Genetic Analysis of Complex Disease. Группа авторов

found in >1% of the population. A polymorphism may be a change in a single nucleotide, known as a single nucleotide polymorphism, an insertion or deletion (indel), or a duplication or deletion of a large segment of DNA, sometimes referred to as a copy number variant (CNV). Much research is currently underway to evaluate the effects of such polymorphisms on common and complex diseases, such as multiple sclerosis, cancer, and heart disease.

      Point Mutations

      A point mutation is defined as an alteration in a single bp in a stretch of DNA, thereby changing the 3‐bp codon. Since the genetic code is degenerate, many such changes do not necessarily alter the resulting amino acid. However, if the single bp change leads to the substitution of one amino acid for another, the result can significantly affect the final protein product. Point mutations can be classified as transition mutations (purine → purine or pyrimidine → pyrimidine) or as the less common transversion mutations (purine → pyrimidine or pyrimidine → purine). In general, transitions are less likely than transversion mutations to change the resulting amino acid. Five effects of point mutations have been described:

       Synonymous or silent mutations are single bp changes in the DNA that do not affect the resultant amino acid

       Nonsense mutations result in a premature stop codon, leading to a polypeptide of reduced length

       Missense mutations lead to the substitution of one amino acid for another

       Splice site mutations affect the correct processing of the mRNA strand by eliminating a signal for the excision of an intron

       Mutations in regulatory genes alter the amount of material produced

      Several examples of point mutations in human diseases are illustrated below.

      Sickle Cell Anemia

      Sickle cell anemia, an autosomal recessive disorder with a carrier frequency in African Americans of approximately 1/12, is a classic example of a point mutation leading to disease. Sickle cell anemia results from a single nucleotide substitution in the HBB gene of an adenine to a thymine, which changes the resultant amino acid from glutamine to valine at codon 6. The pathogenic variant (mutation) leads to the formation of an abnormal form of hemoglobin, hemoglobin S, which causes the red blood cell to take on an abnormal form that resembles a sickle. This causes red blood cells to break down prematurely, leading to anemia. In addition, the sickled red blood cells may accumulate in blood vessels and lead to episodes of severe pain. Interestingly, the carrier state for sickle cell trait may lead to a selective advantage in certain environments: carriers have a resistance to malaria that is useful in tropical climates, which explains the high carrier rate in certain populations.

      Achondroplasia

      Achondroplasia, the most common type of short‐limbed dwarfism, is an autosomal dominant disorder. About 85% of cases are the result of a new mutation. It has been observed that the rate of new dominant mutations increases with advancing paternal age (Penrose 1955; Stoll et al. 1982). Achondroplasia is now known to result from mutations in the fibroblast growth receptor 3 gene (FGFR3), located on chromosome 4p16.3. Interestingly, over 95% of the mutations are the identical G‐to‐A transition at nucleotide 1138 on the paternal allele (Rousseau et al. 1994; Shiang et al. 1994; Bellus et al. 1995). This single change causes a gain of function mutation which results in constitutive activation of the receptor, thereby inhibiting the proliferation of cartilage cells, or chondrocytes, and significantly restricting growth in individuals with this condition. Other pathogenic variants in FGFR3 are also responsible for hypochondroplasia and thanatophoric dysplasia, types of dwarfism that are clinically distinct from achondroplasia.

      Deletion/Insertion Mutations

      Another class of mutations involves the deletion or insertion of DNA into an existing sequence. Deletions or insertions may be as small as 1 bp, or they may involve one or many exons or even the entire gene. Even single bp deletions or insertions can have devastating effects, frequently by altering the reading frame of the DNA strand. A specific type of deletion/insertion mutation is a CNV. A CNV is structural variation in which kilobases to several megabases of DNA have been deleted or added and may encompass numerous genes. It is hypothesized that CNVs may account for 5–13% of the genome (Stankiewicz and Lupski 2010; Zarrei et al. 2015). Most CNVs are expected to be benign, while some are directly tied to a particular disease. Other CNVs may confer an increased risk for a particular condition, and much research is currently taking place about the role of CNVs in complex diseases.

      Duchenne and Becker Muscular Dystrophy

      Duchenne muscular dystrophy (DMD) is a severe, childhood‐onset X‐linked muscular dystrophy. Becker muscular dystrophy (BMD) is allelic with DMD but typically has a later age of onset and a milder presentation. Boys with DMD typically have normal development for the first few years of life, after which rapidly progressive muscle deterioration becomes obvious. Affected males usually lose the ability to walk by age 10–12 years. The eventual loss of muscle strength in the cardiac and respiratory muscles leads to death in early adulthood. Duchenne and Becker muscular dystrophy is caused by mutations in the DMD gene, which codes for the protein dystrophin (Koenig et al. 1988). Large deletions in this gene account for approximately 60–70% of cases of DMD and BMD; however, duplications and point mutations have also been reported (Takeshima et al. 2010). Mutations in this gene that alter the reading frame typically cause DMD, while mutations that preserve the reading frame lead to BMD. Researchers are investigating a variety of therapies including exon‐skipping and read‐through of stop codons.

      Cystic Fibrosis

      Cystic fibrosis (CF), an autosomal recessive disorder, is the most common hereditary disease among Northern Europeans, with a carrier frequency of between 1/25 and 1/30 (Hamosh et al. 1998). This condition affects the function of the pancreas, lungs, and sweat glands, among other organ systems (Ratjen and Doring 2003). In Northern Europeans, a single mutation in the CFTR gene called ΔF508 accounts for about 70% of the abnormal CF alleles. Three bp (codon 508) are deleted, and the resulting amino acid sequence is missing a phenylalanine. Although the reading frame is preserved in this particular mutation, the deletion results in a block in protein processing. CF is an excellent example of allelic heterogeneity in which different mutations, or alleles, at the same locus can cause a disease. In fact, more than 1900 other deleterious mutations in CFTR have been identified (Cystic Fibrosis Mutation Database 2015).

      Charcot‐Marie‐Tooth Disease

      Charcot‐Marie‐Tooth (CMT) Type 1A and hereditary liability to pressure palsies (HNPP) are caused by an abnormal 1.4 megabase CNV on 17p12. CMT is a peripheral neuropathy most commonly caused by a duplication of PMP22, while a deletion of this same gene will result in the phenotypically distinct condition, HNPP. There are numerous types of CMT, many of which are caused by mutations at many different loci, a scenario described as locus heterogeneity.

      Nucleotide Repeat Disorders

      Certain loci in the genome have variable numbers of nucleotide repeats, typically of di‐ or tri‐nucleotide length. Most are not associated with expressed genes but can be exploited as genetic markers since they are highly polymorphic. A few loci with tri‐nucleotide repeats are located near or within a gene and, by expansion beyond a certain threshold, can disrupt gene expression and cause disease.

More than 20 disorders have been shown to be the result of unstable nucleotide repeats (La Spada & Taylor 2010; Polak et al. 2013). The most common of these conditions are summarized in Table 2.4. Expansions may occur in the exon, intron, or regulatory elements of a gene. The phenotypes