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Non-STR DNA Markers: SNPs, Y-STRs, LCN and mtDNA

Statistical Interpretation of a Y-STR Match

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Since the Y-STR (Y-Short Tandem Repeats) loci are located on the NRY part of the Y-chromosome and are inherited as a block of linked haplotypes, estimates of the multilocus frequency cannot proceed by the product rule.  Instead an estimate of the frequency of occurrence of a particular haplotype requires the counting method, which is based upon how many times a particular multilocus haplotype is observed in a particular database.  This is akin to the procedure used to estimate mtDNA haplotype frequencies. The ability to obtain a reliable estimate thus depends upon the nature of the databases that are used.  Specifically, the ethnogeographic composition of the database, the number of individuals deposited therein, and the number of searchable Y-STR loci are factors that should be maximized to increase confidence in the accuracy of a frequency estimate. 

Read more about Population Genetics in course: Population Genetics & Statistics.

A number of web-accessible, searchable databases exist.  A Y-STR haplotype reference database (YHRD) was established by the Institute of Legal Medicine, Berlin in 2000 to generate reliable Y-STR haplotype frequency estimates for MHL Y-STR haplotypes to be used in the quantitative assessment of matches in forensic casework and the assessment of male population stratification among world-wide populations. This worldwide database extends to US populations and permits MHL and the SWGDAM loci searches. The principal commercial vendors of Y-STR kits support Y-STR databases that permit public access and searching using their particular Y-STR marker sets (See Table Below).

Since the basis for the haplotype frequency estimation is the counting method, the application of a confidence interval is recommended to correct for database size and sampling variation. Reporting a haplotype count without a confidence interval may still be acceptable as a factual statement regarding observations in a particular database. If a confidence interval is applied, the following example calculation could be used (SWGDAM Y-STR Interpretation Guidelines). If the haplotype has been observed in the database, the formula for calculation of the upper 95% confidence limit in this case would be:

Formula for calculation of the upper 95% confidence limit
National Institute of Justice (NIJ) (see reuse policy).

where p is x/n, n=database size, and x=number of observations in database. (Due to the enhanced population substructure effects of the Y-chromosome compared to autosomes, it may be necessary to apply an FST -like correction factor to this estimate, similar to the National Research Council-recommended θ for homozygotes. The appropriate studies to determine this are in progress.) If the haplotype has not been previously observed in the database, the formula for calculation of the upper 95% confidence limit in this case would be:


where n is the size of the database. Alternatively a simplified calculation could be 3/n. This value will be close to above formula, and for 95% of the time the real frequency will be less than that estimate.

Empirical studies have confirmed the non-linkage of Y-STR haplotypes and autosomal STR profiles.  Therefore for those cases in which both autosomal and Y-STR profiles exist, it is possible to multiply the autosomal STR profile frequency with the upper confidence limit bounded Y-STR haplotype frequency to give an overall frequency estimate of the genetic profile obtained.

Read more about Population Genetics in course: Population Genetics & Statistics.

Y-STR Analysis Case Example

Eight years after he requested postconviction DNA testing, Wilton Dedge was exonerated and released from Florida prison. In 1982, Dedge was convicted in Brevard County, Florida, of sexual battery, aggravated battery, and burglary. He was sentenced to two concurrent life sentences. The victim was attacked in her home on December 8, 1981. After coming home in the afternoon, she heard a sound while changing clothes and turned to find a man armed with a blade. He cut off her clothes and raped her vaginally and anally. During the assault, the perpetrator cut the victim all over her body. After the assailant left, the victim contacted her boyfriend and was taken to the emergency room, where a rape kit and the victim's clothes were collected. Wilton Dedge was convicted in May 1982 of this crime, despite his protestations of innocence, largely based upon eyewitness evidence. His conviction was reversed in 1983, but he was again convicted in August 1984. At trial, the prosecution relied on the victim's eyewitness identification, microscopic hair comparison, snitch testimony, and dog-sniffing evidence to secure the conviction.  The prosecution's hair expert testified that two pubic hairs were found on the victim's bed. One was similar to hairs taken from the victim. The other was from a male and, based upon a microscopical hair analysis, Dedge could not be eliminated as a possible source of that hair. The hair proved to be the only physical evidence linking Dedge to the crime. Although sperm were found on a swab in the rape kit, it did not yield the ABO blood type of the semen donor. In 1996, Dedge was one of the first Florida inmates to seek postconviction DNA testing, several years before the state passed its 2001 law providing for such testing. He won that motion in 2000, and, in June 2001, mitochondrial DNA testing proved that the pubic hair did not come from Dedge. After more legal wrangling, further testing was ordered by the Court of Appeal on the semen evidence found on the anal swab recovered from the rape kit.  Initial testing had yielded only two markers because the sample was degraded. Y-chromosome STR testing was utilized in the final round of testing. The Y-STR results excluded Dedge as the contributor of the spermatozoa, conclusively proving his innocence for a second time.

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