Genebase Glossary (90 terms)
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Glossary last revised: Jan 21, 2009
Allele: The alternative forms of a genetic marker at a single locus. In the Y-DNA, each allele is the numeric result for each STR marker tested. Each STR marker is a single locus.
Anthropology: The study of humanity, including the origins, physical and cultural development, biological characteristics, and social customs and beliefs of humankind.
Atlantic Modal Haplotype: A Y-DNA STR haplotype found frequently in male individuals from western Europe: DYS19 = 14, DYS388 = 12, DYS390 = 24, DYS391 = 11, DYS392 = 13, DYS393 = 13.
Autosomal DNA: A chromosome that is not a sex chromosome, normally appearing in pairs in somatic cells. Humans have 23 pairs of chromosomes: 22 pairs of autosomal chromsomes and one pair of sex chromosomes (X and Y sex chromosomes). The X chrosomosome and Y chromosome are not autosomes.
Backbone SNP Test: A SNP test which specifically examines the SNP markers required to confirm an individual's Y-DNA or mtDNA Haplogroup.
Base: An important component of DNA consisting of a purine linked by hydrogen bonds to a pyrimidine. The bases found in DNA are A (adenine), T (thymine), G (guanine) and C (cytosine).
Base Pair (bp): The pair of bases, consisting of a purine linked by hydrogen bonds to a pyrimidine, that connects the complementary strands of DNA or of hybrid molecules joining DNA and RNA. The base pairs in DNA are A (adenine) which pairs with T (thymine) , and G (guanine) which pairs with C (cytosine).
Branch: In reference to the SNP Y-DNA and mtDNA phylogenetic tree, a branch is the point of divergence in the tree. For example, R1 and R2 are branches of R. R1a and R1b are further "sub-branches" of R1.
Carrier: An individual who carries a DNA marker of interest.
Chromosome: The threadlike linear strand of DNA and its associated proteins. Carries the genes and functions in the transmission of hereditary information. Humans have 22 pairs of chromosomes plus the sex chromosome (X and Y). Found in the nucleus of the cell.
Clade: Also known as a haplogroup. In relation to genetic genealogy, refers to the grouping of humans traced to common ancestors detected through shared SNP markers in the mtDNA and Y-DNA phylogenetic tree.
Coding Region: The region of mtDNA which is functional and codes for protein. SNP markers are not as abundant in the Coding region compared to the Control region but markers found here are often critical for mtDNA Haplogroup and subclade determination.
CODIS (Combined DNA Index System): CODIS is a distributed database system for documenting and comparing genetic profiles. CODIS specifies the following 13 autosomal DNA loci as a standard: (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, THO1, TPOX, CSF1PO). Genetrack tests all CODIS loci and also 2 additional loci (D2S1338 and D19S433), resulting in a more informative result than using the CODIS loci alone.
Cohen Modal Haplotype: A Y-DNA STR haplotype found frequently in male individuals of Jewish Cohanim descent: DYS393 = 12, DYS390 = 23, DYS19 = 14, DYS391 = 10, DYS385a = 13, DYS385b = 15, DYS426 = 11,, DYS388 = 16, DYS439 = 12, DYS389I = 13, DYS389II = 30, DYS392 = 11.
Confirmed Haplogroup: A mtDNA or Y-DNA haplogroup designation for an individual which has been confirmed through SNP backbone testing.
Control Region: A region of the mtDNA which does not code for functional proteins. Contains the HVR1 and HVR2 regions which are abundant in SNP markers which are useful for maternal ancestral analysis.
CPI (Combined Paternity Index): The CPI is calculated by multiplying the PI values for each independent locus and is the total paternity index for the loci examined. A CPI of 0 corresponds to a 0% probability of paternity (paternity exclusion) whereas a CPI of >1000 corresponds to a probability of paternity of >99.9% (paternity inclusion).
CRS (Cambridge Reference Sequence): The first human mtDNA ever fully sequenced and published. All mtDNA sequences are compared against the CRS and any differences from CRS are noted as positive (mutations).
Cytoplasm: The part of the cell enclosed within the cell membrane and contains organelles such as mitochondria and the nucleus of the cell.
D-Loop: A non-functional region of the mtDNA which contains the HVR1 and HVR2 region. This region contains an abundance of SNP markers which are important for maternal ancestral analysis.
Deep Ancestry: A study of the ancestry over a time frame of tens of thousands of years to our common roots in Africa. Tested using SNP markers for mtDNA and Y-DNA Haplogroup and Subclade determination.
Deletion: When refering to SNPs, a deletion refers to the remove of one or more than one nucleotides (A, C, T, or G) from a defined location in the DNA.
DNA (deoxyribonucleic acid): The molecule that carries the genetic information of all living organisms. In human, DNA is found in two locations: as chromosomes in the nucleus of the cell and in mtDNA in the mitochondrial of the cell.
DNA Fingerprint: The data obtained from a DNA test, represented by numbers. The genetic profile of an individual does not vary with the age or tissue type of that individual. The genetic profile can therefore be used in forensic investigations to determine if two samples are derived from the same person. Note that identical twins will share identical genetic profiles.
DYS, DYF, DYZ: The prefix found in the naming method for many Y-DNA STR markers, usually followed by numbers. D stands for DNA and Y stands for Y-Chromosome.
Gene: A segment of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism by directing the formation of a protein. Genes undergo mutation when their DNA sequence change.
Genetic Distance: When refering to Y-DNA STR markers, genetic distance refers to the total net difference between the markers compared.
Genetic Event: A detectable change (mutation) in the DNA which is passed down to further generations. SNP mutations are considered genetic events and mark the branches of the phylogenetic tree.
Genetic Genealogy: The use of DNA testing to help individuals to trace their ancestry.
Grandparentage Index: A statistical likelihood ratio representing a comparison of the probability that the individuals are related versus the probability that the individuals are unrelated. A kinship index is calculated for each locus and is used to calculate the Combined Grandparentage Index.
Haplogroup: Also known as a Clade. In relation to genetic genealogy, refers to the grouping of humans traced to common ancestors detected through shared SNP markers in the mtDNA and Y-DNA phylogenetic tree. Named by alphanumeric labels, such as R1a, I1b, etc.
Haplotype: The combination of alleles at multiple loci that are on the same chromosome. In Y-DNA, refers to the combined results of all of the Y-DNA STR markers that are tested.
Heteroplasmy: The presence of a mixture of more than one type of mtDNA and an individual's cytoplasm.
HVR1 Region: Locations 16,000 to 16,579 of the mtDNA hypervariable region (D-Loop). Contains abundant SNP markers which are informative for maternal ancestral testing.
HVR2 Region: Locations 1 to 400 of the mtDNA Hypervariable region (D-Loop). Contains abundant SNP markers which are informative for maternal ancestral testing.
Hypervariable Region (HVR-1, HVR-2): Specific regions of the mtDNA that do not code for protein. In humans, the HVR region typically contains a large number of mutations which can be used to derive ancestry. The entire mtDNA is 16,569 base pairs in length. The HVR1 region is found within base pairs 16001 to 16569, and the HVR2 region is found between base pairs 1 to 574. Testing the HVR1 and HVR2 regions of the mtDNA is usually the starting point for ancestral studies.
Indigenous DNA: The DNA type of an individuals from populations or ethnic groups who have historically inhabited a geographical region.
Indigenous DNA Database: A database consisting of DNA types from indigenous populations. Data in such database is not the same as the data from participants as participants in the project are not considered indigenous peoples. Only data from peer reveiwed journals are included in the indigenous DNA database.
Insertion: When refering to SNPs, an insertion refers to the addition of one or more than one nucleotide (A, C, T, or G) in a defined region of the DNA.
Kinship Index: A statistical likelihood ratio representing a comparison of the probability that individuals are related versus the probability that the individuals are unrelated. A kinship index is calculated for each locus and is used to calculate the Combined Kinship Index.
Locus (plural Loci): A fixed position on a chromosome. In Y-DNA, each STR marker is tested is a locus and the numeric result obtained for each STR marker is an allele, and the combined results of all of the alleles tested on the Y-DNA is called the haplotype (not to be confused with haplogroup).
Marker: A detectable genetic mutation type that can be measured through DNA testing. STR and SNP markers are commonly tested on the Y-DNA and SNP markers are detected on the mtDNA.
Match Probability: The probability of a random match of a genetic profile within a population. For example, a match probability of 1:10 (i.e., 0.1) indicates that there is a 0.1 (i.e., 10%) chance of a random match in the population, whereas a match probability of 1:100 (i.e., 0.01) indicates that there is only a 0.01 (i.e., 1%) chance of a random match in the population. A 1:100 match probability is therefore a better indication that two samples are derived from the same individual than a match probability of 1:10.
Matching Markers: When comparing Y-DNA STR markers between two or more individuals, matching markers refers to the number of STR markers that have identical allele values versus the total number of overlapping markers compared.
Maternal Lineage: The direct maternal line ie mother's, mother's, mother's.... line. This line can be traced by testing an individual's mtDNA since mtDNA is passed down from mother to child.
Meiosis: A type of cell division that produces gametes (spern and egg) which have a haploid chromosome number (23 single unpaired chromosomes instead of 23 pairs of chromosomes).
Microsatellite Repeats: Also known as STR (Short tandem repeats). Short stretches of DNA usually 2 to 4 base pairs in length that repeat over and over again and the number of repeats can differ between different individuals or families.
Minimal Haplotype: In reference to the DNA Clans indigenous DNA database, minimum haplotype refers to the STR profiles that have been tested in common for a group of populations.
Mitochondria: An energy producing organelle which is found in the cytoplasm of our cells. Contains mtDNA.
Mitosis: Cell division in which the resulting cells maintain the same number of chromsomes (23 pairs of chromosomes).
Modal Haplotype: A haplotype which has been identified to occur at high frequencies in a particular population and is thus strongly associated with people from that population group. Examples include the Atlantic Modal Haplotype and Cohen Modal Haplotype.
Motif: A defined DNA sequence. In genetic genealogy, a motif refers to the sequence in the Y-DNA that is counted as a repeat when assigning allele numbers. The motif is especially important for individuals wishing to compare Y-DNA STR markers between different laboratories. If the motif and counting method used by a laboratory is openly published, comparison is permitted between different labs.
MRCA (Most Recent Common Ancestor): The most recent ancestor from which the individuals compared descended.
mtDNA: The type of DNA found in mitochondria in the cytoplasm of cells. Passed down from mother to child along the maternal line. Contains markers for tracing maternal ancestry.
mtDNA Tests: Genetic tests which examine the DNA sequence in mtDNA either through sequencing or SNP analysis.
Mutation: A change in the DNA sequence. Examples of mutation types important in genetic genealogy include changes at a single base pair called "SNP" mutation or changes in the number of short repeats called "STR" mutation.
Negative SNP Marker: When refering to mtDNA, refers to single locations in the mtDNA which are the same as CRS. If someone is negative for 16223, that means that at location 16223 of the mtDNA, their marker is the same as CRS. When refering to Y-DNA, refers to SNP markers which the same as the ancestral type.
NIST (National Institute of Standards and Testing): Federal agency within the U.S. Department of Commerce with the mission to promote U.S. innovation and industrial competitiveness by advancing measurement science, standards, and technology. NIST maintains STRBase and standards for Y-DNA STR markers.
Nomenclature: Rules used for forming names for genetic markers.
Nucleotide: The basic structural unit of DNA and RNA consisting of a deoxyribose or ribose sugar, joined with a purine (A or G) or pyrimidine (T or C) base and a phosphate group. When linked together, the chain of nucleotides form the DNA strand.
Nucleus: A membrane enclosed structure found in the central region of the cell which contains most of the cell's DNA (chromosomes).
Organelle: Membrane bound compartments within the cell that have specific functions such as the mitochondria.
Overlapping Markers: Markers which you have tested which someone else have also tested. When comparing two or more individuals, overlapping markers are compared.
Paternal Lineage: The direct paternal line ie father's, father's, father's .... line. This line can be traced by testing an individual's Y-DNA since Y-DNA is passed down from father to son.
Paternity Index (PI): A likelihood ratio representing a comparison of the probability that the alleged father is the biological father versus the probability that a random man in the population is the biological father. A PI is calculated for each locus and is used to calculate the combined paternity index and probability of paternity.
Phylogenetic Tree: A tree which shows evolutionary relationships between organisms that have a common ancestor. In human ancestry, the Y-DNA phylogenetic tree is constructed based on SNP markers in the Y-DNA and the mtDNA phylogenetic tree is constructed based on SNP markers in the mtDNA and shows how all humans descendend from common paternal and maternal ancestors respectively.
Polymerase Chain Reaction (PCR): Technique for amplifying specific regions of DNA by multiple cycles of DNA polymerization. PCR is the method used by the DNA laboratory to amplify specific loci for analysis, and is capable of producing a genetic profile from very small amounts of sample.
Polymorphism: The genetic variation between individuals or populations.
Population Genetics: The study of differences in genetic material between different populations.
Positive SNP marker: When refering to mtDNA, refers to single locations in the mtDNA which differs from CRS. If someone is positive for 16223, that means that at location 16223 of the mtDNA, their marker differs from CRS. When refering to Y-DNA, refers to SNP markers which are not the ancestral type.
Power of Exclusion (PE): The ability of an assay to discriminate between a real match and a non-match.
Predicted Haplogroup: In reference to Y-DNA, a Y-DNA haplogroup that is predicted through Y-DNA STR testing but not yet confirmed through Y-DNA SNP backbone testing. In reference to mtDNA, a mtDNA haplogroup that is predicted through HVR1 and/or HVR2 testing but has not yet been confirmed by testing the Coding Region through mtDNA SNP backbone testing.
Prior Probability: This is a value ranging from 0 (impossible) to 1 (absolute certainty). A prior probability value of 0.5 is commonly used.
Probability of Paternity: A statistical percentage based upon the combined paternity index and prior probability, describing the probability that the alleged father is the biological father of the child. A 0% probability of paternity indicates a paternity exclusion and a probability of paternity of 99.9% or greater is indicative of a paternity inclusion.
RMI (Relative Match Index): A measure of how closely your Y-DNA STR haplotype matches those of a defined population group as compared to all other population groups in the comparison. For example, a RMI of 100 means that you are 100 times more likely to belong to that population set as compared to the rest of the populations.
Sequencing: A laboratory process to read an entire length of DNA, usually up to 500 base pairs at a time. mtDNA HVR1 and HVR2 are tested using Sequencing technology.
Sibling Index: A statistical likelihood ratio representing a comparison of the probability that the individuals are related as siblings (full or half) versus the probability that the individuals are unrelated. A sibling index is calculated for each locus and is used to calculate the Combined Sibling Index.
SNP (Single Nucleotide Polymorphism): A change (mutation) in the DNA sequence involving a single nucleotide (A, C, T, or G).
SNP Test Panel: A specially selected panel of SNP markers designed for a specific purpose. Examples of SNP test panels include the mtDNA and Y-DNA Backbone SNP Panels to confirm an individual's haplogroup and the Subclade SNP Test Panels, designed to provide further resolution by determining the subclade once the haplogroup has been confirmed.
Somatic: The cells of the body with the exception of the reproductive cells (gametes). Examples of somatic cells are blood cells and buccal cells.
STR (Short Tandem Repeat): Short stretches of DNA usually 2 to 6 base pairs in length that repeat over and over again and the number of repeats can differ between different individuals or families. Also known as Microsatellite Repeats.
Sub-branch: Refers to the further branching of a main branch in the Y-DNA or mtDNA phylogenetic tree into. For example, E1 and E2 are sub-branches of Y-DNA Haplogroup E. E1a and E1b are sub-branches of E1. Also see Subclade.
Subclade: Refers to the sub-classification of Clades (Haplogroups) in the Y-DNA or mtDNA phylogenetic tree into further sub-branches. For example, E1 and E2 are subclades of Y-DNA Haplogroup E. E1a and E1b are subclades of E1.
Subclade SNP Test Panel: A specially selected panel of SNP markers which allows and individuals who have confirmed their haplogroup to gain further resolution by further deriving their subclade. Each haplogroup has its own designated Subclade test panel.
Substitution: When refering to SNPs, a substitution is a single change in which the nucleotide (A, C, T, or G) is replaced with a different nucleotide.
TMRCA (Time to Most Recent Common Ancestor): A measure of how long ago two or more individuals compared shared a common ancestor.
X Chromosome: One of the two sex determining chromosomes, it's counterpart is the Y Chromosome. Females have two X Chromosomes (XX) and males have one X Chromosome and one Y Chromosome (XY).
Y Chromosome: One of the two sex determining chromosomes, it's counterpart is the X Chromosome. Females have two X Chromosomes (XX) and males have one X Chromosome and one Y Chromosome (XY). The Y Chromosome is passed down from father to son along the paternal lineage. Also known as Y-DNA.
Y-DNA Test: Genetic tests which examine STR markers or SNP markers in the Y Chromosome.
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