variant of a gene or genetic marker.
For STR markers, each allele is designated by
the number of repeats
of the short base sequence.
autosome
one of the non-sex-determining chromosomes.
Autosomes occur in nearly identical pairs.
See also X and Y.
base
the building block of DNA, one of four molecules that
link up to make a DNA chain. The four are named
adenine, cytosine, guanine, and thymine (A, C, G, T for short).
These are also called nucleotides.
buccal
pertaining to the cheeks or the mouth cavity in general. Buccal cell
samples for analysis can be obtained easily and painlessly by a gentle
brushing or scraping of the inside of the mouth.
chromosome
one of the DNA macromolecules found in the cell
nucleus. Humans have 46 chromosomes. See also X and Y.
CRS
the Cambridge Reference Sequence for mtDNA,
used for convenience to compare with all human mtDNA sequences, such that any
sequence can be expressed concisely as a relatively short list of
difference from the reference
DNA
deoxyribonucleic acid. The chemical constituent of genes and chromosomes.
DNA has four different base units, designated A, C, G, and T, which are
connected in long double chains, and the sequence of these bases encodes
the genetic information.
DYS
DNAY-chromosome
Segment. A label for loci or genetic markers on the Y
chromosome. Each marker is designated
by a number, according to international conventions.
Virtually all DYS designations discussed in the context of genetic
genealogy are those of STR
markers (which are useful for genealogy because of their
relatively high mutation rate).
electropherogram
the record produced by the analytic technique called electrophoresis,
which segregates complex molecules in a mixture by applying an electric
field. The molecules migrate at different rates, according to molecular
weight. In the case of DNA analysis, this determination
of molecular weights is equivalent to measuring the length of each DNA
segment in a batch, as well as the relative amount (subject to issues
of calibration) of each type of DNA segment.
a process replacing one allele of a pair with a
copy of the other. This term is used by extension for all kinds of
loci, not just genes.
See also recLOH.
genome
the entire inventory of nuclear DNA in an organism.
genotype
a set of allele values of one or
more markers for one individual. Since most of the
DNA consists of nearly identical
pairs of chromosomes, a genotype
typically has two alleles for each marker, one from each parent.
See also haplotype.
haplogroup
a classification comprising many
different haplotypes thought to be related.
Haplogroups are defined in terms of markers
that mutate so slowly they are treated as if they have occurred
only once in all time.
The major haplogroups originated thousands or tens of
thousands of years ago.
haplotype
a set of allele values of one or more markers
for one individual and identified as coming just from one
parent, particularly markers on the Ychromosome or in
mitochondrial DNA.
See also genotype.
heterozygous
having two different alleles in the two
copies of the same marker or locus
existing on a pair of chromosomes.
By extension, this term
is sometimes applied to the two copies of a locus found on opposite
arms of a palindrome on the Y
chromosome. See also homozygous.
homozygous
having the same allele in the two copies of the
same marker or locus existing on
a pair of chromosomes. By extension, this term
is sometimes applied to the two copies of a locus found on opposite
arms of a palindrome on the Y
chromosome. See also heterozygous.
Hypervariable Region 2. (See HVR1.) The limits of
HVR2 are even more vague than for HVR1. HVR2 is generally said to start at location
1 and to extend for a few hundred bases, but part
of this region is often called HVR3.
indel
A type of polymorphism characterized by the
insertion or deletion of a sequence of DNA at a particular
place.
a distinctive sub-unit of DNA, often not part
of a gene. Often used interchangeably with
locus, but referring to the contents of the site,
rather than the site itself.
organelles within the cell responsible
for converting food into
usable energy. Each mitochondrion has its own DNA.
The mitochondria in a child come entirely from the mother, and so
mitochondrial DNA ("mtDNA" for short) is a tracer of female-line
ancestry, just as Y DNA is a tracer for male-line ancestry.
motif
a sequence of DNAbases
(typically three or four) that is repeated in multiple copies in
a microsatellite or STR. The term is also used
for a combination of several mutations associated
with a particular haplogroup,
especially for mitochondrial DNA.
An event in which the DNA chain alters. In the case
of STR markers, a mutation is almost invariably the gain
or loss of one repeat of the basic short sequence (or, rarely, two repeats).
Other types of mutations include the substitution of
one base for another (known as a SNP)
and the insertion or deletion of
a whole segment (known as an indel.
See also recombination.
any small, compact, and cohesive entity within a cell. An organelle
is to a cell what an organ is to a multi-celled creature.
palindrome
a sequence of letters (or DNA bases) that reads the same forwards and
backwards.
PCR
Polymerase Chain Reaction. A chemical process that replicates a given
sample of DNA many times, in imitation of
natural replication. The process
cycles between two stages: splitting the two strands of DNA apart and then
forming new double strands by adding a mixture of the enzyme polymerase and the
four DNA bases. By adding primers
as well, the process can be used to replicate just the one or more DNA
segments of interest.
poly-C
consisting of many contiguous cytosine ("C") bases.
Such segments of DNA are prone to mutation by the
insertion (or sometimes the deletion) of one or more cytosines, presumably
by the same process that produces ordinary STR mutations.
polymorphism
The occurrence of more than one form of DNA in
different individuals, or even in different cells within one individual.
Such diversity arises through the occurrence of
mutations.
primer
a reagent consisting of a relatively short DNA sequence
exactly matching the sequence flanking a marker of
interest. A primer needs to be long enough that (in principle) it matches only
one spot in the entire human genome,
but, in practice, many segments of human
DNA appear more than once, through a poorly understood process of duplication.
Two primers, one for each end of the desired marker, are used in
the PCR amplification step
to selectively amplify that marker. The primers are often
tagged with a flourescent dye to help in detecting the amplified DNA
segments.
a process of "mixing and matching" of paired
chromosomes that takes place at cell division.
One or more segments may be swapped between the two chromosomes, or
occasionally a
segment may replace the corresponding segment on the other chromosome.
This process can also occur on palindromic segments of the
Y chromosome and may affect paired loci,
such as DYS385a and DYS385b.
Short Tandem Repeat. Also known as microsatellite. This is a genetic
marker
consisting of multiple copies of a short motif,
(a sequence of DNAbases). Occasionally, a microsatellite will
mutate by the gain or loss of one repeat.
So-called "simple" STRs have just one contiguous set of repeats; "complex"
STRs may have multiple sets of repeats separated by short patches of
non-repeating DNA and may even have repeats of more than one motif.
umbilical
in genealogy, referring to the straight maternal line of ancestry
(child to mother to mother's mother to mother's mother's mother and
so on)
X
one of the two sex-determining chromosomes,
See also Y.
Y
one of the two sex-determining chromosomes.
A person with the combination XX is female, while a person with XY is male.
Most of the Y chromosome, unlike the others, does not trade DNA
with a "partner chromosome," and it therefore passes essentially
intact from father
to son. This property leads to a minimum of ambiguity in interpreting the
results of Y DNA analysis.
