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  • Genetic/Genomic Jargon

    Edwin M. Knights Jr., M.D.

    Scientists love to specialize -- it’s exciting and rewarding to develop expertise in a chosen field. Your peers all speak a common language and you feel comfortable in that environment. Just don’t try to communicate with an expert from some other field!

    The genealogist who is researching family medical history can be confronted with an array of obsolete medical and quasi-medical terms which can be very bewildering, especially as many of these represent long-abandoned concepts about the causes or treatments of human illnesses. Definitions have to be assessed in the context of the historical era, the way in which the symptoms presented and the customs of the times. A very useful reference of obsolete medical terminology was written by Jeanette L. Jerger. It’s a lexicon of medical terms that were used in past years. Published by Heritage Books, it’s entitled A Medical Miscellany for Genealogists. From ague to Zwischentrager, the book is a fascinating and valuable source for obscure descriptions of illness.

    FISH AND CHIPS

    These problems seem insignificant, though, when compared to the vast array of scientific terms encountered when researching in the new and sometimes intimidating field of genetic genealogy. Take, for example, the common terms “fish and chips.” When Marshall Field employed a genealogist to travel to England for two years and pursue his family’s pedigree, the gentleman probably spent a fair amount of time in the pubs sampling the local brews and munching on fish and chips. But to the molecular biologist, FISH stands for fluorescence in situ hybridization in which DNA probes labeled with fluorescent dye are used to study biological specimens to find molecular genetic events, such as gene deletion, chromosome translocation or aneuploidy. CHIPS have also assumed a new meaning, referring to microarray methods of analysis using cells containing gene fragments to predict the outcome of DNA-related diseases and helping clinicians to pick out the most appropriate methods of treatment.

    It’s apparent that molecular genealogy is the language of the present and the foreseeable future future as well. DNA’s features are expressed in complex terminology that is quite familiar to the geneticist but may be puzzling to a genealogist who cringes at the mention of a chromosome. Even using as non-technical approach as possible, these concepts require appropriate scientific definitions and descriptions. We offer a short selection of words, pharases and abbreviations which pervade the current literature, especially when dealing with the medical applications of molecular biology. This list is by no means all-inclusive. Acronyms proliferate faster than rabbits, but we hope you’ll find it useful to refresh your memory about a confusing array of terms used in a rapidly expanding science.

    GENOSPEAK FOR GENEALOGISTS

    Adenine:
    Purine base designated by “A” -- one of 4 base molecules in DNA.
    Allele: Genes can be in several forms, or alleles at a single locus, or marker, on a chromosome. If similar alleles are present in a pair of chromosomes, the person is homozygous. Differing alleles make one heterozygous. In Y-chromosome genealogical studies, repeating units, STR’s, are measured and recorded for comparison with other males.
    AMH: Atlantic Modal Haplotype -- 6 markers; most common haplotype in Western Europe.
    Amino acid: Any of a class of 20 molecules which combine to make proteins.
    Antigen: Proteinaceous product detectable by immunological methods employing matching antibodies.
    -ase: Suffix describie enzyme functions, e.g., lipase, dealing with fats.
    Association studies: Seeking a version of a gene which varies between affected and non-affected individuals.
    Autoradiogram (autorad): X-ray film recording, e.g., as used to display polymorphic DNA fragments present in mother, child and the alleged father.
    Autosome: Any chromosome other than sex or mitochondrial chromosomes. Humans have 22 pairs of autosmes (numbered 1-22), l pair of sex chromosomes.
    B-DNA: A naturally occurring form of DNA within cells.
    Beta-DNA: A branched form of DNA.
    Bacteriophage: A virus which infects certain bacteria, using host cell components in its reproduction.
    Base: Human DNA consists of 4 bases: adenine (A), cytosine (C), guanine (G) and thymine (T), derived from either purine or pyrimidine.
    Base pairs: Complementary bases pair up via hydrogen bonds to form DNA in “complementary strands.” Base-pairing occurs between purines and pyrimidines, e.g., A to T and G to C.
    Base sequence: Order of nucleotides in a DNA molecules, e.g. AGTACGT.....
    Bayes’ theorum: Statistical means of assessing the relative probability of two alternative possibilities, based upon acquired information. Can be applied to parentage testing.
    Bipolar disorder: Manic-depressive psychosis.
    BRCA1, BRCA2: Mutated genes associated with some types of heritable breast, ovarian and other cancers.
    Carrier: Person (usually symptomatic) having recessive mutated gene plus its normal allele. Also can refer to autosomal dominant conditions, denoting people who have inherited predisposition(s) conferred by mutations.
    Centromere: Constricted portion near center of a chromosome having a significant role in cell division.
    Chromosome: Threadlike DNA structure, consisting of the nucleotides adenine (A), guanine (G), thymine (T) and cytosine (C), carrying linear sequenced genetic information. Nucleated human cells have 23 pairs, including 22 pairs of autosomes and 2 sex chromosomes.
    Chromosome translocation: Abnormalitites which occur when chromosomes exchange portions, or in reciprocal translocation. Or they may fuse, called “centric fusion.” Translocation can occur in cancer. In chronic myelogenous leukemia, a balanced chromosome translocation occurs (Philadelphia chromosome).
    Clone (n): Genetically identical genes, or organisms derived from a single ancestor. Clone (v): Molecular cloning involves isolating a gene of DNA and inserting it into a cloning vector, which could be bacterial, viral or a yeast cell. When this grows, it makes multiple copies useful for research.
    Complementary sequences of DNA: Double-stranded DNA paired up according to certain rules, A with T, C with G.
    CRS: Cambridge reference sequence, referring to the mtDNA of a European female in Cambridge and used for genetic comparison. The parts of the mtDNA in the hypervariable region (HVR) which show maximum variation are called hypervariable sequences 1 and 2 (HVS1, HVS2).
    Cytosine: Pyrimidine base designated as “C” -- one of 4 bases in human DNA.
    Diploid: Containing a complete set of similar chromosomes, one from each parent.
    DNA: Deoxyribonucleic acid. The molecule that encodes genetic information. A double-stranded helix held together by weak bonds between base pairs of nucleotides.
    DNA bank: Preservation and secure storage of DNA of known origin for future profiling, diagnostic testing and research about human physiology, defects and diseases.
    DNA fingerprinting: Refers to identity, paternity, profiling and forensic analysis of DNA.
    DNA probe: Small piece of DNA tagged with a chemical or radioactive tracers, used to locate a DNA sequence by hybridization to its complementary sequence.
    DNA repair: Carried out by intracellular proteins which repair damaged DNA.
    Double helix: The structure of DNA, consisting of two strands of complementary sequences of DNA coiled to form a structure resembling a spiral staircase.
    DYS: Designated Y-chromosome segment. These markers are valuable in demonstrating genetic association. Unique identifying numbers are assigned by the Human Gene Nomenclature Committee (HUGO).
    Electrophoresis: Means of identification of proteins and DNA by migration and separation across an electrical field in porous material, such as agar, with speed inversely proportional to weight.
    Enzyme: Protein which catalyzes a chemical reaction.
    Epigenetic: Factors other than mutation which modify gene expression.
    Eukaryotes: Organisms having DNA in true nuclei bounded by nuclear membranes.
    Exon: Region of a gene that codes for a protein.
    Gene: Sequential array of DNA nucleotides on a chromosome; the basic unit of heredity.
    Genetic drift: Random change in allelic frequency due to chance, especially evident in small populations.
    Genetics: Study of genes and their influences on inheritance in a genome and their interactions with environmental factors.
    Genomics: Research and technology involving all genetic material in the chromosomes of a particular organism, e.g., 46 chromosomes in humans, containing 3 billion base-pairs within the nucleus of a cell.
    Genotype: Genetic make-up of a person, as determined by subject’s DNA sequence.
    Germ-line mutation: Abnormality in a germ-line cell which can be transmitted to subsequent generations.
    Guanine: Purine base designated (G) -- one of 4 base molecules in DNA.
    Haplogroup: Large genetically similar population group found in a recognized geographic area.
    Haplotype: Contraction of “haploid genotype.” Set of nearby genes or DNA polymorphisms (alleles) inherited as a unit, containing one of each pair of the 46 human chromosomes. A Y-DNA haplotype is an arbitrary set of STR markers used to check a genetic relationship. “Haplotype diversity” refers to the uniqueness of one haplotype within a defined population.
    Hardy-Weinberg law: Mathematical expression of the equilibrium of allelic genetic markers within a population.
    Heterozygous: Individual having 2 different alleles of a specific gene.
    Homologous: Members of a pair of chromosomes having similar genes, inherited one from each parent.
    Homozygous: Individual having identical alleles of a given gene.
    HVR: Hypervariable region of mitochondrial DNA used for identification of haplogroups and genetic mutations (see CRS)
    Hybridization: Formation of a double-stranded DNA molecule between a probe and target DNA.
    Indirect exclusion: A presumed exclusion of parentage based upon the finding that the child and the alleged father are homozygous for different alleles. Not considered 100 percent conclusive.
    Intron: Region of a gene that doesn’t code for a protein.
    Junk DNA: Much of the human DNA is non-coding and its medical functions are either non-existent or limited in scope. Markers found in junk DNA are often useful for genetic genealogy.
    Karyotype: Description of number and structures of a individual’s chromosomes.
    LCR: Ligase chain reaction, a nucleic amplification method developed by Abbott Laboratories. Includes tests for Chlamydia (causing trachoma, an eye disease) and Neisseria (causing gonorrhea). Tests involve probes which combine with DNA in enlarging cycles to form amplicons (ligated molecules).
    Linkage: Linked genes or markers so closely located on a chromosome that they are rarely separated by recombination (significantly less than 50 percent).
    Linkage analysis: Statistical tracking of known genetic markers and diseases in families.
    Linkage disequilibrium: Isolated populations having genealogical evidence of one or more founders having transmitted a genetic condition, or, nonrandom association in a population of alleles at nearby loci.
    Locus: A recognized gene site on a chromosome. Genealogists refer to this as a “marker”.
    Marker: In genetic genospeak, a “locus”; a recognized gene site on a chromosome. Loci are listed as “markers” for the benefit of genealogists. See also “STR marker.”
    Maternal Match: Determination of probability of the generation of occurrence of your most recent common ancestor, as demonstrated by mtDNA markers.
    MCRA: Most common recent ancestor shared by two people.
    Meiosis: Process by which a diploid cell goes through 1 round of chromosome replication and 2 rounds of nuclear division into 4 haploid cells or nuclei, each having only 1 set of chromosomes.
    Mean probability of exclusion: Probability that a single genetic system with excluse a non-father from paternity prior to testing.
    Messenger RNA (mRNA): DNA is transcribed into mRNA, which ultimately is translated into a protein.
    Microsatellites: Short sequences of nucleotides (e.g., ATCG) replicated multiple times in tandem.
    Minisatellites: Longer sequences of nucleotides replicated multiple times in tandem.
    Mitochondrial DNA (mtDNA): DNA found in organelles within a cell’s cytoplasm, inherited clonally only from mother to all offspring. mtDNA sequences are used for genealogical studies -- compared with the Standard Reference Sequence (CSR) for recent events and deep sequences for occurrences dating several thousand years.
    Mitochondrial clock: Concept of a molecular clock based upon mtDNA mutations occurring at a regular rate, with very slow rate of nucleotide substitution. The exact rate is controversial.
    Mitoses (human): Nuclear division in humans, with genetic material divided into 2 chromosomes that have been produced by fusion of 2 gametes, 1 from the male and 1 from the female parent. The fusion produces a diploid zygote which then undergoes embryological development.
    MODY: Maturity-onset diabetes of the young -- autosomal dominant diabetes of insulin-deficiency type.
    Molecular biology: Study of DNA, RNA and proteins at the molecular level. Includes molecular genetics (inheritance) and molecular pathology (disease processes).
    Molecular phylogeny: The inference of lines of ancestry based upon DNA, RNA or protein sequences obtained in a laboratory.
    Monogenetic: Caused by a single gene mutation.
    MRCA: Most recent common ancestor.
    Multiplexing: Using the polymerase chain reaction (PCR) plus chemicals to amplify markers in DNA so they are simulatenously copied and tagged.
    Mutation: An abnormal alteration in which DNA affects a genetic coding sequence or genetic regulatory function. DNA mutations include base substitutions, transposition, insertions, deletions and exon shuffling.
    Mutation rate: Estimated frequency of genetic mutations. STR markers change at about 1 mutation/500 transmission events (0.2%), but changes are random and can occur at any time.
    Nucleic acid: Long polymer structers comprised of nucleotides, such as DNA and RNA.
    Nuclease: Protein which digests nucleic acids or nucleotides, either by internal or external actions.
    Nucleus: Intracellular, confined portion of a cell, containing genetic material which controls cellular functions and reproduction.
    NASBA: Nucleic acid sequence-based amplification. DNA amplification method developed by Cangene Corp., using 3 enzymes: reverse transcriptase, RHaseH and T7RNA polymerase. Useful in detection of viruses containing RNA, such as hepatitis C and HIV.
    Nucleotide: Single unit of nucleic acid. In DNA the building blocks are pyrimidines C and T, purines A and G, plus phosphate and deoxyribose.
    Oligonucleotide: Short string of nucleotides, used as primers in polymerase chain reactions (PCR).
    Oncogene: Gene capable of causing cancer when mutated.
    Paternity index: Genetic odds in favor of paternity, based upon findings in the mother, child and alleged father.
    PCR: Polymerase chain reaction -- a biochemical method for in vitro nucleic acid amplification, producing millions of copies. Carefully selected primers bind to selected ends to create large amounts of identical DNA for analysis.
    Penetrance: The genetic expression of recognizeable symptoms. Likelihood that a person carrying a mutation will develop the characteristics carried by that mutation.
    Phenocopy: Phenotype that mimics genetic influence but is environmentally related.
    Phenotype: Appearance or clinical presentation of one or more genes, environmental factors, or any combination of these.
    Plasmid: Spherical piece of DNA outside of the chromosome in a bacterium. May replicate independently from the rest of the bacterial DNA. Commonly used as cloning vectors to reproduce quantities of a particular DNA.
    Polymerase: Enzyme concerned with production, e.g., DNA or RNA. The 4 varieties are DDDP, DDRP, RDRP and RDDP (also known as reverse transcriptase).
    Polymorphism: Presence of more than 2 form of a genetic trait.
    Population database: Random sampling of alleles for a given probe used to determine the frequency of an allele in a population.
    Power of exclusion: Ability of a genetic test to exclude a falsely accused man of paternity.
    Preimplantation genetic testing: One or 2 cells from a live embryo created by in vivo fertilization checked to rule out genetic disorders.
    Primers: Small segments of double-stranded DNA used to “prime” the site of initiation of DNA synthesis by DNA-polymerase.
    Probability of paternity: Statistical calculation showing the likelihood that an alleged father is the biological father of a child.
    Proband: Founder or individual through whom a pedigree is established; male is propositus, female is proposita.
    Probe: Small segment of radioactively or chemically tagged DNA or RNA used to locate another piece of DNA via hybridization to its complementary sequence.
    Pseudogene: Vestige of a gene which no longer functions but remains in the genome.
    Recessive: A trait partially or completely masked by a dominant allele.
    Recombinant DNA (rDNA): Shuffling of segments of homologous genes during sex cell formation, passing on alleles from each parent.
    Replication: Process of making more DNA.
    Restriction endonucleases (REs): Restriction enzymes produced by bacteria (now commercially), capable of cleaving DNA at specific sites. Used in genetic engineering of diagnostic tests by creating a recombinant DNA.
    Bacteria contain hundreds of enzymes which recognize and cut over 100 DNA sequences.
    Retrovirus: Virus containing an RNA genome which is converted into a DNA intermediate by reverse transcriptase enzyme. RNA-containing retroviruses can cause T-cell leukemia, lymphomas and AIDS.
    Reverse transcriptase: An RNA-dependent DNA polymerase (RDDP) making DNA as directed by an RNA template. It reverses the flow of genetic information of DNA to RNA to protein, causing it to go from protein to RNA to DNA.
    RFLP: Restriction enzyme fragment length polymorphism. Variation in the size of DNA fragments produced by a restriction endonuclease at a polymorphic locus.
    RNA: Ribonucleic acid; intermediary for the flow of genetic information. A macromolecule composed of small building blocks called nucleotides. Each nucleotide consists of ribose attached to adenine, guanine, cytosine and uracil.
    Ribosomal RNA (rRNA): A constituent of the protein-synthesizing machinery of a cell.
    Sequencing: Determing the order of nucleotides (a base sequence) in a DNA or RNA molecule. Also describes the order of amino acids in a protein.
    Sex chromosomes: Chromosomes which determine sexuality; females have two X chromosomes, males have one X and one Y chromosome.
    Short tandem repeats: Repeats of short base pairs arranged in tandem.
    Single locus probe: DNA probe that detects a single DNA region.
    Somatic cells: All human body cells except for germ-line sex cells.
    Southern blot: Method of studying DNA sequences developed by Dr. E. Southern. Variations include dot blot, slot blot.
    SNP: Polymorphisms in which a single nucleotide is altered, e.g., A changed to G.
    STR marker: Short tandem repeat marker. An area of DNA where a small base sequence showing a base sequence TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA. Genetic markers identified by allelic profiling, used in Y-DNA testing to identify your haplotype.
    Telomeres: Sequences at the end of chromosomes: TTAAGG
    Transmission event: Birth of a male infant passes on the Y-chromosome to the next generation.
    Transcription: Synthesis of RNA from a DNA template. RNA becomes messenger RNA (MRNA) and is translated into a protein.
    Transfer RNA (tRNA): RNA molecule transports amino acids to a ribosome for protein systhesis.
    Translocation trisomy: Type of Down syndrome in which material from a chromosome 21 becomes adherent or translocated to another chromosome.
    Trisomy: Presence of an additional chromosome, so there are 3 copies instead of 2.
    VNTR: Variable number of tandem repeats. DNA locations comprised of short repeats, or 10-70 base pairs arranged in tandem.
    X-Chromosome: Female sex chromosome; females have two X chromosomes; males have one X, one Y.
    YHRD: Database of haplotypes including predominantly Eurasian samples, but also American, East Asian, Eskimo Aluet and Amerindian, using up to 11 markers.
    X-linked inherited disease: Single X-chromosome may carry a recessive mutation which doesn’t become manifest in the mother but can cause X-linked disease, such as hemophilia or colorblindness, in a male offspring.
    Y-chromosome: Male sex chromosome, transmitted only via the male line.


    SELECTED REFERENCES

    Jerger JL: A Medical Miscellany for Genealogists. Bowie, Md., Heritage Books, 1995

    Carmichael T; Kuklin A: How to DNA Test Our Family Relationships, Moutain View CA, AceN Press, 2002

    Cold Spring Harbor Laboratory

    DNA Heritage Tutorial

    Duerinck K: Genetic Definitions

    Farkas, DH: DNA Simplified: The Hitchhiker’s Guide to DNA. Washington DC, AACP Press, 1996

    Guttmacher AE, Collins FS: Genomic Medicine -- A Primer. N Engl J Med 347, 19 Nov. 7 2002

    Russell PJ: Genetics, Ed. 4, New York NH, HarperCollins, 1996

    Genetic terminology can be found in any standard textbook of genetics. Genetic and genomic glossaries are on the internet, including http://www.nejm.org

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