Genetic Glossary Terms Flashcards
1
Q
ACMG
A
American College of Medical Genetics
2
Q
Allele
A
Alternative form of a genetic locus; a single allele for each locus is inherited from each parent
3
Q
Amino Acid
A
Any of a class of 20 molecules that are combined to form proteins in living things. The sequence of amino acids in a protein and hence protein function are determined by genetic code
4
Q
Amniocentesis
A
Prenatal diagnosis method to obtain amniotic fluid for diagnostic purposes
5
Q
Amplification
A
Any process which increases the number of copies of a specific DNA fragment; can be in vivo or in vitro
6
Q
Autosomal dominant
A
A gene on one of the non-sex chromosomes that can be expressed, even if only one copy is present. The chance of passing the gene to offspring is 50% for each pregnancy
7
Q
Autosome
A
A chromosome not involved in sex determination. The diploid human genome consists of a total of 46 chromosomes: 22 pairs of autosomes and 1 pair of sex chromosomes (the X and Y chromosome)
8
Q
Base pair (bp)
A
two nitrogen bases (adenine and thymine or guanine and cytosine) held together by weak bonds. two strands of DNA are held together in the shape of a double helix by the bonds between base pairs
9
Q
base sequence
A
the order of nucleotide bases in a DNA molecule; determines structure of proteins encoded by that DNA
10
Q
candidate gene
A
a gene located in a chromosome region suspected of being involved in a disease
11
Q
carrier
A
an individual who possesses a mutant allele but does not express it in the phenotype, either because of a dominant allelic partner or because the mutation is nonpenetrant
12
Q
cell
A
the basic unit of any living organism that carries on the biochemical processes of life
13
Q
chorionic villus sampling
A
an invasive prenatal diagnostic procedure involving removal of villi from the human chorion to obtain chromosomes and cell products for diagnosis of disorders in the human embryo
14
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chromosome
A
in the eukaryotic nucleus, one of the threadlike structures consisting of chromatin which carries genetic information arranged in a linear sequence
15
Q
clinical performance
A
a term encompassing clinical sensitivity, clinical specificity, penetrance and gene/environmental modifiers
16
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clinical sensitivty
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the proportion of individuals who do not have a specified clinical disorder and whose test results indicate that the disorder is not present
17
Q
clinical utility
A
the value a test in diagnosing/ruling out a disease, in suggesting treatment or prevention strategies, and in evaluating risks and benefits associated with the test
18
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clinical validity
A
the ability of a test to distinguish affected and unaffected populations, including a determination of the probability of being affected. the clinical sensitivity, specificity and predictive value of a test
19
Q
clone
A
a genetically engineered exact copy of biological material such as a DNA segment, a whole cell or a complete organism
20
Q
cloning
A
using specialized DNA technology to produce multiple, exact copies of a single gene or other segment of DNA to obtain enough material for further study. this process, used by researchers in the Human Genome Project, is referred to as cloning DNA. the resulting cloned (copied) collections of DNA molecules are called clone libraries. a second type of cloning exploits the natural process of cell division to make many copies of an entire cell. the genetic makeup of these cloned cells, called a cell line, is identical to the original cell. a third type of cloning produces complete, genetically identical animals such as the famous sheep, Dolly
21
Q
complex trait
A
trait that has a genetic component that does not follow struct Mendelian inheritance. may involve the interaction of two or more genes or gene environment interactions
22
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confirmatory testing
A
repeat testing generally performed to corroborate a positive test result
23
Q
congenital
A
any trait present at birth, whether the result of a genetic or non-genetic factor
24
Q
contiguous genes
A
genes physically close on a chromosome that, when acting together, express a phenotype
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cytogenetics
the study of the physical appearance of chromosomes
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deletion
the loss of a segment of the genetic material from a chromosome; can lead to a disease or abnormality
27
diagnostic test
a test performed to determine the presence or absence of a specific medical condition
28
DNA (deoxyrionucleic acid)
the molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. the four nucleotides in DNA contain the bases adenine (A), guantine (G), cytosine (C) and thymine (T). in nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner
29
DNA probe
any biochemical used to identify or isolate a gene, a gene product or a protein
30
DNA sequence
the relative order of base pairs, whether in a DNA fragment, gene, chromosome, or an entire genome
31
DNA sequencing
in the plus and minus or primed synthesis method, DNA is synthesized in vitro in such a way that it is radioactively labeled and the reaction terminates specifically at the position corresponding to a given base; in the chemical method, single stranded DNA is subjected to several chemical cleavage protocols that selectively make breaks on one side of a particular base
32
dominant
an allele that is almost always expressed, even if only one copy is present
33
ELSI
ethical, legal and social implications (of Human Genome Project)
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equivocal result
a test result that cannot be interpreted as either negative or positive
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ethics
the study of fundamental principles which defines values and determines moral duty and obligation
36
eugenics
the study of improving a species by artificial selection; usually refers to the selective breeding of humans
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exon
the protein-coding DNA sequence of a gene
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false negative
does have the abnormality or disease and is incorrectly classified by the test
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false positive
does not have the abnormality or disease and is incorrectly classified by the test
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fluorescence in situ hybridization (FISH)
a physical mapping approach that uses fluorescein tags to detect hybridization of probes with metaphase chromosomes and with the less-condensed somatic interphase chromatin
41
gene
a hereditary unit that occupies a certain position on a chromosome; a unit that has one or more specific effects on the phenotype, and can mutate to various allelic forms. the fundamental physical and functional unit of heredity. a gene is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product
42
gene amplification
any process by which specific DNA sequences are replicated disproportionately greater than their representation in the parent molecules; during development, some genes become amplified in specific tissues. repeated copying of a piece of DNA; a characteristic of tumor cells
43
gene product
the biochemical material, either RNA or protein, resulting from expression of a gene. the amount of gene product is used to measure how active a gene is; abnormal amounts can be correlated with disease-causing alleles
44
gene therapy
an experimental procedure aimed at replacing, manipulating, or supplementing nonfunctioning or misfunctioning genes with healthy genes
45
gene transfer
incorporation of new DNA into and organisms cells, usually by a vector such as a modified virus. used in gene therapy
46
genetic code
the sequence of nucleotides, coded in triplets (codons) along the mRNA, that determines the sequence of amino acids in protein synthesis. a genes DNA sequence can be used to predict the mRNA seuqnece, and the genetic code can in turn be use to predict the amino acid sequence
47
genetic counseling
the educational process that helps individuals, couples or families to understand gentic information and issues that may have an impact on them
48
genetic discrimination
prejudice against those who have or are likely to develop an inherited disorder
49
genetic engineering
altering the genetic material of cells or organisms to enable them to make new substances or perform new functions
50
genetic marker
a gene or other identifiable portion of DNA whose inheritance can be followed
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genetic modifers
other genes that can influence the phenotype associated with the gene of interest
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genetic polymorphism
difference in DNA sequence among individuals, groups or populations
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genetic predisposition
a genotype that increases the risk but is insufficient to result in disease. impaired expression of alleles at other gene loci and/or environmental factors are needed before the disease appears
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genetic screening
testing a group of people to identify individuals at high risk of having or passing on a specific genetic disorder
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genetic testing
analyzing an individuals genetic material to determine predisposition to a particular health condition or to confirm a diagnosis of genetic disease
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genetic variation
a phenotypic variability of a trait in a population attributed to genetic heterogeneity
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genetics
the study of inheritance patterns of specific traits
58
genome
all the genetic material in the chromosomes of a particular organism; its size is generally given as its total number of base pairs
59
genome project
research and technology-development effort aimed at mapping and sequencing the genome of human beings and certain model organisms
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genotype
the genetic constitution of an organism, either overall or at a specific locus, as distinguished from its physical appearance (its phenotype); the specific allelic composition of a gene, or set of genes, established at DNA level
61
Hardy-Weinberg Law
the concept that both gene frequencies and genotype frequencies will remain constant from generation to generation in an infinitely large, interbreeding population in which mating is at random and there is no selection, migration or mutation
62
homozygote
having two alleles on homologous chromosomes that are identical for a given gene
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heterozygote
having two alleles on homologous chromosomes that are different for a given gene
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human genome project
collective name for several projects begun in 1986 by the department of energy to create an ordered set of DNA segments from known chromosomal locations, develop new computational methods for analyzing genetic map and DNA sequence data, and develop new techniques and instruments for detecting and analyzing DNA. this DOE initiative is now known as this. the joint national effort, led by DOE and NIH, is known as this
65
hybridization
the pairing of a single-stranded, labeled probe (usually DNA) to its complementary sequence
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in situ hybridization
the pairing of a single-stranded, labeled probe (usually DNA) to its complementary sequence within intact, banded chromosomes
67
in vitro
studies performed outside a living organism such as in a laboratory
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in vivo
studies carried out using living organisms
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incidence
number or proportion or new cases of a specified condition in a population over a specified time period
70
incomplete penetrance
the gene for a condition is present, but not obviously expressed, in all individuals with the gene in a family
71
inherit
in genetics, to receive genetic material from parents through biological processes
72
karyotype
a set of photographed, banded chromosomes arranged in order from largest to smallest in a standard format showing the number, size, and shape of each chromosome type; used in low-resolution physical mapping to correlate gross chromosomal abnormalities with the characteristics of specific diseases
73
kilobase (kb)
unit of length for DNA fragments equal to 1000 nucleotides
74
locus (pl. loci)
the position on a chromosome of gene or other chromosome marker; also the DNA at that position. the use of locus is sometimes restricted to mean expressed DNA regions
75
megabase (Mb)
unit of length for DNA fragments equal to 1 million nucleotides
76
Mendelian inheritance
one method in which genetic traits are passed from parents to offspring. named for Gregor Mendel, who first studied and recognized the existence of genes and this method of inheritance
77
molecular biology
the study of the structure, function and makeup of biologically important molecules
78
molecular genetics
the study of macromolecules important in biological inheritance
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monogenic disorder
a disorder caused by mutation of a single gene
80
multifactorial
a characteristic influenced in its expression by many factors, both genetic and environmental
81
mutation
any heritable change in DNA sequence. a process by which genes undergo a structural change
82
nucleus
the cellular organelle in eukaryotes that contains most of the genetic material
83
oligonucleotide
a molecule usually composed of 25 or fewer nucleotides; used as a DNA synthesis primer
84
patent
in genetics, conferring the right or title to genes, gene variations, or identifiable portions of sequences genetic material to an individual or organization
85
PCR
see polymerase chain reaction
86
pedigree
a family tree diagram that shows how a particular genetic trait or disease has been inherited through many generations of a family
87
penetrance
the frequency with which a genotype manifests itself in a specific phenotype; the proportion of individuals who manifest that genotype at the phenotypic level. for example, if 100 females have two D mutations and 70 have symptoms of the disorder, the penetrance is 70%
88
phenotype
the biochemical, physiological and physical characteristics of an individual, as determined by the genotype and the environment in which it is expressed; also in a more limited sense, the expression of some particular gene or genes
89
polymerase
any enzyme that catalyzes the formation of DNA or RNA from deoxyribonucleotides or ribonucleotides
90
polymerase chain reaction (PCR)
a method for amplifying a DNA base sequence using a heat-stable polymerase and two 20-base primers, one complementary to the positive strand at one end of the sequence to be amplified and one complementary to the negative strand at the other end. because the newly synthesized DNA strands can subsequently service as additional templates for the same primer sequences, successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample
91
polymorphism
frequently occurring (common), usually normal variation, in a defined nucleotide sequence. these in genes may result in protein polymorphisms. a protein polymorphism is said to occur when the most common allele has a frequency of no greater than 99%
92
prevalence
the proportion of individuals in a population having a disease
93
primer
short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase
94
proband
individual in a family who brought the family to medical attention
95
probe
single-stranded DNA or RNA molecules of specific base sequence, labeled either radioactively or immunologically, that are used to detect the complementary base sequence by hydridization
96
protein
a large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nucleotides in the gene that codes for the protein. proteins are required for the structure, function, and regulation of the body's cells, tissues, and organs; and each protein has unique functions, examples are hormones, enzymes and antibodies
97
public policy
a set of action guidelines or rules that results from the actions or lack of actions of governmental entities
98
recessive gene
a gene which will be expressed only if there are 2 identical copies or, for a male, if 1 copy is present on the X chromosome
99
recombinant DNA technology
procedure used to join together DNA segments in a cell-free system (an environment outside a cell or organism). under appropriate conditions, a recombinant DNA molecule can enter a cell and replicate there, either autonomously or after it has become integrated into a cellular chromosome
100
restriction fragment length polymorphism (RELP)
variation between individuals in DNA fragment sizes cut by specific restriction enzymes; polymorphic sequences that result in RFLPs are used as markers on both physical maps and genetic linkage maps. RLFPs usually are caused by a mutation at a cutting site
101
screening test
a test designed to identify subjects who are at sufficient risk of a specific disorder to benefit from further investigation or preventive action, among those who have not sought medical attention on account of symptoms of that disorder
102
sensitivity
the proportion of individuals with the abnormality or disease that will have a positive test
103
single nucleotide polymorphism (SNP)
DNA sequence variations that occur when a single nucleotide (A, T, C or G) in the genome sequence is altered
104
single gene disorder
hereditary disorder caused by a mutant allele of a single gene
105
Southern blotting
transfer by absorption of DNA fragments separated in electrophoretic gels to membrane filters for detection of specific base sequences by radio-labeled complementary probes
106
specificity
the proportion of individuals without the abnormality or disease that will have a negative test
107
syndrome
the group or recognizable pattern of symptoms or abnormalities that indicate a particular trait or disease
108
trait
any detectable phenotypic property of an organism
109
true negative
does not have the abnormality or disease and is correctly classified by the test
110
true positive
does have the abnormality or disease and is correctly classified by the test
111
validation
the action (or process) of proving that a procedure, process, system, equipment or method used works as expected and achieves the intended result (can be performed at both analytical and clinical level)
112
verification
confirmation by examination and provision of objective evidence that specified requirements have been fulfilled
113
wild type
the form of an organism that occurs most frequently in nature
114
alternative splicing
use of different exons in formation of mRNA from initially identical transcripts. this results in the generation of related proteins from one gene, often in a tissue or developmental stage-specific manner
115
candidate gene
a gene believed to influence expression of complex phenotypes due to known biological and/or physiological properties of its products, or to its location near a region of associated or linkage
116
complementary DNA
a DNA copy of the messenger RNA (mRNA) transcribed from a gene. the cDNA is made from the mRNA using the enzyme reverse transcriptase
117
codon
three bases in a DNA or RNA sequence that specify a single amino acid
118
copy number variants
stretches of genomic sequence of roughly 1000 base pairs (1kb) to 3 million base pairs (3Mb) in size that are deleted or are duplicated in varying numbers
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comparative genomic hybridization
tech wherein a DNA test sample is competitively hybridized with a reference sample of DNA of known sequence to a DNA microarray, used to detect copy number changes in the test sample
120
coverage
the number of times a portion of the genome is sequenced in a sequencing reaction. often expressed as "depth of coverage" and numerically as 1X, 2X, 3X etc.
121
DNA barcoding
a method that uses a short genetic marker in a DNA sequence to identify it as belonging to a particular species or group of otherwise-related sequences
122
exome
the entire portion of the genome consisting of protein-coding sequences (as opposed to introns or noncoding DNA between genes)
123
exon
any segment of a gene that is represented in the mature messenger RNA (mRNA) product
124
frame shift mutation
any mutation that disrupts the normal sequence of triplets causing a new sequence to be created that codes for different amino acid. frame shift mutations are usually caused by an insertion or deletion of DNA and typically eventually produce a premature stop codon
125
GC content
the percentage of nucleotides in a DNA sequence that are either guanine (G) or cytosine (C)
126
genome
the sum total of the genetic material of a cell or an organism
127
genome-wide analysis
a genetic study evaluating the potential linkage of genetic markers located throughout the genome to a specific trait. this approach has been used for mendelian disorders as well as complex traits (genome-wide association study)
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genomics
the study of genes and their function
129
genotype
the specific set of 2 alleles inherited at a genetic locus
130
haplotype
the combination of linked marker alleles (may be polymorphisms or mutations) for a given region of DNA on a single chromosome
131
HapMap
the international hapmap project developed a haplotype map of the human genome, the hapmap, that describes the common patterns of human DNA sequence variation. the hapmap is a key resource for finding genes affecting health, disease, and responses to drugs and environmental factors. the frist release of the hapmap was made in 2005
132
hybridization
the bonding of single-stranded DNA or RNA into double-stranded DNA or RNS. the ability of complementary stretches of DNA or RNA to hybridize with each other is dependent on the base-pair sequence
133
intron
a segment of DNA that is transcribed into RNA but is ultimately removed from the transcript by slicing together the sequences on either side (exons) to produce messenger RNA (mRNA)
133
library
a complete set of clones that contains all the genetic material from an organism, tissue, or specific cell type at a specific stage of development
134
linkage
two loci that reside close enough to each other that recombination rarely occurs between them. alleles at the 2 loci do not assort independently at meiosis but are likely to be inherited together
135
locus (loci)
the physical site on the chromosome occupied by a particular gene or other identifiable DNA sequence characteristic
136
Mendelian disorder
a trait or disease that follows the patters of inheritance that suggest the trait or disease is determined by a gene at a single locus
137
methylation
covalent attachment of methyl groups to DNA, usually at cytosine bases.
138
missense mutation
a mutation that is typically the change of a single nucleotide that results in the substitution of one amino acid for another in the final gene product
139
mutation
any alteration of a gene or genetic material from its natural state. generally mutations refer to changes that alter the gene in a negative sense causing the protein product of the gene to have an altered function
140
next generation/high-throughput sequencing
DNA sequencing technology that permits rapid sequencing of large portions of the genome; so called because it vastly increases the throughput over classic sanger sequencing
141
nonsense mutation
any mutation that results directly in the formation of a stop codon
142
oncogene
a gene, 1 or more forms of which is associated with cancer. many of these are involved, directly or indirectly, in controlling the rate of cell growth
143
plasmid
circular extrachromosomal DNA molecules in bacteria that can independently reproduce. plasmids can be used as vectors in recombinant DNA research, and they can contain genes important to bacterial virulence such as antibiotic resistance in nature
144
polymerase chain reaction
a procedure in which segments of DNA can be amplified using flanking oligonucelotides called primers and repeated cycles of replication by DNA polymerase
145
polymorphism
difference in DNA sequence among individuals that may underlie differences in health. genetic variations occurring in more than 1% of a population would be considered useful polymorphisms for genetic linkage analysis. the vast majority of DNA polymorphisms are benign and not associated with a detectable phenotype
146
proband
that affected person whose disorder, or concern about a disorder, brings a family or pedigree to be genetically evaluated
147
promoter
the sequence of nucleotides located 5' to the coding sequence of a gene that determines the site for binding of RNA polymerase and the initiation of transcription. more than 1 promoter may be present in a gene and may give rise to different versions of the protein
148
pyrosequencing
a method of determining the ordering of nucleotide bases in a DNA molecule by measuring the synthesis of the complementary DNA strand
149
quantitative PCR
a PCR-based lab technique that allows the accurate measurement of the amount of specific nucleic acids (usually RNA) in a sample
150
read
a discrete segment of sequence information generated by a sequencing instrument; read length refers to the number of nucleotides in the segment
151
recombination
the formation of a new set of alleles on a single chromosome that is not the same as either parent owing to a crossover during meiosis
152
restriction fragment-length polymorphism (RELP)
a type of polymorphism that results from variation in the DNA sequence recognized by restriction enzymes. RFLPs can be used in linkage and gene association studies of traits and diseases
153
single-nucleotide polymorphism (SNP)
DNA sequence variation that occur when a single nucleotide in the genome sequence is altered. SNPs are the most abundant variant in the human genome and are the most common source of gnetic variation, with more than 10 million SNPs present in the human genome, representing a density of 1 SNP for approximately every 100 bases
154
stop codon
the DNA triplet that causes translation to end when it is found in messenger RNA. the DNA stop codons are TAG, TAA and TGA
155
TagSNP
a readily measured SNP that is in string linkage disequilibrium with multiple other SNPs so that it can serve as a proxy for these SNPs on large-scale genotyping platforms
156
translocation
a chromosomal segment that has been broken off and reinserted in a different place in the genome
157
uniparental disomy
the inheritance of both parental copies of a chromosome from one parent and no homologous chromosome from the other parent. the resulting offspring could be affected with a recessive disease if the parent contributing both copies is a carrier
158
variant of unknown significance (VUS)
genetic variant that cannot be definitively determined to be associated with a specific phenotype
