This tutorial is Part 3 of a 9 part series.
Part 1, What is Y-DNA?
Part 2, Types of Ancestral Markers in Y-DNA
Part 3, STR Markers in Y-DNA <<== You are here
Part 4, STR Markers in Y-DNA - Y-DNA STR Marker Testing
Part 5, STR Markers in Y-DNA - What is Genetic Distance?
Part 6, STR Markers in Y-DNA - What is the Time to Most Recent Common Ancestor (TMRCA)?
Part 7, STR Markers in Y-DNA - Why test more STR markers?
Part 8, SNP Markers in Y-DNA - Y-DNA Haplogroup and Subclade Determination
Part 9, SNP Markers in Y-DNA - Summary of Y-DNA Test Types
What is a STR marker?
STR stands for "short tandem repeat". STR is a type of DNA polymorphism where short sequences of DNA are repeated over and over again. STRs are usually considered “junk DNA” because they are introns and do not code for protein. The number of times a DNA sequence is repeated for a given STR is variable between different individuals.
The STR markers found in the Y-DNA are very useful for examining paternal line connections. A male individual’s Y-DNA STR marker set is unique to his paternal line. All males who are descendents from the same male lineage will have exactly the same or a very similar Y-DNA STR marker pattern. The combined results for the panel of Y-DNA STR markers tested is considered the individual's Y-DNA "haplotype". Please note that "haplotype" is not the same as "haplogroup (we will be discussing "haplogroups" later in the tutorial).
The Y-DNA STR Test examines several different STR Marker Types:
A. Single-Copy Y-DNA STR Markers
Single-copy STR markers are STR markers that occur only once in the human genome. That means that when this marker type is tested, only one allele value will be obtained for each marker in your report.
B. Multi-Copy Y-DNA STR Markers
Multi-copy STR markers are markers that occur more than once (ie more than one copy) in the human genome. That means that when this marker type is tested, more than one allele value can be obtained for each of these markers in your report.
For example, the markers DYS385, DYS459 and YCAII are typically present at two different locations on the Y-chromosome; therefore, they are also termed “duplicated markers”. The allele values for each copy are not reported in any specific order, as the exact order of copies cannot be determined, but typically, the smaller allele value is reported first, followed by the larger allele value.
C. Special Multi-Copy Marker DYS389
DYS389 is a special marker. Unlike other multi-copy STR markers, only one location is amplified. The forward primer for DYS389 binds at a specific location on the Y-chromosome, whereas the reverse primer binds at two different locations. Such amplification yields two PCR products: the shorter DYS389I fragment and the longer DYS389II fragment.
D. Special rules for reporting Marker DYS464
DYS464 is a special Y-DNA STR marker which is known to have 4 to 7 alleles (a to d for 4 or a to g for 7). Previously, the “genotype” is reported. When the genotype is reported, identical repeats are reported multiple times if that same repeat is present more than once. For example, someone may be reported as having the following markers for DYS464:
DYS464a = 17
DYS464 b= 18
DYS464c = 18
DYS464 d = 19
As shown above, the value “18″ is reported twice. This type of reporting is known as “genotype” reporting. However, recent policies implemented by the American Association of Blood Banks mandates that all Accredited DNA testing laboratories must report the “phenotype” instead of “genotype” for multi-copy markers, especially if the marker has more than 2 alleles. Though the requirements of AABB refers to apparent homozygotes detected on autosomal DNA, the interpretation concerns are similar for multicopy alleles on the Y-Chromosome because peak height ratio detection of STR fragment analysis results is not a validated method for copy number detection in the absence of real time PCR and sequencing. ref: Guidance for Standards for Relationship Testing Laboratories 8th Edition, 220.127.116.11.
If the phenotype is reported for the above individual, then his results will be shown as follows:
DYS464a = 17
DYS464b = 18 (duplicate repeat values are only reported once when reporting phenotypes, so when reporting by phenotype, “18″ is only reported once)
DYS464c = 19
Phenotype reporting is especially important in cases with more than 2 alleles such as DYS464 which is known to have up to 7 alleles. Currently, only the phenotype will be reported for Y-DNA STR marker DYS464.