17 terms

SMU Genetics Chapter 11

Genome-Wide Variation and Trait Analysis
DNA polymorphism
a DNA sequence that occurs in 2 or more variant forms
a combination of alleles at multiple tightly linked loci that are transmitted together over many genereations
variation in the length of a restriction fragment detected by a particular probe due to nucleotide changes at a restriction site
a short oligionucleotide probe that hybridize to one allele at a chosen SNP locus
SNP definition
2 different nucleotides appear at the same position in genomic DNA from different individuals
DNA fingerprinting
detection of genotype at a number of linked highly polymorphic loci using one probe
DNA element composed of tandemly repeated identical sequences
location on a chromosome
4 classes of DNA polymorphisms
-single nucleotide polymorphism
-insertion/ deletion
-simple sequence repeat (useful for making DNA fingerprints)
-copy number variation/ copy number polymorphism
-single bp difference
-most have no direct effect on activity of genes
-very stable (low mutation rate)
SNP alleles detected via Southern blots
-only works if SNP changes restriction site
Restriction Fragment Length Polymorphisms
-gain or loss of a restriction site
SNP detection via PCR
-use PCR primers flanking SNP to amplify SNP-containing region
-cut PCR product with restriction enzyme & run on gel
SNP detection using ASOs (Allele Specific Oligionucleotides)
-short probes (<21 nts) hybridize only to perfectly complementary DNA
-single bp mismatch prevents hybridization (@ higher temp)
SSRs/ Microsatellites
Simple Sequence Repeats
-Repeat unit lengths:2-5 bp
-Mutate by replication errors (repeated sequences have increased tendency to loop out during replication)
-most do not affect genes
-useful as highly polymorphic markers
Huntington's disease
-one exception to SSRs not affecting genes
-caused by increased number of CAG repeats in coding region of HD gene
DNA fingerprints
-total number of SSR alleles at multiple unlinked loci