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The Use and Significance of Y-STR Testing

By Julie Heinig, Ph.D.
October 1, 2007

While many legal professionals may be well acquainted with the conventional autosomal Short Tandem Repeat (STR) analysis that is typically associated with forensic cases involving DNA, some may be less familiar with the technique of Y-chromosome STR analysis (commonly referred to as Y-STR). One may ask, why should Y-STR testing be used instead of autosomal STR analysis? Using the Y-STR technique, scientists are often able to identify genetic information that may otherwise be difficult or impossible to detect, especially in sexual assaults and other cases that involve mixed male/female DNA samples.

Y-STR DNA Testing
An individual's genetic information, which includes autosomal DNA markers such as the 13 CODIS core STR loci, is inherited from both biological parents. Everyone receives exactly half of his or her genetic markers from each parent. Because of the unique combination of the mother's and father's DNA, genetic information is different for each child (except identical twins). The Y chromosome DNA markers, however, are conserved and passed down paternally from a father to all of his male offspring without changing (except when mutations occur).

Forensic DNA evidence is rarely pristine; in fact, analysis is often difficult because of partial DNA profiles, sample degradation, and male/female DNA mixtures. In the past five years, there has been an increase in the use of Y-short tandem repeat loci (Y-STRs) by forensic laboratories, especially in cases where using conventional autosomal STRs has achieved limited success. When autosomal STRs are used in sexual assault cases, the amplification and eventual detection of male DNA in a mixture sample may be masked by the presence of high levels of female DNA. The application of Y-STRs simplifies the analysis of these mixtures by removing the female contribution from the amplification profile. These situations include sexual assault evidence from azoospermic or vasectomized males and blood-to-blood or saliva-to-blood mixtures where the absence of sperm prevents a successful differential extraction of male DNA. In addition, the number of individuals involved in a "gang rape" may be easier to decipher with Y-STR results than with the complicated mixtures associated with autosomal STR results.

Y-STR markers are useful in the analysis of the following types of evidence:

  • Rape kit samples with limited male genetic material or from cold cases
  • Evidence where seminal fluid has been identified but few or no sperm is present
  • Fingernail scrapings from a female assault victim
  • Ligatures from the strangulation of a female victim

Cases Involving Y-STR Testing

Fingernail swabs from assault victim:

DDC has experienced a number of cases in which DNA has been extracted from the swabs of fingernails. For example, the results obtained from autosomal STR analysis included a strong profile from the female victim with no sign of male DNA. Subsequent Y-STR testing yielded a full male profile. In fact, in some cases, more than one male donor has been observed through Y-STR testing.

There are a number of possible sources of DNA found on fingernails. DNA may be from the victim scratching her assailant or from the victim sticking her fingers in his mouth, nose, or eyes during the assault. The DNA could also simply be from sweat on the perpetrator's body. Using Y-chromosome-specific markers can improve the chances of detecting low levels of the perpetrator's DNA in a high background of the victim's DNA.

Trace amounts of seminal fluid on victim's underwear:
Our laboratory receives a number of forensic cases from crime labs in which they have identified seminal fluid on the victim's underwear with no sperm present. The autosomal DNA test results from the non-sperm fraction produced a female profile only, but after performing a Y-STR test, we were able to observe a male profile that was then used for comparison purposes.

A limitation of Y-STRs compared with autosomal STRs is a reduced power of discrimination due to a lack of recombination throughout most of the Y chromosome. In an effort to increase the power of discrimination of current Y-STR multiplexed systems, a 17-plex Y-STR system has been developed by Applied Biosystems called the Yfiler TM PCR amplification kit. The significance of a match between genetically typed samples depends on the frequency at which a haplotype occurs in a population. If the suspect and evidence samples have the same haplotype, then the suspect (and his paternal relatives) cannot be excluded as a possible source of the evidence sample. In spite of the accuracy of this type of statement, courts are likely to require some kind of statistic to give meaning to the match. Since the product rule cannot be applied to Y-STR markers, a counting method is used to empirically determine how many times a particular haplotype is observed in a population database (Budowle, B., Sinha, S.K., Lee, H.S., Chakraborty, R. Utility of Y-chromosome STR haplotypes in forensic applications . Forensic Sci Rev 2003; 15(2): 153-64). Confidence intervals may then be used to reflect the uncertainty involved in population database samplings of unrelated individuals.

In conclusion, unlike autosomal STRs, a Y-STR profile cannot uniquely identify an individual. In addition, the observation of a Y-STR match does not possess the power of discrimination or impact a courtroom in the same way an autosomal STR match would. However, if the evidence has a very small amount of male DNA, the Y-STR information can provide extremely valuable information in the genetic identification of the male contributor.



Autosomal From "autosome," which is any chromosome that is not a sex chromosome. The human has 22 pairs of (or 44) autosomal chromosomes and 1 pair of (or 2) sex chromosomes.

DNA Markers – DNA markers, also called genetic markers, are specific portions of DNA that consist of short, repeating sequences of DNA. The number of times these sequences are repeated is highly variable among individuals, and it is this fact that makes DNA markers effective for human identity and family relationship testing.

Haplotype – The genetic information from one set of chromosomes (compared to genotype from autosomal chromosomes) representing single alleles.

Recombination – The process by which progeny derive a combination of genes different from that of either parent. During the process of meiosis or gamete cell production, each reproductive cell receives at random one representative of each pair of chromosomes, or 23 in all. Since there are two chromosomes in each pair, meiosis results in about 8.4 million (223) different possible combinations of chromosomes in human eggs or sperm cells. The union of egg and sperm cells therefore results in over 70 trillion different possible combinations – each one representing half of the genetic material from the father and half from the mother. In this manner, human genetic material is effectively shuffled with each generation producing the diversity seen in the world today. (Definition from Forensic DNA Typing by Butler, p. 22)