Polymorphisms, Ch. 10, p.260
- Compare and contrast the different types of polymorphisms
Polymorphism Structure Detection Method
1 or more nucleotide changes that
Restriction fragment length
affect the size of restriction enzyme Southern blot
(RFLP)
products
Variable-number tandem Repeats of 8-50 base sequences in Southern blot,
repeats (VNTR) tandem PCR
Repeats of 1-8 base sequences in Southern blot,
Short tandem repeats (STR)
tandem PCR
Sequencing,
Single-nucleotide (SNP) Alterations of a single nucleotide
other
- Define RFLPs and discuss how they are used in parentage testing and human ID
● Restriction fragment length polymorphisms
● Differences in the sizes and number of fragments generated by restriction enzyme
digestion of DNA
● Polymorphisms are inherited from each parent
○ Fragment sizes of an individual are a combination of those from each
parent
○ Paternity testing: alleles or fragments of the child and mother are analyzed
and the remaining fragments have to belong to the father
■ 8 loci needed
○ Human ID: HaeIII (GGCC), HinfI (GANTC), Southern blot
- Interpret an RFLP assay when given data
Figure 10.5, p 265
- Describe short tandem repeat structure and nomenclature
● Different alleles contain different numbers of repeats
● Mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide
● Nomenclature
○ Within genes: gene name
○ Non-gene assoc: D#S#
■ DNA, chromosome
■ Segment
■ Ex. D8S1179, D18S51
- Explain how allelic ladders are used to interpret electrophoresed results for STRs
, ● Allelic ladders: sets of fragments representing all possible alleles of a repeat
locus
● Helps determine the size of your amplicons by comparing the co-size migration
with specific alleles in the ladder.
● Allow accurate ID of the sample alleles
- Describe how Y-STR can be used in forensic and lineage studies
● Developed for surname testing and forensic ID of male offenders or victims
● Primer set only amplifies STR located on the Y chromosome
○ There is only 1 allele at each locus
■ Linked and inherited together
○ Y chromosome is inherited as a single haplotype
■ Paternally related men share all Y loci
● Autosomal STRs provide stronger analytical power because of homologous
recombination
○ Y chromosome does not
- Differentiate informative, noninformative, donor informative, recipient informative loci
Informative Loci - one locus in which donor alleles differ from the recipient alleles
Noninformative Loci - loci in which the donor and the recipient have the same alleles
Donor informative Loci - the donor and recipient share one allele for which the donor is
heterozygous and the donor has a unique allele
Recipient Informative Loci - the unique allele is in the recipient
- Define mitochondrial STRs and summarize briefly their clinical use
● Sequence differences in the hypervariable regions (HV) of the mitochondrial
genome
● Follow maternal inheritance patterns
○ Typing can be used for legal exclusion or confirmation of maternal lineage
Summary
● Four types of polymorphisms are used for a variety of purposes in the laboratory:
RFLP, VNTR, STR, and SNP
● Polymorphisms are used for human identification and parentage testing
● Y-STR haplotypes are paternally inherited; maternal relatives share mitochondrial
alleles
● Polymorphisms are used to measure engraftment after allogeneic bone marrow
transplants
● Single-nucleotide polymorphisms are detected by sequencing, melt curve
analysis, or other methods
● Mitochondrial DNA typing is performed by sequencing the mitochondrial HV
regions
- Compare and contrast the different types of polymorphisms
Polymorphism Structure Detection Method
1 or more nucleotide changes that
Restriction fragment length
affect the size of restriction enzyme Southern blot
(RFLP)
products
Variable-number tandem Repeats of 8-50 base sequences in Southern blot,
repeats (VNTR) tandem PCR
Repeats of 1-8 base sequences in Southern blot,
Short tandem repeats (STR)
tandem PCR
Sequencing,
Single-nucleotide (SNP) Alterations of a single nucleotide
other
- Define RFLPs and discuss how they are used in parentage testing and human ID
● Restriction fragment length polymorphisms
● Differences in the sizes and number of fragments generated by restriction enzyme
digestion of DNA
● Polymorphisms are inherited from each parent
○ Fragment sizes of an individual are a combination of those from each
parent
○ Paternity testing: alleles or fragments of the child and mother are analyzed
and the remaining fragments have to belong to the father
■ 8 loci needed
○ Human ID: HaeIII (GGCC), HinfI (GANTC), Southern blot
- Interpret an RFLP assay when given data
Figure 10.5, p 265
- Describe short tandem repeat structure and nomenclature
● Different alleles contain different numbers of repeats
● Mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide
● Nomenclature
○ Within genes: gene name
○ Non-gene assoc: D#S#
■ DNA, chromosome
■ Segment
■ Ex. D8S1179, D18S51
- Explain how allelic ladders are used to interpret electrophoresed results for STRs
, ● Allelic ladders: sets of fragments representing all possible alleles of a repeat
locus
● Helps determine the size of your amplicons by comparing the co-size migration
with specific alleles in the ladder.
● Allow accurate ID of the sample alleles
- Describe how Y-STR can be used in forensic and lineage studies
● Developed for surname testing and forensic ID of male offenders or victims
● Primer set only amplifies STR located on the Y chromosome
○ There is only 1 allele at each locus
■ Linked and inherited together
○ Y chromosome is inherited as a single haplotype
■ Paternally related men share all Y loci
● Autosomal STRs provide stronger analytical power because of homologous
recombination
○ Y chromosome does not
- Differentiate informative, noninformative, donor informative, recipient informative loci
Informative Loci - one locus in which donor alleles differ from the recipient alleles
Noninformative Loci - loci in which the donor and the recipient have the same alleles
Donor informative Loci - the donor and recipient share one allele for which the donor is
heterozygous and the donor has a unique allele
Recipient Informative Loci - the unique allele is in the recipient
- Define mitochondrial STRs and summarize briefly their clinical use
● Sequence differences in the hypervariable regions (HV) of the mitochondrial
genome
● Follow maternal inheritance patterns
○ Typing can be used for legal exclusion or confirmation of maternal lineage
Summary
● Four types of polymorphisms are used for a variety of purposes in the laboratory:
RFLP, VNTR, STR, and SNP
● Polymorphisms are used for human identification and parentage testing
● Y-STR haplotypes are paternally inherited; maternal relatives share mitochondrial
alleles
● Polymorphisms are used to measure engraftment after allogeneic bone marrow
transplants
● Single-nucleotide polymorphisms are detected by sequencing, melt curve
analysis, or other methods
● Mitochondrial DNA typing is performed by sequencing the mitochondrial HV
regions
