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Genomics Glossary
Like any other scientific field, the study of genetics and genomics brings with a slew of buzzwords and terms. Some key ones are listed below.
A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - R - S - T - U - V - W - X - Y - Z
-A-
- Allele
- alternative DNA sequence at the same physical gene locus, which may or may not result in different phenotypic traits
- Allele Frequency
- the fraction of the gene copies that share a particular form
-B-
- Bioinformatics
- the large-scale storage, retrieval and assessment of data from biological studies. This field draws on high-performance computing, software and information technology
- Biomarker
- a substance used as an indicator of a biological state. It is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention
-C-
- Candidate gene
- gene that is mutated at a higher rate in disease than predicted by random chance. Mutations in these genes are called ‘driver mutations’
- Chromosomal locus
- location of a gene on a chromosome. For example, for a gene whose chromosomal location is listed as 5p14.2, ‘5’ refers to the chromosome number, ‘p’ refers to the chromosome’s short arm (p for ‘petit’ in French; q indicates the long arm), 14.2 represent the position on the arm (in this case, band 14, sub-band 2). Bands are numbered, with band 1 located nearest the centromere.
- Chromosomal inversion
- reversing the orientation of a chromosomal segment
- Codon
- a tri-nucleotide sequence which encodes for an amino acid
- Copy number variant (CNV)
- a segment of DNA in which copy-number differences have been found by comparison of two or more genomes. CNVs may either be inherited or caused by de novo mutation. CNVs can be caused by genomic rearrangements such as deletions, duplications, inversions, and translocations.
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-D-
- Deletion
- removal of one or more nucleotides from the DNA. Note that a deletion is not the exact opposite of an insertion: the former is quite random while the latter consists of a specific sequence inserting at locations that are not entirely random or even quite narrowly defined. Large-scale deletions lead to loss of the genes within those regions
- DNA Microarray
- a multiplex technology, consisting of an arrayed series of thousands of microscopic spots of DNA oligonucleotides each containing picomoles (10−12 moles) of a specific DNA sequence (‘probes’ or ‘reporters’). This can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample (‘target’) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. Since an array can contain tens of thousands of probes, a microarray experiment can accomplish many genetic tests in parallel.
- DNA mismatch repair
- a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage
- Driver and passenger mutations
- Many somatic mutations accumulate during the process of tumor development. Small subsets of these mutations contribute to tumor development and are referred to as ‘driver mutations’, whereas the majority are effectively neutral and are called ‘passenger mutations’
- Duplication
- large-scale mutation leading to multiple copies of all chromosomal regions, increasing the dosage of the genes located within them. Also called amplification
-E-
- Epigenetics
- study of the changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence. These changes may remain through cell divisions for the remainder of the cell's life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism; instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently.
- Epistasis
- an interaction between genotypes at two different gene loci, which sometimes resembles a dominance interaction at a single locus. For example, in the determination of flower color, one gene locus determines whether the pigment is red (‘AA’ or ‘Aa’) or white (‘aa’), while another locus determines whether the pigment is produced (‘BB’ or ‘Bb’) or not (‘bb’). In a ’bb’ plant, the flowers will be white, irrespective of the genotype of the other locus as ‘AA’, ’Aa’, or ’aa’.
- Exome
- the 1% of the human genome that is the most functionally relevant and most likely to cause noticeable phenotypes. Comprised of short segments of DNA called exons, the exome provides the genetic blueprint for proteins.
- Exon
- a nucleic acid sequence that is represented in the mature form of an RNA molecule after either portions of a precursor RNA (introns) have been removed by cis-splicing or by two or more precursor RNA molecules have been ligated by trans-splicing. The mature RNA molecule can be a messenger RNA or a functional form of a non-coding RNA such as rRNA or tRNA. Depending on the context, exon can refer to the sequence in the DNA or its RNA transcript.
-F-
- Fusion gene
- a hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion. Often, fusion genes are oncogenes; examples include BCR-ABL, and TMPRSS2-ERG. Most fusion genes are found from hematological cancers, sarcomas and prostate cancer.
-G-
- Gene
- the basic unit of heredity in a living organism. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring. A gene is an ordered sequence of molecules located in a particular position on a particular chromosome that encodes a protein or other molecule.
- Genetics
- study of inheritance patterns for specific traits
- Genetic (allelic) drift
- the change in the relative frequency in which a gene variant (allele) occurs in a population due to random sampling and chance
- Genetic linkage
- phenomenon occurring when particular genetic loci or alleles for genes are inherited jointly. Genetic loci on the same chromosome are physically close to one another and tend to stay together during meiosis, and are thus genetically linked. This is called autosomal linkage. Alleles for genes on different chromosomes are usually not linked, due to independent assortment of chromosomes during meiosis.
- Genetic mapping
- the process of determining the locus for a particular biological trait
- Genetic screening
- testing a group of people to identify individuals at high risk of having or passing on a genetic disorder
- Genetic testing
- analysis of an individual’s genetic material to determine predisposition to a particular health condition
- Genome
- the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA
- Genomics
- the study of genes and their function
- Genotype
- the genetic constitution of a cell, an organism, or an individual (i.e., the specific allele makeup of the individual) usually with reference to a specific character under consideration
- Germ-line cells
- line of cells that have genetic material that may be passed to a child. For example, sex cells such as the sperm or the egg, are part of the germline. So are the cells that produce sex cells, called gametocytes, the cells that produce those, called gametogonia, and all the way back to the zygote, the cell from which the individual developed.
- Glycomics
- the comprehensive study of glycomes (the entire complement of sugars, whether free or present in more complex molecules, of an organism), including genetic, physiologic, pathologic, and other aspects
- GWAS
- Genome Wide Association Study; an examination of genetic variation across the human genome
-H-
- Heritability
- the proportion of phenotypic variation in a population that is attributable to genetic variation among individuals. Variation among individuals may be due to genetic and/or environmental factors.
- Heterozygous
- characteristic of a particular gene when two different alleles occupy the gene's position on the homologous chromosomes. Heterozygous genotypes are represented by a capital letter (representing the dominant allele) and a lowercase letter (representing the recessive allele), such as ‘Rr’. The capital letter is usually written first.
- Homozygous
- characteristic of a particular gene when identical alleles of the gene are present on both homologous chromosomes. Homozygous dominant genotypes are represented by double capital letters (‘RR’) if the allele codes for the dominant trait and double lowercase letters (‘rr’) if the trait is recessive.
-I-
- Indel
- a mutation resulting in a colocalized insertion and deletion and a net gain or loss in nucleotides, and microindel is defined as an indel that results in a net gain or loss of 1 to 50 nucleotides.
- Insertion
- mutation which adds one or more extra nucleotides into the DNA. It is usually caused by transposable elements (‘transposons’), or errors during replication of repeating elements (e.g. AT repeats). Insertions in the coding region of a gene may alter splicing of the mRNA (splice site mutation), or cause a shift in the reading frame (frameshift), both of which can significantly alter the gene product.
- Interstitial deletion
- an intra-chromosomal deletion that removes a segment of DNA from a single chromosome, thereby apposing previously distant genes
- Intron
- a DNA region within a gene that is not translated into protein. These non-coding sections are transcribed to precursor mRNA (pre-mRNA) and some other RNAs (such as long non-coding RNAs), and subsequently removed by a process called splicing during the processing to mature RNA. After intron splicing (i.e., removal), the mRNA consists only of exon derived sequences, which are translated into a protein.
-J-
-K-
- Karyotype
- the characteristic chromosome complement of a eukaryote species
-L-
- Locus
- the specific location of a gene or DNA sequence on a chromosome
- Loss of heterozygosity
- loss of one allele, either by a deletion or recombination event, in an organism that previously had two different alleles
-M-
- Metabolomics
- the analysis of low molecular weight molecules involved in primary or intermediary metabolism and metabolites found in cells, tissues, and body fluids
- Microsatellite
- repeated sequences of DNA
- Microsatellite instability
- In cells with mutations in DNA repaire, some microsatellites accumulate erros and become longer or shorter
- Mutation
- changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. They can also be induced by the organism itself, by cellular processes such as hypermutation.
- Mutation: back
- a point mutation that restores the original sequence and hence the original phenotype. Also called a reversion.
- Mutation: dominant-negative
- mutation where an altered gene product that acts antagonistically to the wild-type allele. These mutations usually result in an altered molecular function (often inactive) and are characterized by a dominant or semi-dominant phenotype. Also called an antimorphic mutation. [e.g., Marfan syndrome]
- Mutation: gain-of function
- mutation where the result of gene product gains a new and abnormal function. These mutations usually have dominant phenotypes. Often called a neomorphic mutation.
- Mutation: lethal
- mutation that leads to the death of the organisms which carry the mutation
- Mutation: loss-of function
- mutation where the result of gene product has less or no function. When the allele has a complete loss of function (null allele) it is often called an amorphic mutation.
- Mutation: missense
- protein point mutation resulting in a change in nucleotide sequence which results in a change in amino acid product. Also called a nonsynonymous mutation.
- Mutation: nonsense
- protein point mutation resulting in a change in nucleotide sequence which results in a stop codon which can truncate the protein
- Mutation: silent
- protein point mutation resulting in a change in nucleotide sequence which does not alter the amino acid product. Also called a synonymous mutation.
-N-
- Non-coding sequence
- describes DNA which does not contain instructions for making proteins. In eukaryotes, a large percentage of many organisms' total genome sizes is non-coding DNA. Some non-coding DNA is involved in regulating the activity of coding regions. However, much of this DNA has no known function and is sometimes referred to as "junk DNA".
- Nucleotides
- molecules that, when joined together, make up the structural units of RNA and DNA. In DNA, the purine bases are adenine (‘A’) and guanine (‘G’), while the pyrimidines are thymine (‘T’) and cytosine (‘C’). RNA uses uracil (‘U’) in place of thymine.
-O-
- Oncogene
- a gene that, when mutated or expressed at high levels, helps turn a normal cell into a tumor cell
- Open reading frame
- a reading frame that contains a start codon, a subsequent region which usually has a length which is a multiple of 3 nucleotides, and a stop codon at its end
-P-
- Pathway analysis
- an approach that assigns the genes mutated in pathology (e.g. cancer) to known biological signaling pathways and then determines the pathways that are most commonly mutated
- Pharmacogenomics
- the branch of pharmacology which deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity. By doing so, pharmacogenomics aims to develop rational means to optimize drug therapy, with respect to the patients' genotype, to ensure maximum efficacy with minimal adverse effects. Such approaches promise the advent of "personalized medicine"; in which drugs and drug combinations are optimized for each individual's unique genetic makeup.
- Phenotype
- any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior. Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and possible interactions between the two.
- Protein isoform
- any of several different forms of the same protein. Different forms of a protein may be produced from related genes, or may arise from the same gene by alternative splicing. A large number of isoforms are caused by single nucleotide polymorphisms or SNPs, small genetic differences between alleles of the same gene.
- Proteomics
- the large-scale study of the structure, quantity, and function of proteins
-Q-
-R-
- Recombination
- the process by which genetic material is broken and joined to other genetic material
- Reading frame
- a contiguous and non-overlapping set of three-nucleotide codons in DNA or RNA. There are 3 possible reading frames in an mRNA strand and six in a double stranded DNA molecule due to the two strands from which transcription is possible. This leads to the possibility of overlapping genes.
-S-
- Single nucleotide polymorphisms
- Single Nucleotide Polymorphisms or “snips”; a DNA sequence variation occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared sequence) differs. Scientists are studying how single nucleotide polymorphisms, or SNPs (pronounced "snips"), in the human genome correlate with disease, drug response, and other phenotypes.
- Somatic cells
- refers to cells of the body, rather than gametes (eggs or sperm)
- Splicing (RNA)
- modification of an RNA after transcription, in which introns are removed and exons are joined
- Splicing (gene)
- joining pieces of genetic material in genetic engineering
- Splicing (protein)
- an intramolecular reaction of a particular protein in which an internal protein segment (called an intein) is removed from a precursor protein with a ligation of C-terminal and N-terminal external proteins (called exteins) on both sides
-T-
- Transcription
- the process of creating an equivalent RNA copy of a sequence of DNA. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary, antiparallel RNA strand. Transcription is the first step leading to gene expression.
- Transcriptomics
- the study of the transcriptome, the complete set of RNA transcripts produced by the genome at any one time
- Translation
- the first stage of protein biosynthesis (part of the overall process of gene expression). Translation is the production of proteins by decoding mRNA produced in transcription. Translation occurs in the cytoplasm where the ribosomes are located.
- Translocation
- a chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes
- Transposon
- sequence of DNA that can move around to different positions within the genome of a single cell, a process called transposition. In the process, they can cause mutations and change the amount of DNA in the genome. Transposons were also once called ‘jumping genes’, and are examples of mobile genetic elements. Also called a transposable element.
