DNA Polymorphisms

What is a DNA polymorphism?

A sequence difference compared to a reference standard that is present in at least 1-2% of a population.

What are the different types of polymorphisms?

Types include single nucleotide polymorphisms (SNPs), restriction fragment length polymorphisms (RFLPs), variable number tandem repeats (VNTRs), and short tandem repeats (STRs).

Define restriction fragment length polymorphisms (RFLPs).

RFLPs are variations in DNA sequences that result in different sizes and numbers of fragments when DNA is cut with restriction enzymes.

What is the structure of short tandem repeats (STRs)?

STRs consist of repeating units of 1-8 base pairs.

How is gender identification achieved using the amelogenin locus?

The amelogenin locus contains variations that can indicate gender based on the presence of specific alleles.

What is the significance of STRs in bone marrow engraftment monitoring?

STRs can be used to track the presence and proportion of donor cells in a recipient's bone marrow.

What are single nucleotide polymorphisms (SNPs)?

SNPs are variations at a single nucleotide position in the DNA sequence that may occur in both coding and non-coding regions.

What is mitochondrial DNA typing used for?

Mitochondrial DNA typing is used for maternal lineage tracing and forensic identification.

What is the Human leukocyte Antigen (HLA) locus?

The HLA locus is a highly polymorphic region of human DNA important for immune system compatibility.

What are variable number tandem repeats (VNTRs)?

VNTRs are sequences that consist of repeating units of 8 to over 50 base pairs.

What are the characteristics of mobile elements in the genome?

Mobile elements, such as LINES and SINES, can replicate and spread throughout the genome, potentially forming pseudogenes.

What are Alu elements?

Alu elements are a type of SINE that are present in over 1,000,000 copies per genome and are associated with specific restriction enzyme recognition sites.

What is the role of RFLPs in genetic analysis?

RFLPs are used to detect polymorphisms by analyzing changes in the restriction map of a DNA region.

How are RFLPs visualized?

RFLPs are visualized using techniques like Southern blotting, which shows differences in fragment sizes.

What does it mean for a locus to be homozygous?

A locus is homozygous if both alleles inherited from the parents are the same.

What does it mean for a locus to be heterozygous?

A locus is heterozygous if the alleles inherited from the parents are different.

What is the significance of recombination in genetic diversity?

Recombination increases genetic diversity by mixing alleles from both parents during gamete formation.

How are RFLP genotypes inherited?

RFLP genotypes are inherited such that one allele is passed from each parent, resulting in a unique combination in the offspring.

What is the first step in using RFLPs for analysis?

The first step is to construct a restriction enzyme map of the DNA region under investigation.

How can VNTRs be resolved?

By gel electrophoresis of a restriction digest, allowing detection of gains or losses of repeats.

What role do frequent cutters like HaeIII or HinfI play in DNA analysis?

They generate fragments small enough to resolve different numbers of repeats in VNTRs.

What is the advantage of using multiple probes in DNA analysis?

It produces highly variable patterns between individuals by analyzing three to five loci simultaneously.

What is the difference in analysis complexity between one locus and multiple loci?

Analyzing one locus yields a simpler pattern compared to multiple loci, which can be more complex.

What is the significance of analyzing multiple loci in RFLP?

The probability of two individuals having the same RFLP profile decreases as more loci are analyzed.

What are short tandem repeats (STRs)?

Similar to VNTRs but consist of smaller repeat units of 1 to 7 base pairs.

How are STRs amplified for analysis?

They are efficiently amplified using PCR, requiring less specimen than traditional methods.

What are the different types of nucleotide sequence repeats in STRs?

Mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide repeats.

How can STR alleles be analyzed?

By fragment size using Southern blotting or by amplicon size using PCR.

What is an allelic ladder?

Standards representing all alleles observed in a population, used for comparison in genotyping.

What is multiplex PCR?

A method that allows multiple loci to be genotyped in the same reaction.

What is the designation system for non-gene associated STRs?

The D#S# system, where 'D' indicates DNA, the first number indicates the chromosome, and 'S' indicates a unique segment.

What is the amelogenin locus and its significance?

A useful marker located on the X and Y chromosomes, analyzed alongside STRs for sex determination.

How does the Y allele of the amelogenin gene differ from the X allele?

The Y allele is six base pairs larger than the X allele.

What is the HUMAMEL gene?

It codes for amelogenin-like protein and is located at Xp22.1-22.3 and Y.

What is the role of STRs in forensic genetics?

They provide a means to differentiate individuals based on variations in repeat numbers.

What are microvariants in STRs?

Repeat units that contain altered sequences, such as missing bases from the repeat.

Why is PCR preferred over Southern blotting for STR analysis?

PCR is much faster and requires a lower amount of specimen.

What is the relationship between repeat number and allele size in STR analysis?

Different alleles contain different numbers of repeats, affecting the fragment size.

What is the importance of computer analysis in DNA fragment sizing?

It allows for accurate sizing of restriction fragments in DNA analysis.

What is the length of the X allele?

212 bp

What is the length of the Y allele?

218 bp

How are females represented in terms of alleles?

Females are homozygous (X, X).

How are males represented in terms of alleles?

Males are heterozygous (X, Y).

What does the discovery of shared alleles between individuals indicate?

It is strong evidence of identity, paternity, or relatedness.

What do DNA testing results produce for comparison?

Peak or band patterns converted to genotype for comparison.

How is an STR locus genotype defined?

By the number of repeats in the alleles.

How is a heterozygous locus genotype designated?

As 7/8 or 7,8, indicating different repeat numbers on each chromosome.

How is a homozygous locus genotype designated?

By a single number of repeats, such as 7/7 or 7,7.

What indicates microvariant alleles?

The number of complete repeats followed by a decimal and the number of bases in the partial repeat, e.g., 9.3.

What is a genotype or profile of a specimen?

The collection of alleles in all the locus genotypes tested.

What does genetic concordance express?

The situation where all locus genotypes from two sources are the same.

When are two samples considered different?

If at least one locus genotype differs, except in paternity testing due to potential mutations.

What is the product rule in genetics?

The frequency of a genotype is the product of the frequency of each allele separately.

What does linkage equilibrium assume?

That the loci are not genetically linked in the genome.

How is the overall frequency (OF) of a locus genotype calculated?

OF = F1 x F2 x F3 x Fn, where F is the frequency of each allele.

What is the expected occurrence of a genotype with a frequency of 1/500?

It would be expected to occur in 1 out of 500 randomly chosen members of that population.

What is the significance of testing more loci?

It increases the certainty that the profile is unique to a single individual.

What method is used to analyze STR genotypes?

Gel or capillary gel electrophoresis.

How are Y chromosome STRs inherited?

Paternally as a haplotype without recombination.

What is a chimera in the context of bone marrow transplants?

A recipient with donor marrow.

What are the two parts of chimerism testing?

Pretransplant informative analysis and post-transplant engraftment analysis.

What is stutter in PCR reactions?

A technical artifact producing minor products of n-1 repeat units.

What is the formula for calculating % recipient or % donor DNA?

A(R) / (A(R) + A(D)) x 100 for recipient; A(D) / (A(R) + A(D)) x 100 for donor.

What is the average number of base differences in mitochondrial HV sequences of unrelated individuals?

8.5 base differences.

What types of polymorphisms are used for human identification?

RFLP, VNTR, STR, and SNP.

How are SNPs detected?

By sequencing, melt curve analysis, or other methods.

What is the purpose of the Human Haplotype Mapping Project?

To identify SNP haplotypes throughout the human genome.