Term
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Definition
DNA sequences that are shared by a certain percentage of the population but differ from the majority. May be 1 - 1,000 bp long.
The probability of polymorphisms in the human genome is great, due to the large size, 98% of which doesn't code for anything. Individuals genome sequences probably differ by 1 nucleotide every 1000-1500 bases. |
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Term
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Definition
| A highly polymorphic region of the human genome. The variable sequences at this locus code for peptides that establish self-identity of the immune system. Similarity/compatibility between donors/recipients can be determined by comparing DNA sequences. |
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Term
| Single Nucleotide Polymorphisms |
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Definition
SNPs. Single nucleotide differences among different individual's genomes. May occur in gene coding regions or intergenic sequences. Genome sequences differ by 1 nucleotide every 1000-1500 bases.
Detected by sequencing and other methods. |
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Term
| Long Interspersed Nucleotide Sequences |
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Definition
| LINEs. Highly repeated DNA sequences 6-8 kbp in length. Encode RNA polymerase promoters and open reading frames related to RT or retroviruses. More than 50,000 LINEs making up more than 15% of the human genome. |
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Term
| Short Interspersed Nucleotide Sequences |
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Definition
| SINEs. 1,000,000 copies per genome. 0.3 kbp in length. Include ALU elements, which have the recognition site for the Alu restriction enzyme. |
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Term
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Definition
| LINEs and SINEs. Can be copied and spread throughout the genome by recombination and reverse transcription. May form pseudogenes (intronless, nonactive copies of genes). |
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Term
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Definition
| STRs. Short blocks (1-10 bp) of repeated sequences in tandem that can undergo expansion or shrinkage over the generations. Detected by PCR. |
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Term
| Variable Number Tandem Repeats |
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Definition
| VNTRs. 10-50 bp sequences that can undergo expansion or shrinkage over generations. Detected by Southern Blot, PCR. |
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Term
| Restriction Fragment Length Polymorphisms |
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Definition
| RFLPs. One or more nucleotide changes that change the length of a restriction enzyme product. The restriction map of a DNA region can be used to detect SNPs, larger sequence variants, and tandem repeats. Detected by Southern Blots. |
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Term
| DNA Restriction Enzyme Maps |
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Definition
| Restriction enzymes are used to create a DNA map of the region being inestigated. The number of fragments and their sizesfrom the test DNA are compare to the expected numbers and sizes for that restriction enzyme. Polymorphisms are detected when number of fragments and their length differ from the prediction. |
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Term
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Definition
| Mutations, recombination within and between chromosomes, gene conversion, etc. have contributed to human genetic diversity. A single locus can have different versions (alleles) across the population. A person is homozygous for a given locus if they have the same allele on both chromosomes, and heterozygous for a locus if they have different alleles on each chromosome. |
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Term
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Definition
| Used in RFLP analysis after gel electrophoresis. A membrane on which DNA products are blotted, followed by a probe that attaches to a specific DNA sequence. Won't show all restriction fragments, but will show a distinctive band pattern depending on the combination of alleles inherited from each parent. |
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Term
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Definition
Common restriction enzymes used to fragment genomic DNA in the U. S. for human identification purposes.
HinfI is used in Europe.
Over 2000 RFLP loci have been found in the human genome. |
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Term
| RFLPs for Genetic Mapping |
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Definition
| The locations of many polymorphisms in the human genome are known. These polymorphisms can be used to judge the location of unknown genes. Statistical methods are used to show the probability that an unknown gene is located close to a known marker in the genome. If a particular polymorphism is frequently found in diseased individuals it is probable that an affected gene is located near that polymorphism. |
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Term
| Parentage Testing using RFLP |
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Definition
| A child will have two alleles for any given gene (including polymorphisms), one from each parent. The combination of alleles in the child can be compared to those in the parents. The fragment sizes of the loci in the child are a combination of those from the parents. Maternal and child fragment sizes are compared, and the remaining fragments must come from the father. Possible fathers are ones that could have contributed the remaining alleles (inclusion). A difference of one allele excludes paternity. At least 8 loci must be tested. |
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Term
| First Genetic Human ID Tools |
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Definition
ABO blood group typing was used first, but can only show exclusion and was informative in only 15-20% of cases.
Analysis of the HLA locus could provide exclusion in 90% of cases.
Together, exclusion could be shown in 97% of cases, but positive identification was elusive. |
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Term
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Definition
| RFLPs can arise from point mutations, mutations creating new restriction sites, insertions/deletions of repeating events. This happens frequently in repeated sequences of DNA. Repeats of over 8 bp are VNTRs, minisatellites. The loss or gain or one repeat will show up on gel electrophoresis. HaeIII and HinfI generate fragments small enough too see differences on a Southern blot and give an informative pattern. |
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Term
| Single Locus Probe System |
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Definition
| SLP systems were developed in 1990 fo simplified DNA profiling. Analyzing just one loci is easier and produces simpler patterns. Data analysis also easier in this case if a sample might contain DNA from multiple individuals. |
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Term
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Definition
| Short tandem repeats (STRs) of 1-7 bp. STRs with repeat units with altered sequences are microvariants, missing some bases of the repeat. Arise via mutation. Degraded samples can be analyzed be used because long intact DNA fragments are unnecessary. PCR only needs 10 ng of DNA for STR (instead of 1 ug). Primers are designed to select sequences of 100-400 bp that contain STRs. If the primer is labeled the PCR products can be visualized. |
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Term
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Definition
| STRs that are amplified with primers closer to the STR sequence than usual. This produces smaller amplicons that are more easily extracted from difficult sources (fixed tissue, degraded sources). |
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Term
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Definition
Amplification requires test DNA, primers, buffer, and polymerase. A control may also be amplified. Samples are then combined with allelic ladders (specific to that locus) and internal size standards (molecular weight markers) in formamide.
STRs are a discrete allele system where there are a finite number of alleles defined by the number of repeats. |
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Term
| Capillary Electrophoresis of STRs |
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Definition
| Automation enables quick electrophoresis via capillary systems, but a single run on such a system with only a single dye can only resolve loci whose allelic ranges don't overlap in size. Multicolor dye labels allow multiple products of similar lengths to be resolved in the same run. Primers labeled with dyes can generate products that emit different wavelengths. Size standards and allelic ladders are always run at the same time as samples, allowing automatic results. |
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Term
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Definition
| STR "mathes" are made by comparing profiles and making probability calculations. The chance that a set of alleles will occur in 2 unrelated individuals at random is 1 in 10^6 - 7 x 10^8 in Caucasians and 1 in 3 x10^6 - 3x10^8 for African Americans. |
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Term
| Amount of DNA in One Cell |
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Definition
Minimal requirements for DNA amplification is from one cell, which contains 6 pg of DNA. A/T bp are 617 g.mol, and G/C are 618 g/mi=ol. There are 3 billion bp in one copy of the human genome.
One genome copy:
3x10^9 bp x 618 g/mol/bp = 1.85 x 10^12 g/mol 1.8 Tg x 10^12 g/mol x 1 mol/6.023 x 10^23 molecules = 3.07 x 10^-12g = 3 pg
Each cell contains two copies, so 6 pg. One ng of DNA (1000 pg) should contain 333 copies of each locus. |
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Term
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Definition
| With genes, referred by gene name (e.g., TH01 is intron 1 of the human tyrosine hydroxylase gene on Chromosome 11). STRs have no phenotypic effects on genes. Non-gene STRs have a D#S# system, D is for DNA, the # is the chromosome. S is the unique sequence and # is a number registered in the international genome database. |
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Term
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Definition
| Frequently analyzed along with STRs (although not an STR). Located on the X and Y chromosomes, functions in embryonic development and tooth maturation. It is 6 bp longer in the second intron on the Y chromosome than on the X, so XY shows up as 2 bands on a gel, and XX shows as one. |
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Term
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Definition
The number of repeats in that allele.
A heterozygous locus would have two bands of different sizes, designated as 7/8 or 7,8.
A homozygous locus would have one band and be designated 7, 7/7, or 7,7.
Microvariant alleles containing partial repeat units are designated by the number of repeats and then a decimal indicating the number of bases in the partial repeat (e.g., 9.3).
The genotype is the collection of all alleles of all the loci tested. |
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Term
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Definition
When all of the loci examined from two individuals have the same alleles.
If one locus genotype differs, the two samples must be different (exclusion). Paternity tests are an exception (new alleles may be generated in offspring). |
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Term
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Definition
| A PCR anomaly where polymerases miss a repeat when replicating, creating 2 or more species in the amplified product and resulting in extra bands or peaks on a gel. The larger a repeat unit is, the less stutter is observed. |
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Term
| Gel Electrophoresis Variation in Bands |
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Definition
Consistent band migration might be interrupted by air bubbles, crystals, dye blobs, contaminants, temperature variations, and voltage spikes.
For PCR, some polymerases add additional non-template adenine residues to the 3' end of the product. If the 3' addition doesn't get added to all PCR products, mixed amplicons will result in extra bands or peaks close together. |
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Term
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Definition
| Tiny variations persist in bands on a gel. Bins are acceptable ranges of sizes for bands to fall in. To establish a range of observed sizes, the same fragments can be run over and over. A bin is the uncertainty window surrounding the main position of multiple runs of a band. Collecting these bands in the characteristic distribution is binning. All peaks within a bin are considered as the same locus. |
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Term
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Definition
The proportion of alleles that fall within an uncertainty window exactly is a fixed bin, and approximately is floating bins.
Locus-specific brackets can be used to assess allele certainty by running artificial alleles at the high and lows ends of the allele size. |
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Term
| Hardy-Weinberg Equilibrium |
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Definition
A set of conditions under which the relative frequency of 2 alleles in the population remains constant.
p^2 + 2pq + q^2 = 1.0
Conditions:
1. Large population
2. Random mating
3. No immigration or emigration
3. No mutation
5. No natural selection |
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Term
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Definition
When looking at a set of alleles, its frequency in the population is the product of each individual allele's frequency. This rule works because of linkage equilibrium, which assumes that loci are not associated with each other (linked) in the genome, and that observed frequencies of haplotypes are concordant with the haplotype frequencies predicted by multiplying the frequency of individual loci within a haplotype.
Overall frequency (OF) = F1 x F2 x F3 ... Fn |
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Term
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Definition
| Discordance of the observed frequencies of haplotypes in a population and the predicted haplotype frequencies. When this happens it implies that the loci being examined are physically close to one another on the chromosome so that recombination is unlikely. Used for mapping loci. |
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Term
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Definition
| Likelihood ratio of paternity. Calculated for each loci tested. Common alleles have low paternity indices, rare alleles have high paternity indices. |
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Term
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Definition
CPI. If tested loci are not linmked (e.g., on different chromosomes) the occurrence of each allele can be considered separate. The paternity index of each allele can be multiplied to calculate CPI.
CPI = P1 x P2 x P3 .... Pn |
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Term
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Definition
| Unlike RFLP paternity testing, a paternity index of 0 for a locus would not demonstrate nonpaternity because of the possibility of mutation. Mutations are rare in RFLP systems but can shows up if over 12 loci are tested with STRs. u = observed mutation rate of locus is used instead of the paternity index in these cases. |
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Term
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Definition
CPI is accompanied by this, a number calculated from the paternity index and prior odds (assumed by the lab to be 50/50
CPI x prior odds/(CPIx0.5) + (1-0.5) |
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Term
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Definition
| Probability of sibling relationships can be calculated using polymorphisms. This is louder statistically than a paternity test. The likelihood ratio can be called a kinship ratio, sibling index, or combined sibling test. |
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Term
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Definition
| Testing determining the probability of aunt or uncle relationship. Based on number of shared alleles. Probabilities can be increased if other known relatives are available for testing. This kind of testing is important in genetic studies because linkage mapping of genes in populations can be affected by unknown family relationships. |
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Term
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Definition
The majority of STR mutations are gains or losses of one repeat. Brenner said PI for mutant alleles must take into account the nature of the mutation (one or more repeats lost or gained). The loss of one repeat is much more likely.
PI for mutant allele - u/(4P[q]) for one repeat
PI for mutant allele - u/(40P[q]) for two repeats |
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Term
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Definition
| Only in men, and only one allele (paternally derived). Y-STR allele sets are inherited whole and together, since Y chromosomes don't recombine with X or Y chromosomes. Haplotypes for Y-STRs can have frequencies determined for the whole population. Y-STRs are always less definitive than autosomal STRs. |
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Term
| Y-STR Paternity Lineage Testing |
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Definition
All men in a family (brothers, uncles, cousins, grandfather) will have the same Y-STR haplotype (except for rare mutation events).
Tests can be done to see if two males have a common ancestor. |
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Term
| Y-STRs in Forensic Testing |
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Definition
In forensic crime scenes with much female and little male evidence, autosomal STRs are of little use. Y-specific primers can be used to specifically amplify male DNA from a mix, giving results of only male origin.
Also used in missing person's cases where reference paternity samples are available, since the Y chromosome has low mutation rates (1.72-4.27 mutations/1000 alleles) with mutations occurring once every 500 generations/locus. |
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Term
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Definition
| Calculated from the frequency of occurrence of a given haplotype in a tested population. 1-HD represents the probability of two random males sharing the same Y haplotype. If the HD is high, the odds of two random men in the population having the same haplotype is low. |
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Term
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Definition
| Measure of Y profile uniqueness. Determined by number of different haplotypes seen in a population and the number of samples in a population. Expresses number of males in a population that can be identified with a given haplotype. DC is increased by increasing the number of loci used to determine the haplotype. |
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Term
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Definition
Many STRs have known locations in the genome, so they can be used to map the locations of other genes (particularly disease-associated genes).
If the STR is closely linked to the gene, the STR can be a target of testing, since screening large genes for point mutations is hard. |
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Term
| Family History STR Linkage Analysis |
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Definition
| A single family with members affected by a disease can be analyzed. All members are tested for certain alleles, and unaffected members results are compared to results of members with the disease. If a certain allele at a particular locus is always present in affected members, that locus is closely linked to the gene of interest's location. |
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Term
| Population Studies for STR Linkage Analysis |
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Definition
| Large numbers of unrelated individuals can be tested for a set of STRs. If an STR shows up in commonly diseases individuals, the STR is likely linked to a disease gene. The results are addressed in probability terms that an individual with that STR is likely to have the disease gene. |
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Term
| Population Studies for STR Linkage Analysis |
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Definition
| Large numbers of unrelated individuals can be tested for a set of STRs. If an STR shows up in commonly diseases individuals, the STR is likely linked to a disease gene. The results are addressed in probability terms that an individual with that STR is likely to have the disease gene. |
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Term
| Sibling Studies for STR Linkage Analysis |
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Definition
Sets f twins, both identical and fraternal, can be used to study environmental and genetic affects. Monozygotic (identical) twins have the same DNA, including disease genes. If both have the same genetic disease, they should share the same linked STR alleles.
Fraternal (dizygotic) twins have the same proportion of shared genes as any sibling pair. |
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Term
| Single Nucleotide Polymorphisms |
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Definition
| Individual human genomes differ every 1000-1500 nucleotides. Most of these differences are variations of just one base. Polymorphisms must be present in at least 1% of the population. Haploid genomes usually differ at 1 nucleotide per 1331 bp. There are a predicted 11 million sites in the 3 billion bp genome that differ in 1% of the population, so each person has 11 million SNPs. 5 million have been identified so far, 99% benign and 60,000 in genes. |
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Term
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Definition
| Blocks of closely placed SNPs are usually inherited together with recombination rarely taking place (haplotypes). A sequence of 2000-6000 bp with up to 60 SNPs can compose a haplotype, so just the SNPs can identify a haplotype. Only 4-5 SNPs have to be detected to identify a haplotype, and these are Tag SNPs. |
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Term
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Definition
| Mitochondrial DNA. A circular molecule of 16569 bp. The G and C distribution of the bands is asymmetrical, with a G-rich heavy (H) and a C-rich light (L) strand. mtDNA sequences are always inherited maternally. |
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Term
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Definition
| 22 tRNA genes, 2 rRNA genes, and 12 genes for the oxidation phosphorylation system. Mutations of these genes can cause neuropathies and myopathies. |
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Term
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Definition
| Hypervariable Region I (HVI) and Hypervariable Region II (HVII) are 2 non-coding regions of mtDNA. There is a reference hypervariable sequence called the Cambridge/Oxford/Anderson reference sequence. |
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Term
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Definition
| There is a predominant promoter, Pl, on the L strand and Ph on the H strand where transcription is started. These are located at sequences called the displacement (D) - loop, a triple-stranded region with a short piece of H strand DNA (7s DNA) synthesized from the H strand. L-strand sequence is limited by a bidirectional attenuator so rRNA and mRNA transcripts are usually from the H strand. Mature mtRNAs are coded from a polycistronic transcript from the tRNA gene. |
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