Chapter 20: Autosomal Short Tandem Repeat Profiling

Short Tandem Repeat (STR)

Short Tandem Repeat (STR)

A region of genomic DNA containing an array of short repeating sequences.

core repeat region

The ______ of each STR locus contains tandemly repeated sequences.

flanking regions

The _____ surrounding the core repeat region are also needed for STR analysis.

Repeat Unit Length

The number of nucleotides in a single repeat unit.

Simple Repeats

Consists of tandem repeats with identical repeat unit sequences.

Allele designation

is based on the number of repeat units in the core repeat region.

Complex repeats

Contain several clusters of different tandem repeats with intervening sequences.

Nonconsensus alleles

with partial repeat units also appear in the population. These nonconsensus alleles, also known as microvariants, differ from common alleles by one or more nucleotides.

Quadruplex

The first STR multiplex system, developed by Forensic Science Services in the United Kingdom.

Second-Generation Multiplex (SGM)

The first national DNA database established in the United Kingdom.

European Standard Set (ESS)

Consists of seven loci: TH01, VWA, FGA, D21S11, D3S1358, D8S1179, and D18S51.

Combined DNA Index System (CODIS)

• Established by the FBI.

• It contains 13 core STR loci plus the amelogenin sex-typing locus.

electropherogram

The data collection process generates an _____ that shows a profile of peaks corresponding to each DNA fragment.

Allelic Ladder

A collection of synthetic fragments corresponding to common alleles observed in the human population for a given set of STR loci.

off-ladder allele

If a rare allele fails to match alleles within an allelic ladder, it is considered an ________.

Inclusion (Match)

Peaks of compared STR loci, such as those between the profiles of suspect and crime scene evidence or victim and crime scene evidence, show identical genotypes.

Exclusion

The genotypes of two or more samples differ, and the profile of the sample is determined to be an _____, meaning that the profiles originated from different sources.

Inconclusive Result

The data do not support a conclusion of inclusion or exclusion. In other words, insufficient information is available to reach a conclusion.

Mutations at STR Core Repeat Regions

If a mutation occurs in the germ cells, the mutant allele will be transmitted to and be present in all cell types of the progeny.

Germ-Line Mutation

A type inheritable mutation in germ cell lineage.

mutation rate

The frequency of germ-line mutation can be measured by the ____, expressed as the number of mutations per generation.

Somatic Mutations

Involves the mutation of only somatic cells.

Trisomy

Duplicating one of the homologous chromosomes results in a total of three copies of a particular chromosome.

triallelic

If the duplicated locus is mutated, a ______ or three-peaks pattern can be detected at a single locus, but not at loci located at other chromosomes in a multiplex STR profile.

Point Mutations

It involve the changing of a nucleotide sequence through nucleotide substitution, insertion, or deletion.

Null Allele

If a mutation at a primer-binding sequence prevents the primer from annealing to the template, this leads to a complete failure of the amplification of the allele.

Stutter

A minor allele peak, whose repeat units are shorter or longer than the parental allele peak.

Stutter Ratio

The area of the stutter peak divided by the area of the parental peak.

Nontemplate Adenylation

During PCR amplificationn, DNA polymerase often adds an extra nucleotide, usually an adenosine, to the 3′-end of an amplicon.

Heterozygote Imbalance

It occurs when one of the alleles has greater peak area or amplitude than the other allele within the same locus in which the two alleles of a heterozygote are compared.

Preferential amplification

Refers to an event where a smaller allele is amplified more efficiently than larger ones.

Allelic Dropout

It occurs when an allele, usually one of the heterozygote alleles, fails to be detected.

Pull-Up Peaks

Occurs when a minor peak of one color on an electropherogram is pulled up from a major allelic peak in another color when the colors have overlapping spectra.

Spikes

These are sharp peaks that are present in all color panels of an electropherogram. It is caused by by air bubbles and urea crystals in the capillary of an electrophoretic platform.

Low Copy Number DNA Testing

• It involves the testing of very small amounts of DNA in a sample.

  • It is often needed for samples derived from evidence such as fingerprints and tools and weapons handled by perpetrators.

Mixture Interpretation

The interpretation of DNA profiles of mixed stains.