Can the Rapidly Mutating Loci in the Yfiler Plus® Amplification Kit Differentiate the Members of a Large Family?

There are some forensic cases where Y STRs are the only useful evidence.  For example, if a female victim scratches her male attacker as she struggles with him, she may pick up some male DNA under her fingernails, but it would be expected that there will be a large amount of her own female DNA in her fingernail scrapings.  In the lab we would quantitate the amount of total human DNA versus the amount of male DNA, and we know that at some point, it is not feasible to amplify the autosomal DNA because we would only see the female’s DNA profile.  In those cases it is useful to amplify Y STR DNA because it zeroes in on the male DNA and can ignore even very high amounts of female DNA.

However, since the Y chromosome is handed down from father to son as a whole, paternal relatives are expected to have the same Y STR DNA profile.  In a case where there might be brothers or other family members who are all possible suspects, it is not possible to differentiate them with traditional Y STR amplification kits.  The YFiler Plus kit has these loci that are considered highly mutating, so it becomes more possible that there might be a mutation between father and son, or between brothers, which would allow these individuals to be differentiated.

Although there are published mutation rates for the Y STR DNA loci, there is not necessarily a lot of data for each locus, and these mutation rates may change as more data is collected.  The mutation rates of the highly mutating loci in this kit are only approximately ten times higher than the other loci, and so mutation is still a rare occurrence.  This project was intended to see whether in a practical instance if we could differentiate a group of related men.


Written by: Tamara Camp, DuPage County Forensic Science Center



The Yfiler Plus® (YFP) PCR amplification kit amplifies 27 Y-STRS, including seven highly polymorphic rapidly-mutating loci: DYF387S1a/b, DYS449, DYS518, DYS570, DYS576, and DYS627.  The kit is advertised as having “powerful discrimination capacity, particularly between closely related males”, which could be of use in casework where multiple related males are named as suspects.

Shortly after our lab worked on the internal validation of YFP, I found myself at an event where I knew a large number of men were related. We know the published mutation rates of these loci, but I thought it would be interesting to see, in practice, if I could actually differentiate these men from one another using this kit.  These men consented to buccal swab collection for the purposes of this study.

In an effort to determine whether father-son pairs, siblings, paternal uncle-nephew pairs or paternal cousins can be differentiated in routine casework, standards from a large family set, including three generations of male relatives, were acquired and their Y-STR DNA profiles were determined using the Yfiler Plus kit.

Standards were collected on sterile cotton swabs and portions of these swabs were extracted with the PrepFiler® Automated Forensic DNA Extraction Kit (ThermoFisher Scientific) on the Automate® Express DNA Extraction System (ThermoFisher Scientific).  Extracts were quantified with the Investigator Quantiplex Hyres Kit (Qiagen) and the male values were used to normalize the samples on the QIAgility® liquid handling robot (Qiagen).  Normalized samples were amplified with the Yfiler Plus® (YFP) PCR amplification kit on the GeneAmp 9700 PCR System (ThermoFisher Scientific).  Amplicons were analyzed on an Applied Biosystems® 3500 Genetic Analyzer (ThermoFisher Scientific).

Nineteen male relatives from 3 generations of a large family were analyzed with the Yfiler Plus amplification kit.  All four of the first generation sons who were typed share the same 27 locus Y-STR DNA profile.  We can assume that this Y-STR DNA profile would have been shared by their father, who passed it on to these sons.  This profile will be called the family profile for simplicity.

Most of the remaining family members also share the family profile, with some exceptions.  All of the sons of one first generation son who was not tested, demonstrate a difference at the DYS627 locus, one of the rapidly mutating loci.  While the family profile has a 25 at DYS627, the sons of this untested man have a 26 at this locus.  It can be assumed that this mutation originated at the untested man, who passed it on to each of his sons.  Interestingly, a grandson of the untested man, types as a 25 at DYS627, indicating a back mutation to the family profile.  In addition, a member of the third generation demonstrates a difference from the family profile at the DYS456 locus.  While the family profile has a 16 at this locus, this man has a 15 allele.  DYS456 is not considered a rapidly mutating locus.

Out of 19 typed male relatives, 3 mutation events were observed, for an overall mutation rate of 0.5% [27 loci x 19 individuals = 513; 3/513 = 0.00585].  According to the Y-HRD website, the highest mutation rate in the YFP kit is at DYS518 with a mutation rate of 0.018.  The lowest mutation rate in the YFP kit is at the DYS438 locus with a mutation rate of 0.000375.  Our results fall within these values.

If the results from this family set can be assumed to be typical, it will be rare to be able to differentiate family members with the YFP amplification kit.  Some mutations may be observed, allowing some father-son pairs, siblings, paternal uncle-nephew pairs or paternal cousins to be differentiated from one another, but most paternally related individuals will be expected to have the same Y-STR DNA profile.


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