KAPLAN_USMLE_STEP_1_LECTURE_NOTES_2018_BIOCHEMISTRY_and_GENETICS
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Part II ● Medical Genetics
•Heritability represents the contribution of genes to the liability curve. Heritability can be estimated by twin studies and adoption studies.
•For many common diseases, subsets of cases exist in which genetic factors play an especially important role. These subsets tend to develop disease early in life (e.g., BRCA1 and BRCA2 mutations in breast cancer), and they often tend to have a more severe expression of the disease.
•In some cases, genes involved in the less common, strongly inherited subsets of common diseases (in cancer, specific oncogenes and tumor suppressor genes) are also involved in the common noninherited cases (but in different ways, such as a somatic mutation instead of a germline mutation).
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Part II ● Medical Genetics
Answers
1.Answer: D. Because the trait in this case is 5 times more common in males in females, it means that males are found lower on the liability curve. Fewer factors are needed to cause the disease phenotype in the male. Therefore, a female with the disease is higher on the liability curve and has a larger number of factors promoting disease. The highest risk population in this model of multifactorial inheritance would be the sons (the higher risk group) of affected mothers (the lower risk group). The affected mother had an accumulation of more disease-promoting liabilities, so she is likely to transmit these to her sons, who need fewer liabilities to develop the syndrome.
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Recombination Frequency |
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Learning Objectives
Solve problems concerning polymorphic markers and linkage analysis
Demonstrate understanding of determining recombination frequency accurately
Explain information related to LOD scores
OVERVIEW
An important step in understanding the basis of an inherited disease is to locate the gene(s) responsible for the disease. This chapter provides an overview of the techniques that have been used to map and clone thousands of human genes.
POLYMORPHIC MARKERS AND LINKAGE ANALYSIS
A prerequisite for successful linkage analysis is the availability of a large number of highly polymorphic markers dispersed throughout the genome. There are several classes of polymorphic markers; over 20,000 individual examples of these polymorphic markers at known locations have been identified and are available for linkage studies. Collectively, these markers provide a marker map of each chromosome, so when one wishes to map the position of a gene—often one involved in a disease process—the gene’s position can be located relative to one or more markers by recombination mapping. These high-density marker maps allow genome-wide screening for mapping genes.
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Chapter 5 ● Recombination Frequency
RFLPs (restriction fragment length polymorphisms)
Restriction endonuclease (RE) sites—palindromes recognized by specific restriction endonucleases—can serve as 2-allele markers. A specific site may be present in some individuals (allele 1) and absent in others (allele 2), producing different-sized restriction fragments that can be visualized on a Southern blot.
Alternatively, the area containing the restriction site can be amplified by using a PCR (polymerase chain reaction) and treating the PCR product with the restriction enzyme to determine whether one (RE site absent) or two (RE site present) fragments are produced. The PCR product(s) can be separated by agarose gel electrophoresis and visualized directly without using a blot.
VNTRs (variable number of tandem repeats)
These polymorphisms are the result of varying numbers of minisatellite repeats in a specific region of a chromosome. The minisatellite repeat units typically range in size from 20 to 70 bases each. The repeat is flanked on both sides by a restriction site, and variation in the number of repeats produces restriction fragments of varying size. VNTRs are used infrequently in current genetic mapping, as they tend to cluster near the ends of chromosomes.
STRPs (short tandem repeat polymorphisms, or microsatellites)
Short tandem repeat polymorphisms are repetitive sequences in which the repeated unit is generally 2–6 bases long. An example of a dinucleotide repeat (CA/TG) is shown above. These markers have many alleles in the population, with each different repeat length at a locus representing a different allele. STRPs can be amplified with a PCR by using primers designed to flank the repeat block. Variation in the number of repeats produces PCR products of varying length, which can then be visualized on agarose gel electrophoresis. STRPs are distributed throughout the chromosomes, making them very useful in mapping genes. STRPs are used in paternity testing and in forensic cases, but these sequences can also be used in gene mapping.
SNPs (single nucleotide polymorphisms)
SNPs represent nucleotide positions in the human genome where only two nucleotides—for example, C or G—are found. These occur on average about once in every 1,000 base pairs (bp) and, like STRPs, are very useful in mapping genes. Unlike STRPs, which have multiple alleles at each locus, SNPs are usually two-allele markers (either G or C in the above example). These can be typed by PCR amplification and identification by sequencing or through the use of probes on DNA chips, a process which can be automated.
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Part II ● Medical Genetics
GENE MAPPING: LINKAGE ANALYSIS
Crossing Over, Recombination, and Linkage
The first step in gene mapping is to establish linkage with a known polymorphic marker (one with at least two alleles in the population). This can be done by recombination mapping to determine whether the gene is near a particular marker. Multiple markers on different chromosomes are used to establish linkage (or the lack of it).
Recombination mapping is based on crossing over during meiosis, the type of cell division that produces haploid ova and sperm. During prophase I of meiosis, homologous chromosomes line up and occasionally exchange portions of their DNA. This process (shown in Figure II-5-2) is termed crossover.
Figure II-5-2. The Process of Crossing Over Between
Homologous Chromosomes
When a crossover event occurs between two loci, G and M, the resulting chromosomes may contain a new combination of alleles at loci G and M. When a new combination occurs, the crossover has produced a recombination. Because crossover events occur more or less randomly across chromosomes, loci that are located farther apart are more likely to experience an intervening crossover and thus a recombination of alleles. Recombination frequency provides a means of assessing the distance between loci on chromosomes, a key goal of gene mapping.
This process is illustrated in Figure II-5-3.
•If the gene of interest (with alleles G1 and G2) and the marker (with alleles M1 and M2) are on different chromosomes, the alleles will remain together in an egg or a sperm only about 50% of the time. They are unlinked.
•If the gene and the marker are on the same chromosome but are far apart, the alleles will remain together about 50% of the time. The larger distance between the gene and the marker allows multiple crossovers to occur between the alleles during prophase I of meiosis. An odd number
of crossovers separates G1 from M1 (recombination), whereas an even number of crossovers places the alleles together on the same chromosome (no recombination). The gene and marker are again defined as unlinked.
•If the gene and the marker are close together on the same chromosome, a crossover between the two alleles is much less likely to occur.
Therefore, G1 and M1 are likely to remain on the same chromosome more than 50% of the time. In other words, they show less than 50% recombination. The gene and the marker are now defined as linked.
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