Page 92 - Genetics_From_Genes_to_Genomes_6th_FULL_Part3

386 Chapter 11 Analyzing Genomic Variation

transporting chloride ions across the membrane. Ivacaftor 11.5 The Era of Whole-Genome
interacts specifically at the cell surface with the G551D mutant
CFTR protein, enhancing its ability to transport chloride. Sequencing
This treatment has been remarkably effective in preventing
the symptoms of cystic fibrosis from developing in young
children, but unfortunately G551D accounts for only about learning objectives
4% of all mutant CFTR alleles in the human population. 1. Describe a high-throughput, automated method by
More recently (in 2015), researchers developed a which millions of DNA templates may be sequenced
treatment for the much more prevalent ΔF508 mutation. simultaneously.
This allele encodes a protein that cannot fold properly and 2. Summarize a sequence of investigative steps that can
thus is not inserted into cell membranes. The new drug, narrow the candidates for a disease-causing variant.
called lumacaftor, ameliorates the folding problem, 3. Explain how databases that catalog sequence variation
resulting in an increase in the number of CFTR molecules in many people can facilitate the diagnosis of genetic
in cell membranes. The mutant proteins are still partially diseases.
defective in chloride ion transport. Remarkably, a combi-
nation pill containing lumacaftor and ivacaftor prevents
the development of cystic fibrosis in many patients homo-
zygous for ΔF508. DNA microarrays with millions of SNPs sample only a small
proportion of the variation between human genomes and can
suggest only a disease gene’s general chromosomal location.
Locus heterogeneity: Mutations in different As we just saw, disease gene identification eventually re-
genes cause the same disease quires DNA sequencing to correlate the disease phenotype
In this chapter, we deal exclusively with Mendelian genetic with actual mutations. Suppose now that we could cheaply
diseases caused by mutations in a single gene, but you and accurately sequence all of the nucleotides—not just
already know that many other conditions display locus those of candidate genes—in an affected person’s genome.
heterogeneity: They are caused by mutations in one of two The whole-genome sequence must somewhere include the
or more different genes. A previously discussed example of causative mutation. Thus, unlike positional cloning, where
a heterogeneous condition is deafness (review Fig. 3.23). the first goal is to find a molecular marker linked to the dis-
In confronting a new genetic disease, researchers must al- ease gene, the goal in the whole-genome approach is to find
ways be aware of the possibility of locus heterogeneity. directly a DNA alteration that is the disease allele.
Startling developments are making the idea of routine
In complex traits (also called quantitative traits) such as and affordable whole-genome sequencing into a reality.
high blood pressure, many different genes can influence Chapters 9 and 10 explained that the Human Genome Project,
the phenotype even in a single person. Chapter 22 outlines completed in 2003, sequenced the complete human ge-
some methods geneticists can use to study the genetic basis nome at a cost of 3 billion dollars. Researchers have since
of these complex traits. invented imaginative new methods that have rapidly driven
down the cost of DNA sequencing. In 2016, it is possible to
sequence a person’s whole genome (at a high coverage that
essential concepts will still miss some small regions) for about $2000, and the
cost will undoubtedly fall under $1000 within a few years.
• Positional cloning identifies DNA polymorphisms that are Whole-genome sequencing is still costly enough that
linked to disease genes. researchers often economize by sequencing just that portion
• Lod scores allow statistical assessment of linkage when of the genome corresponding to the protein-coding exons.
data are limited, as in human pedigrees. This is often informative because many, though far from all,
• After a disease gene is mapped approximately, disease-causing mutations alter the amino acid sequence of
researchers sequence candidate genes in the region to a protein. In whole-exome sequencing, investigators first
identify one that is altered consistently in affected enrich (by hybridization to cDNA sequences) for genomic
individuals. DNA fragments that correspond to the exons of all genes,
• In allelic heterogeneity, a variety of mutations in a single and then sequence these fragments. The exome, that is, the
gene cause disease. Compound heterozygotes with two collection of all exons of all genes, constitutes less than 2%
different recessive loss-of-function mutations in the same of whole-genome DNA, so whole-exome sequencing re-
gene may display the mutant phenotype. quires many fewer sequencing reads than whole-genome
• In locus heterogeneity, mutations in one of two or more sequencing. When DNA sequencing becomes even cheaper,
different genes can cause the same disease. enriching for the exome will likely no longer have a signifi-
cant cost advantage over whole-genome sequencing.