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--- chapter_21 [2024/09/18 19:47] – mike
+++ chapter_21 [2026/10/25 01:20] (current) – [Single nucleotide polymorphisms (SNPs)] mike
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-Of course, to many people humans are the organism in which they are most interested, either for their intrinsic interest in themselves or for biomedical applications. Humans are also more difficult to study compared to the other model organisms we have discussed in this book. The human genome is much larger and less gene dense than invertebrates such as Drosophila or //C. elegans//. More importantly, we cannot study human genetics by designing experiments using true-breeding mutants that can generate large quantities of data to test hypotheses prospectively the way we can with model organisms; for ethical reasons we can only study human genetics retrospectively, using whatever meager quantity of data natural human populations provide. Human geneticists therefore rely on non-invasive DNA tests, genetic mapping, and statistical analyses to make connections between genotype and phenotype. There are, whoever,  some advantages to studying human genetics. First, humans are self-screening; they will self-report interesting phenotypes (usually these are genetic diseases). Second, subtle phenotypes may be more recognizable, as affected individuals may be able to talk directly with researchers.
+Of course, to many people humans are the organism in which they are most interested, either for their intrinsic interest in themselves or for biomedical applications. Humans are also more difficult to study compared to the other model organisms we have discussed in this book. The human genome is much larger and less gene dense than invertebrates such as Drosophila or //C. elegans//. More importantly, we cannot study human genetics by designing experiments using true-breeding mutants that can generate large quantities of data to test hypotheses prospectively the way we can with model organisms; for ethical reasons we can only study human genetics retrospectively, using whatever meager quantity of data natural human populations provide. Human geneticists therefore rely on non-invasive DNA tests, genetic mapping, and statistical analyses to make connections between genotype and phenotype. There are, however,  some advantages to studying human genetics. First, humans are self-screening; they will self-report interesting phenotypes (usually these are genetic diseases). Second, subtle phenotypes may be more recognizable, as affected individuals may be able to talk directly with researchers.
 ===== Polymorphisms and mapping =====
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 The vast majority (probably 99%) of SNPs are selectively “neutral” changes of little or no functional consequence. This is mostly because they likely exist outside coding or gene regulatory regions (>97% of human genome). They can also be silent substitutions in coding sequences, or amino acid substitutions that do not affect protein stability or function. A small minority of SNPs are of functional consequence and are selectively advantageous or disadvantageous; this can affect the allele frequency of these SNPs.
-SNPs can be detected in a variety of ways. Conceptually, all you need to detect a SNP is knowledge of the DNA sequence surrounding the SNP. Armed with this information, you could use PCR to amplify a DNA fragment that contains the SNP from individuals and sequence the DNA ([[chapter_07|chap. 7]]). In practice, you would likely use a device called a DNA microarray that is specifically designed to detect SNPs. Or, you could simply use NGS sequencing technology to sequence the genome of the individual to identify SNPs.
+SNPs can be detected in a variety of ways. Conceptually, all you need to detect a SNP is knowledge of the DNA sequence surrounding the SNP. Armed with this information, you could use PCR to amplify a DNA fragment that contains the SNP from individuals and sequence the DNA ([[chapter_07|Chap. 7]]). In practice, you would likely use a device called a DNA microarray that is specifically designed to detect SNPs. Or, you could simply use NGS sequencing technology to sequence the genome of the individual to identify SNPs.
 ==== Simple sequence repeats (SSRs) ====