	Identification of a gene based on its map position and on the availability of candidate genes mapped to the same region.
Human	Knowledge of the phenylalanine hydroxylase amino acid sequence and screening of cDNA libraries using degenerate oligonucleotides.	Identification of mutations in the rhodopsin gene from patients with retinitis pigmentosa.	Mapping of the Duchenne muscular dystrophy locus to Xp21 and cloning of the dystrophin gene from this region.	Mapping of both the Marfan syndrome locus and the fibrillin gene to 15q and identification of mutations in the fibrillin gene from patients with Marfan syndrome.
Mouse	Screening of an expression library with antibodies to identify the tyrosinase gene.	Identification of mutations in the β subunit of rod cGMP phosphodiesterase in the mouse retinal degeneration mutation.	Mapping of the shaker-1 locus and cloning of the mutated myosin VII gene from the critical region.	Mapping of the leptin receptor to the region of the diabetes mutation and identification of abnormal splicing of this gene in diabetic mice.

Homologous Recombination

1. Two homologous chromosomes pair and crossover events (recombinations) occur between homologous chromatids.
   
2. Homologous chromosomes segregate.
   
3. Duplicate chromosomes segregate yielding cells containing only one copy of each homologous chromosome.

Figure 15.2

 

Figure 15.3

A recombination frequency of 1% (1 centiMorgan) means that two genes recombine on average once in every 100 meiotic events. This is equal to about 1000kb (1 Mb) of DNA sequence.

Analysis of recombination frequencies among genes establishes their linear order and the distance between them.

Genes that are close to each other on a chromosome tend to be inherited together. This allows for the use of polymorphic loci near a candidate gene to be used as markers to examine whether they cosegregate with a phenotype (see linkage analysis below).

Association of a marker allele with a disease gene. A mutation (blue line) takes place that produces a disease gene. This mutation occurs in a DNA background that contains other polymorphisms. During subsequent meiotic events allelic markers that are further away from the mutation will segregate away from it, while those that are close by will cosegregate, allowing an association between the disease gene and the cosegregating polymorphic markers. The associated region will depend on the number of meiotic events occurring after the mutation and the probability of recombination events in this stretch of DNA.