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Molecular Diagnostics > DNA Polymorphisms and Human Identification > Flashcards

DNA Polymorphisms and Human Identification Flashcards

1
Q

SNPs

A

Single Nucleotide Polymirohisms. A single nucleotide variation from the reference sequence.

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2
Q

LINEs

A

Long Interspersed Nucleotide Elements. Highly repeated sequences located throughout the human genome that contain RNA polymerase promoters and open reading frames related to the reverse transcriptase of retroviruses. 6-8 kilobases long.

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3
Q

SINEs

A

Short Interspersed Nucleotide Elements. Highly repeated sequences .3 kilobases long located throughout the human genome. Present in over 1mil copies per genome.

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4
Q

Alu Elements

A

Short interspersed nucleotide sequences containing recognition sites for the Alu restriction enzyme.

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5
Q

Psuedogenes

A

Intronless, nonfunctional copies of active genes.

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6
Q

STRs

A

Short Tandem Repeats. Shorter blocks of repeated sequences that undergo expansion or shrinkage through generations. 1-10bp.

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7
Q

VNTRs

A

Variable-Number Tandem Repeats. Shorter blocks of repeated sequences that undergo expansion or shrinkage through generations. 10-150bp.

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8
Q

RFLPs

A

Restriction Fragment Length Polymorphisms. A sequence variation that results in creating, destroying, or moving a restriction site.

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9
Q

Locus

A

Gene or region of DNA.

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10
Q

Allele

A

Version of a gene, sequence, or locus.

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11
Q

Homozygous

A

A pair of alleles in a human is the same.

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12
Q

Heterozygous

A

A pair of alleles in a human is different.

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13
Q

Inclusion

A

Alleles from a father that a child inherits.

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14
Q

Exclusion

A

In human identification, elimination of a person. Difference of one allele from a reference source.

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15
Q

MLP

A

Multiple-Locus Probe. Southern blot that utilizes three to five probes to analyze three to five loci on the same blot.

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16
Q

SLP

A

Single-Locus Probe. Analysis of one locus at a time. Yields better results than MLPs.

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17
Q

Continuous Allele System

A

Sizes of fragments define alleles. RFLP.

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18
Q

Profile

A

A set of RFLP. A set of markers, alleles, or other characteristics in an individual.

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19
Q

Microsatellites

A

DNA from highly repeated short sequences (STRs) such that it differs in density from nonrepeated DNA.

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20
Q

Minisatellites

A

DNA from highly repeated short sequences (VNTRs) such that it differs in density from nonrepeated DNA.

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21
Q

Microvariants

A

A repeated sequence with altered DNA, missing one or more bases of the repeat.

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22
Q

Mini-STR

A

STRs amplified with PCR primers located closer to the tandem repeat than in the standard STR.

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23
Q

Y-STR

A

Short tandem repeats located on the Y chromosome. Can be used for surname testing and forensic identification of males.

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24
Q

Allelic Ladders

A

Set of fragments representing all possible alleles of a population.

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25
Q

Discrete Allele Fragments

A

A set of alleles that can be classified by a finite number of types.

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26
Q

Amelogenin Locus

A

A marker often analyzed along with STR. Located on the X and Y chromosome.

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27
Q

CODIS

A

Combined DNA Indexing System. A set of 13 STR loci and amelogenin used for positive identification.

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28
Q

Locus Genotype

A

The set of inherited alleles at a particular site on homologous chromosomes, such as STR repeats or SNPs.

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29
Q

Stutter

A

An anomaly of PCR amplification in which the polymerase may miss a repeat during the replication process, resulting in two or more different species in the amplified product.

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30
Q

Bin

A

An acceptable range of sizes in genotyping.

31
Q

Bin

A

In fragment analysis, an acceptable range of sizes in genotyping.

32
Q

Binning

A

In fragment analysis, collection of all peaks or bands within a characteristic distribution of positions and areas.

33
Q

Locus-specific Brackets

A

An alternative assessment of allele certainty. Definition of a high and low limit of migration within which alleles are identified.

34
Q

Match Probability

A

Probability of identity or inheritance of a set of genetic alleles.

35
Q

Hardy-Weinberg Equilibrium

A

The relative frequency of two alleles in a population remains constant.

36
Q

Likelihood Ratio

A

The comparison of the probability that the two genotypes came from the same person with the probability that the two genotypes came from different persons, taking into account different allele frequencies and linkage equilibrium in the population.

37
Q

Paternity Index

A

Likelihood of paternity.

38
Q

Paternity Index

A

Likelihood of paternity. Genetic evidence.

39
Q

Linkage Equilibrium

A

The assumption that two alleles are not genetically linked.

40
Q

Probability of Paternity

A

A number calculated from the combined paternity index and prior odds.

41
Q

Combined Paternity Index

A

CPI. Summarizes and evaluates the genotype information. Multiplies together the paternity index for each locus.

42
Q

Kinship Index

A

AKA sibling index or combined sibling index. The likelihood ratio generated by a sibling test.

43
Q

Prior Odds

A

Nongenetic evidence. Initial probability of an event prior to test results.

44
Q

Kinship Index

A

AKA sibling index or combined sibling index. The likelihood ratio generated by a sibling test to determine if two individuals share one or both parents.

45
Q

Avuncular Testing

A

Another type of relationship analysis that measures the probabilities that two alleged relatives are related as either an aunt or and uncle through genetic polymorphisms.

46
Q

Autosomal STRs

A

Short tandem repeats located on a chromosome other than the X and Y chromosomes.

47
Q

HD

A

Haplotype Diversity. Calculated from the frequency of occurrence of a given haplotype in a tested population.

48
Q

DC

A

Discrimination Capacity. This determines the number of different haplotypes seen in the tested population and the total number of samples in the population. Another measure of profile uniqueness.

49
Q

DC

A

Discrimination Capacity. The power of a locus for use in identification, considering the number of different alleles of the locus and the total number of individuals tested in a given population.

50
Q

Minimal Haplotype

A

8 Y-STR loci used as markers for parental lineage testing and matching.

51
Q

Extended Haplotype

A

All of the loci from the minimal haplotype plus the highly polymorphic dinucleotide repeat. Used for lineage testing and matching.

52
Q

Linkage Analysis

A

Family history, population studies, and sibling analyses can be used to map genes since many of the locations of STRs in the genome are known.

53
Q

Linkage Disequilibrium

A

The assumption that two alleles are genetically linked.

54
Q

Allogenic

A

Between two individuals.

55
Q

Hematopoietic Stem Cells

A

Peripheral blood stem cells.

56
Q

Hematopoietic Stem Cells

A

Peripheral blood stem cells.

57
Q

Hematopoietic Stem Cells

A

HPC. Undifferentiated white blood cells that can differentiate into multiple blood cell lineages.

58
Q

GVT Effect

A

Graft Versus Tumor Effect.

59
Q

GVT Effect

A

Graft Versus Tumor Effect. Immune reaction by donor cells (graft) on residual tumor cells after a bone marrow transplant for treatment of malignant disease.

60
Q

GVHD

A

Graft Versus Host Disease. Phenotypic manifestations of immune reaction by donor cells (graft) to the recipient (host) after a bone marrow transplant.

61
Q

MUD

A

Matched Unrelated Donor. Anonymous unrelated contributors selected from a pool based on HLA typing.

62
Q

Mosaic

A

Cells arising from the same zygote have undergone a genetic event, resulting in two clones of phenotypically different cells in the same individual.

63
Q

Informative Locus

A

One locus in which the donor alleles differ from the recipient alleles.

64
Q

Informative Locus

A

One locus in which the donor alleles differ from the recipient alleles.

65
Q

Noninformative Locus

A

The donor and recipient have the same alleles.

66
Q

Full Chimerism

A

Only the donor alleles were detected in the recipient after transplant.

67
Q

Mixed Chimerism

A

A mixture of donor alleles and recipient alleles are found in the recipient after transplant.

68
Q

Graft Failure

A

Only the recipient alleles were present after transplant.

69
Q

Fragment Analysis

A

Analysis after capillary electrophoresis that looks at peak sizes and peak areas.

70
Q

HV1

A

Hypervariable Region 1. One of the noncoding regions in the mitochondrial genome.

71
Q

HV2

A

Hypervariable Region 2. One of the noncoding regions in the mitochondrial genome.

72
Q

Cambridge Reference Sequence

A

AKA The Oxford Sequence or the Anderson Reference. The reference mtDNA hypervariable region is the sequence published initially by Anderson,

73
Q

Heteroplasmy

A

More than one mtDNA sequence present in the same individual.

74
Q

Paternal Lineage Test

A

Can determine if two or more males have a common paternal ancestor.

Molecular Diagnostics (20 decks)

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