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Terminology Flashcards

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1
Q

Locus

A

A unique chromosomal location

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2
Q

Allele

A

different variants of the same coding sequence (locus)

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3
Q

Homozygous

A

identical maternal and paternal alleles

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4
Q

Heterozygous

A

non-identical maternal and paternal alleles

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5
Q

Hemizygous

A

only having inherited one allele

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6
Q

Genotype

A

genetic characteristics/ combination of alleles in an organism

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7
Q

Phenotype

A

observed genetic characteristics/traits shown by the individual

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8
Q

mutation

A

process that gives rise to chages in base sequences or the outcome i.e. the altered sequence

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9
Q

substitution

A

the change of one nucleotide to another

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10
Q

deletion

A

one or more nucleotides are deleted (can also occur with larger chromosome fragments)

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11
Q

insertion

A

on or more nucleotides are inserted (not a copy of the ones around)
(can occur with both small and larger segments)

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12
Q

duplication

A

a copy of the sequence directly close by is inserted (can occur with both small and larger segments)

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13
Q

inversion

A

original nucleotide sequence is reversed and flipped 180 degrees (can occur with both small and larger segments)

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14
Q

conversion

A

sequence copied from another site in the genome replacing the original sequence

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15
Q

balanced structural variation

A

the DNA variant has the same content but some of it is located somewhere else in the genome

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16
Q

translocation

A

two different DNA molecules (chromosomes) receive a double strand break and exchange fragments without any change in content

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17
Q

Indel

A

collective name for insertion/deletion

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18
Q

unbalanced structural variation

A

DNA variants that differ in DNA content compared to the reference

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19
Q

CNV

A

copy number variation eg. large indels or tandem duplications

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20
Q

De novo mutation

A

a new variant apparent in neither of the biological parents

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21
Q

Genetic mosaicism

A

a state which an individual has 2 or more genetically different sets of cells in his/her body occurs eg if mutations occurs early during embryonic development

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22
Q

SNP

A

single nucleotide polymorphism. A DNA variant that only spans one base pair, Needs to be present in at least 1% of the population

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23
Q

Neutral variation

A

variation which has little to no effect on the phenotype

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24
Q

Population genetics

A

The science of allele frequencies and how they differ between populations and subpopulations

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25
Q

Haplotype

A

combination of alleles at the same chromosomal segment

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26
Q

gene pool

A

all alleles at a given locus across a population

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27
Q

The Hardy Weinberg Equation

A

a mathematical equation that can be used to calculate the genetic variation of a population in equilibrium. p^2+2pq+q^2=1
p+q=1

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28
Q

Linkage Disequilibrium

A

the tendency of some alleles to be transmitted together more or less often than expected by chance alone. usually caused by close proximity of genes on the same chromosome

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29
Q

Haplotype blocks

A

Blocks of the genome that are created by correlated SNPs inherited together

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30
Q

genetic drift

A

changes in allele frequencies due to chance

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31
Q

Heterozygosity measure (Nei’s statistics)

A

probability that two alleles at a locus drawn at random from a population will be different from each other

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32
Q

population mutation parameter Ꝋ

A

the diversity per nucleotide that is expected due to the balance between mutation creating new alleles and drift to fixation eliminating them

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33
Q

Diversity: the bottle neck effect

A

a drastic reduction of effective population size, leaving only a lower random set of alleles

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34
Q

Founder effect/event

A

when a small number of individuals form a new population with their set of alleles

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35
Q

negative selection or purifying selection

A

the selective removal of alleles that are deleterious

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36
Q

dN/dS

A

the ratio of nonsynonymous to synonymous substitutions

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37
Q

positive selection (darwinian selection)

A

promotes frequency of advantagous DNA variants

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38
Q

Fst (st subscripted)

A

a measure of how different two (sub)populations are by considering how much heterozygosity would be gained if the two were a single random-mating population (F= 0 –> identical populations F=1 compleate separation)

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39
Q

genealogical ancestry

A

individuals who would feature in your genealogy if you were able to trace it all the way back

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40
Q

Genetic ancestry

A

Individuals from whom you inherit significant parts of your genome

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41
Q

coefficent of inbreeding

A

the probability that an individual recive two alleles at a given locus that are identical by decent

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42
Q

coefficent of relationship

A

the proportion of alleles two individuals share that are identical by decent

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43
Q

Identical by state (IBS)

A

the same DNA sequence but might not be from the same descent

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44
Q

Identical by descent (IBD)

A

the same DNA sequence (alleles) that are due to same ancestry

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45
Q

effective population size

A

proxy of the number of individuals in a population that contribute their genes to the next generation

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46
Q

Mutation-drift equilibrium

A

variation is gained by mutation at the same rate as it is lost by drift and selection (–> the effective population size stays the same)

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47
Q

autosome

A

A chromosome which is not a sex chromosome

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48
Q

p-arm

A

the short (petite) arm of the chromosome

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49
Q

q-arm

A

the large arm of the chromosome

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50
Q

centromere

A

part of the chromosome which separates the p and the q arm

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51
Q

telomere

A

repetitive DNA sequences at the end of the chromosomes which protects them from damage

52
Q

zygote

A

a fertilized egg

53
Q

karyotype

A

a photomicrograph of the full set of chromosomes in metaphase from a single cell nucleus arranged in pairs in descending order of size

54
Q

Aneuploidies

A

the chromosomal constitution of cells which deviate from the normal by addition or subtraction of chromosomes

55
Q

Trisomy

A

three copies of a chromosome

56
Q

monosomy

A

one copy of a chromosome

57
Q

non-disjunction

A

that a pair of chromosomes has failed to separate or segregate at anaphase –> both chromosomes pass to the same dauther cell

58
Q

sub-microscopic structural rearrangements

A

small deletions, tandem duplications, inversions, insertions etc. (but still on chromosome level?)

59
Q

haploinsufficency

A

a genetic variation that results in reduced gene dosage

60
Q

Contigous gene syndromes

A

Disorders caused by deletion of multiple gene loci that are adjacent to one another. Contiguous gene syndromes are characterized by multiple, apparently unrelated, clinical features caused by deletion of the multiple adjacent genes

61
Q

congenital abnormalities

A

structural or functional abnormalities that occur during intrauterine life

62
Q

gene dosage

A

the number of copies of a single gene within a genome

63
Q

copy number variation (CNV)

A

phenomenon which sections of the genome are repeated and the number of repeats in the genome varies between individuals

64
Q

recombination

A

the process by which genetic material is exchanged between the two homologous chromosomes

65
Q

meiosis

A

cell divisions where haploid germ cells are generated

66
Q

gene

A

region encoding a protein or an RNA molecule

67
Q

homologues

A

the pair of two corresponding chromosomes or genes

68
Q

Chromatide

A

one of the homologous chromosomes

69
Q

Haplotype

A

combination of linked alleles on the same homologue

70
Q

SNV

A

single nucleotide variant. A DNA variant that only spans one base pair. unlike SNP does not have to be present in a specific frequency in the population

71
Q

mutation

A

rare allele. Under 1% of the population has it, often associated with disease

72
Q

polymorphism

A

common allele (above 1% in the population) may be associated with increased disease RISK

73
Q

penetrance

A

percentage of individuals with a specific genotype showing the phenotype

74
Q

dominant

A

alleles which influence the phenotype both in homozygous and heterozygous state

75
Q

recessive

A

alleles that only influence the phenotype in the homozygous state

76
Q

Consanguineous parents

A

parents which are related

77
Q

the two hit model/hypothesis

A

The hypothesis that most tumor suppressor genes require both alleles to be inactivated eg. one inherited mutation and one somatic mutation

78
Q

genetic heterogeneity

A

different genes may if mutated cause the same phenotype

79
Q

allelic heterogeneity

A

different variants in a specific gene may cause variable phenotypes

80
Q

Lyonisation

A

x-chromosome inactivation

81
Q

Imprinting

A

the variable phenotypic expression of a gene depending on whether it is of paternal or maternal origin which is a function of the DNA methylation pattern. Imprinted regions are observed to be more methylated and less transcriptionally active

82
Q

mendelian disease

A

monogenetic disease. difference in a single gene

83
Q

STR markers

A

short tandem repeat markers (microsatellites) eg used in forensics

84
Q

multiplex PCR

A

methods for using more than one primer set in a polymerase chain reaction to amplify more than one segment of the target DNA sequence in a single reaction

85
Q

miniSTRS

A

reduced size STR amplicons which are created by moving the forward and reverse primer in close to the STR repeat region

86
Q

orthologous (genes)

A

genes in different species that derive from a common ancestral gene (the splitting of lineages)

87
Q

paralougous (genes)

A

genes that are homologous due to an ancestral gene duplication event

88
Q

microsatellites

A

non-coding tandem repeats of two to six nucleotides

89
Q

pseudogene

A

genes bearing close resemblance to known genes at different loci but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation

90
Q

retropseudogene/ processed pseudogenes

A

pseudogenes which lacks introns and contain a poly-A segment near the downstream end

91
Q

retrotransposition

A

insertion of DNA sequences mediated by an RNA intermediate

92
Q

alternative splicing

A

a process whereby multiple RNA transcripts are generated from a single gene –> alternative forms of mature messenger RNA

93
Q

ELSI

A

Ethical Legal Social Implications of human genome research

94
Q

ENCODE

A

the ENCyclopeadia Of DNA Elements - a project which aims to identify all functional elements in the human genome

95
Q

GWAS

A

Genome Wide Association Study. A study based on analysis comparing allele frequency of all available polymorphic markers (DNA markers/mutations/SNPs) in unrelated patients with a specific condition and those of healthy controls to identify markers associated with a specific condition

96
Q

HapMap project

A

project aimed to develop a haplotype map of the human genome describing the common patterns of human genetic variation

97
Q

VNTRs/SSRs

A

variable number tandem repeats/ single sequence repeats. Tandem repeats that vary greatly in number among individuals

98
Q

minisatellite

A

non-coding tandem repeats of 10-100 nucleotides

99
Q

copy number neutral loss of heterozygousity

A

a phenomenon whereby one of two homolougous chromosomal regions is lost but various mechanisms have ensured the presence of two identical copies of such region in the genome eg. you get 2 alleles from your mother but non from your father or by mitotic recombination

100
Q

epigenetics

A

the study of heritable changes in gene function that cannot be explained by changes in DNA sequence

101
Q

pharmaco-genomics

A

the science of understanding the correlation between the individual patients genetic make-up and their response to drugs

102
Q

heritability

A

the degree of the phenotypic variation (in a population) that is estimated to be caused by genetic differences

103
Q

oncogene

A

a gene in which gain of function alterations lead to neoplastic cell transformation

104
Q

tumor suppressor gene

A

genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check

105
Q

complex disease

A

difference in multiple genes in addition to environment

106
Q

genetic marker

A

a DNA sequence with a known physical location on a chromosome (e.g. SNVs and microsatellites)

107
Q

genetic mapping

A

the process of establishing the locations of loci on the chromosomes

108
Q

genetic distance

A

the distance between two loci based on recombination fraction. The genetic length over which one crossover occurs in 1% of meioses. Expressed in cM (centi-Morgan)

109
Q

linkage

A

the tendency of genes or other DNA sequences at a specific loci to be inherited together as a consequence of their physical proximity on a single chromosome

110
Q

linkage analysis

A

mathematical model of the extent to which a given marker tends to be co-transmitted with a disease through families. Can result in mapping a disease to a specific chromosome region

111
Q

LOD score

A

a statistical measure of the likelihood of obtaining the test data if the two loci are linked to the likelihood of observing the same data purely by change (likelihood of linkage/likelihood that the loci are unlinked)

112
Q

Autozygosity

A

when you are homozygous due to the fact that your maternal and paternal chromosome are derived from the same common ancestor

113
Q

sensitivity

A

measure of how often a test correctly generates a positive result for people who have the condition (e.g. how rare are false negatives)

114
Q

specificity

A

measure of the ability of a test to correctly generate a negative result for people who don’t have the condition (e.g. how rare are false positives)

115
Q

Precision/accuracy

A

How reproducible or correct a test is

116
Q

utilitarianism

A

an ethical principle that says that actions (good/bad) should be evaluated based on their consequences

117
Q

duty ethics

A

an ethical principle that judges the intention of an action rather than the consequence/ some actions are prohibited regardless of the consequences

118
Q

virtue ethics

A

an ethical principle that judges the character of a person rather than isolated actions i.e. an action is right if it is the kind of action that a virtuous person would do

119
Q

ccffDNA

A

Circulating Cell Free Fetal DNA

120
Q

missense mutation

A

a point mutation leading to an amino acid substitution

121
Q

nonsense mutation

A

a point mutation leading to a premature stop codon in turn leading to a truncated protein

122
Q

splicing mutation

A

a mutation that occur at the boundary of an exon and an intron which disrupts the RNA splicing

123
Q

frame-shift mutation

A

a small deletion or addition (duplication) of nucleotides which causes a shift in the reading frame of the RNA leading to many incorrect amino acids in the protein

124
Q

trinucleotide repeat expansions

A

increased number of a particular series of nucleotides eg. CAG leading to disease

125
Q

(genetic) anticipation

A

The tendency that a disease appears to be more severe in later generations

Molecular genetics (1 decks)

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