Genetic Terms
Cell Biology Terms
Types of Genetic Tests
Types of Genetic Files
Genetic Terms Glossary
Allele
A variant form of a gene. Alleles can be dominant or recessive, and they determine specific traits in an organism.
Autosome
Any chromosome that is not a sex chromosome (X or Y). Humans have 22 pairs of autosomes.
Carrier
An individual who has one copy of a recessive allele for a genetic trait or condition. Carriers typically do not show symptoms of the trait or condition but can pass the allele to their offspring.
Chromosome
A thread-like structure made up of DNA and proteins that carries genetic information. Humans have 23 pairs of chromosomes. You inherit one copy of each chromosome from your father and one copy from your mother.
Copy Number Variation (CNV)
A structural variation in the genome where sections of DNA are repeated or deleted. CNVs can play a role in disease and evolution.
DNA (Deoxyribonucleic Acid)
The molecule that carries the genetic instructions for life. It is made up of nucleotides (A, T, C, and G) arranged in a double helix.
Dominant
Refers to an allele that expresses its trait even when only one copy is present. It “masks” the effect of a recessive allele.
Epigenetics
The study of changes in gene expression that do not involve changes to the underlying DNA sequence. These changes can be influenced by environmental factors and can sometimes be inherited.
Exon
A segment of a gene that contains the instructions for making proteins. Exons are spliced together after the removal of non-coding regions (introns).
Gene
A segment of DNA that contains the instructions for building a specific protein or set of proteins.
Genome
The complete set of genetic material (DNA) in an organism. The human genome contains about 3 billion base pairs of DNA.
Genotype
The genetic makeup of an individual, often in reference to a specific trait. For example, a person might have a genotype of AA, Aa, or aa for a given gene.
Genome-Wide Association Study (GWAS)
A study that looks for associations between genetic variations (often SNPs) and specific traits or diseases across the entire genome.
Genotype
The genetic makeup of an individual, often in reference to a specific trait. For example, a person might have a genotype of AA, Aa, or aa for a given gene.
Heterozygous
Having two different alleles for a specific gene (e.g., Aa). Example: Someone who is heterozygous for the MTHFR C677T variant has one copy of the variant allele and one copy of the typical allele.
Homozygous
Having two identical alleles for a specific gene (e.g., AA or aa). Example: Someone who is homozygous for the MTHFR C677T variant has two copies of the variant allele.
Intron
A non-coding region of a gene that is removed during RNA processing. Introns do not code for proteins but may have regulatory functions.
Mutation
A change in the DNA sequence. Mutations can be inherited or occur spontaneously and can lead to changes in protein function. Generally, mutation is used for variants or changes that are found in less than 1% of the population.
Multifactorial Inheritance
The type of inheritance that results from the interaction of multiple genes and environmental factors. Many common diseases, such as heart disease and diabetes, have multifactorial inheritance patterns.
Nutrigenomics
The study of how foods or specific nutrients affect an individual’s genes and how a person’s genes affect the need for or response to foods or nutrients.
Penetrance
The proportion of individuals with a specific genotype who actually express the associated phenotype. High penetrance means that most individuals with the genotype will show the trait.
Pharmacogenomics
The study of how an individual’s genetic makeup affects their response to drugs. This information can be used to tailor medical treatments to individuals.
Phenotype
The observable traits or characteristics of an individual, determined by both genetic makeup and environmental influences.
Polygenic
This refers to a trait that is influenced by multiple genes. Examples include height, skin color, and many common diseases like type 2 diabetes.
Polymerase Chain Reaction (PCR)
A laboratory technique used to amplify a specific DNA segment, enabling researchers to create millions of copies of a particular DNA sequence for analysis.
Proband
The first individual in a family to be tested or diagnosed with a genetic condition. Also called the index case or propositus.
Recessive
An allele that only expresses its trait when two copies are present (homozygous). It is “masked” by a dominant allele when both are present.
Single Nucleotide Polymorphism (SNP)
A variation in a single base pair in the DNA sequence. SNPs are common and can be associated with various traits and diseases.
Somatic Mutation
A mutation that occurs in somatic (non-reproductive) cells. These mutations are not passed to offspring but can lead to diseases like cancer.
Variant of Uncertain Significance (VUS)
A genetic variation where its association with disease is not yet known. VUS results can complicate the interpretation of genetic testing results.
Cell Biology Glossary
Apoptosis
A form of programmed cell death that occurs in multicellular organisms. It is a controlled process where cells die without causing harm to the surrounding tissue.
Autophagy
A process by which cells break down and recycle their own components, such as damaged organelles or misfolded proteins, through the lysosomal pathway. Autophagy is important for cellular health and survival.
Cell Junctions
Structures that connect adjacent cells and provide mechanical stability or facilitate communication. Types of cell junctions include tight junctions, gap junctions, and desmosomes.
Cell Membrane (Plasma Membrane)
A phospholipid bilayer that surrounds the cell, protecting it from the external environment and regulating the movement of substances in and out of the cell.
Clathrin
A protein that plays a key role in the formation of coated vesicles during endocytosis. Clathrin-coated vesicles are responsible for transporting molecules from the plasma membrane to various intracellular destinations.
Cytokines
Small signaling proteins released by cells that play important roles in immune responses, cell growth, and cell differentiation. They act as chemical messengers to regulate communication between cells.
Cytoplasm
The gel-like substance within the cell membrane that contains the cytosol, organelles, and various molecules necessary for cellular processes.
Cytoskeleton
A network of protein filaments and tubules that provides structural support to the cell, maintains its shape, and aids in intracellular transport and cellular movement.
Endocytosis
A cellular process in which a cell engulfs external substances, such as nutrients or pathogens, by enveloping them with its plasma membrane to form a vesicle.
Endoplasmic Reticulum (ER)
A network of membranes found in eukaryotic cells. It comes in two forms:
- Rough ER: Studded with ribosomes and involved in protein synthesis.
- Smooth ER: Lacks ribosomes and is involved in lipid synthesis and detoxification processes.
Extracellular Matrix (ECM)
A complex network of proteins and carbohydrates that provides structural support to cells and regulates various cellular functions such as adhesion, migration, and differentiation.
Exocytosis
The process by which cells release substances to the external environment by fusing a vesicle with the plasma membrane.
Glycoprotein
A protein that has carbohydrate molecules attached to it. Glycoproteins are found on the surface of cells and play a role in cell-cell interactions, immune recognition, and signaling.
Golgi Apparatus
An organelle in eukaryotic cells responsible for modifying, sorting, and packaging proteins and lipids for secretion or delivery to other parts of the cell.
Ligand
A molecule that binds to a specific receptor on the surface of a cell to initiate a signal transduction pathway. Ligands include hormones, growth factors, and neurotransmitters.
Lysosome
A membrane-bound organelle that contains digestive enzymes. Lysosomes break down waste materials, cellular debris, and foreign pathogens that have entered the cell.
Mitochondria
Double-membrane-bound organelles that produce energy (ATP) through cellular respiration. Often referred to as the “powerhouse” of the cell.
Mitosis
A type of cell division in eukaryotic cells that results in two genetically identical daughter cells, each with the same number of chromosomes as the parent cell. Mitosis is crucial for growth, development, and tissue repair.
Meiosis
A specialized form of cell division that produces four genetically unique daughter cells, each with half the number of chromosomes as the parent cell. Meiosis is essential for sexual reproduction and the formation of gametes (sperm and egg cells).
Nucleus
The membrane-bound organelle in eukaryotic cells that contains the cell’s genetic material (DNA). The nucleus regulates gene expression and controls cellular activities.
Organelle
A specialized subunit within a cell that has a specific function. Examples include the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes.
Peroxisome
A membrane-bound organelle that contains enzymes for breaking down fatty acids and detoxifying harmful substances like hydrogen peroxide.
Phagocytosis
A type of endocytosis in which a cell engulfs large particles or microorganisms. This process is commonly used by immune cells (like macrophages) to remove pathogens.
Plasmid
A small, circular piece of DNA found in bacteria (and sometimes eukaryotes). Plasmids can replicate independently of the bacterial chromosome and often carry genes that provide resistance to antibiotics.
Proteasome
A large protein complex that degrades unneeded or damaged proteins by proteolysis, a process in which proteins are broken down into amino acids.
Ribosome
A molecular machine in cells that synthesizes proteins. Ribosomes can be found floating freely in the cytoplasm or attached to the rough endoplasmic reticulum (rough ER).
Stem Cell
A type of undifferentiated cell that has the ability to develop into different cell types. This is how cells regenerate and replace cells that are old or damaged. Stem cells can divide and differentiate to form specialized cells or maintain their undifferentiated state.
Telomere
A nucleotide sequence that repeats at the ends of chromosomes to protect them from damage when replicating. Telomeres shorten with each round of cell division, and their length is associated with aging and cancer.
Tight Junction
A type of cell junction that tightly brings neighboring cells together in an epithelial sheet to prevent molecules from moving between the cells.
Transcription
The process by which genetic information from DNA is copied into RNA (specifically mRNA) in the nucleus. This is the first step in gene expression. After transcription, genes are translated into proteins.
Translation
The process by which ribosomes use the information in mRNA to synthesize proteins. This occurs in the cytoplasm and is the second step in gene expression.
Vesicle
A small, membrane-bound sac that transports substances within the cell or releases substances to the external environment through processes like exocytosis.
Types of Genetic Tests
Carrier Screening
A type of genetic test that checks if an individual carries a gene for a recessive genetic disorder. It’s often used for couples planning to have children to assess the risk of passing on certain genetic conditions.
Next-Generation Sequencing (NGS)
A high-throughput sequencing technology that allows for the simultaneous sequencing of millions of DNA fragments. NGS is commonly used in clinical diagnostics to identify genetic variants related to disease.
Pharmacogenetic Testing
A test that looks at how genetic variations affect an individual’s response to medications. This type of testing can help doctors choose the best treatment and dosage.
Preimplantation Genetic Diagnosis (PGD)
A genetic test performed on embryos created through in vitro fertilization (IVF) to check for specific genetic conditions before the embryo is implanted in the uterus.
Prenatal Genetic Testing
Testing that is performed during pregnancy to assess the risk of genetic disorders in a developing fetus. Examples include amniocentesis, chorionic villus sampling (CVS), and NIPT.
Targeted Sequencing
A sequencing approach that focuses on specific regions of the genome, such as a set of genes of interest. This approach is often used in clinical diagnostics when a specific genetic condition is suspected.
Whole Genome Sequencing (WGS)
A sequencing technique that determines the complete DNA sequence of an organism’s genome, including both coding and non-coding regions. WGS is useful for identifying mutations in cases where other genetic tests are inconclusive.
Whole Exome Sequencing (WES)
A type of genomic sequencing that focuses on the exons, which are the protein-coding parts of the genome. WES is a cost-effective method to identify disease-causing mutations in genes.
Glossary of Sequencing Data Files
Tab-Delimited File (TXT or TSV)
A plain text file where data is organized into columns separated by tabs. Tab-delimited files are often used in bioinformatics for storing various types of structured data, such as gene lists or variant tables.
BAM (Binary Alignment/Map) File
A binary version of a SAM file, used to store aligned sequencing reads in a compressed format. BAM files are widely used because they are space-efficient and can be indexed to allow for fast retrieval of sequence alignments.
BAI (BAM Index) File
An index file that accompanies a BAM file. It allows for fast searching and retrieval of specific regions in large BAM files without having to read the entire file.
BED (Browser Extensible Data) File
A text-based format that defines genomic regions (such as coordinates for genes, exons, or regulatory elements). BED files are commonly used in genome browsers to visualize annotations.
CRAM (Compressed Read Alignment Map) File
A highly compressed format for storing aligned sequence reads, like BAM but more space-efficient. It achieves this by using external reference sequences and reducing redundancy in the data.
FASTQ File
A text-based file format used for storing raw sequencing data, typically generated by an NGS platform. It contains both the nucleotide sequence and a corresponding quality score for each base call. FASTQ files are the first output in a sequencing workflow and are often large.
FASTA File
A text-based format for storing nucleotide or protein sequences. Each entry in a FASTA file begins with a header line (starting with >), followed by the sequence. FASTA files are often used to store reference genomes.
SAM (Sequence Alignment/Map) File
A text-based format used to store aligned sequence data. SAM files include information about the reads, their alignment to a reference genome, and quality scores. BAM files are the binary equivalent of SAM files.
VCF (Variant Call Format) File
A file format that stores information about genetic variants (SNPs, insertions, deletions) discovered during analysis of sequencing data. VCF files include detailed information about the variants, such as their genomic position, reference and alternate alleles, and genotype information for samples.
BCF (Binary Variant Call Format) File
A binary version of a VCF file. Like BAM files, BCF files are compressed and space-efficient. BCF files can be indexed and allow for faster retrieval and processing of variant data.
MAF (Mutation Annotation Format) File
A format commonly used to represent somatic mutations, especially in cancer studies. MAF files contain information about the mutation type, location, and functional impact. They are used in large-scale cancer genomics projects like TCGA.
IDX (Index) File
A generic term for an index file that allows for rapid searching and retrieval of specific regions in large files like BAM, VCF, or CRAM. Index files (like BAI or TBI) are essential for working with large genomic datasets efficiently.
Annotation File
A general term for any file that contains functional or descriptive information about specific genomic features (e.g., genes, exons, variants). Common annotation formats include GFF, GTF, and BED.
MTX (Matrix) File
A format used in single-cell RNA sequencing (scRNA-seq) analysis to store gene expression data as a sparse matrix. MTX files contain a list of non-zero entries in a large matrix where each row represents a gene, and each column represents a cell.
VCFTOOLS
A toolkit for manipulating VCF files. VCFTOOLS can be used to filter, merge, and analyze VCF files to explore variant data.