Y-chromosome Short Tandem Repeat
Scientific Working Group on DNA Analysis Methods (SWGDAM)
| Preliminary Evaluation of Data | Designation
| Interpretation of Results | Conclusions
and Reporting | Statistical Interpretation | References/Suggested
The interpretation of the results of casework is a matter of professional
judgment and expertise. Not every situation can or should be covered
by a preset rule. It is important that the laboratory develop and
implement written guidelines for the interpretation of analytical
results. This document provides a framework for the laboratory to
develop Y-chromosome short tandem repeat (Y-STR) interpretation
guidelines. The laboratory’s interpretation guidelines should
be based upon validation studies, data from the literature, instrumentation
used, and/or casework experience.
Y-STR data may augment autosomal STR results. In some circumstances,
Y-STR data might be the only data that can be obtained. It is important
to note that a Y-STR haplotype is shared by males from the same
paternal lineage. This fact must be taken into account when drawing
Preliminary Evaluation of Data
1.1. The laboratory
should develop criteria to determine whether the results are of
sufficient intensity/quality for interpretation purposes using methods
appropriate for the detection platform. These criteria should be
determined by evaluating data generated by the laboratory.
1.1.1. When quantitative
results (e.g., peak amplitude) are used to evaluate STR profiles,
the results should be examined to determine if they meet the laboratory’s
empirically defined analytical and interpretational threshold(s).
126.96.36.199. The analytical
thresholds are defined as the minimum and maximum intensity thresholds
between which data are reliable for use in allele designations.
188.8.131.52. The interpretational
threshold, the minimum intensity threshold that an allele must meet
to be included in a biostatistical calculation, should be defined.
1.2. The laboratory
should develop criteria to evaluate internal lane size standards
and/or allelic ladders.
1.3. Controls are required
to assess analytical procedures.
1.3.1. The laboratory
should establish criteria for the evaluation of the controls used
in the testing, for example, reagent blank controls, amplification
blank controls, female positive controls, and male positive controls.
1.3.2. The laboratory
should develop criteria for the interpretation and documentation
of results based on evaluation of the controls.
1.4. A laboratory using
Y-chromosome STR multiplexes that contain redundant loci should
establish criteria regarding the concordance of such data.
2.1. The laboratory
should establish criteria to assign allele designations to appropriate
peaks or bands.
2.1.1. Locus Designation:
The laboratory should establish criteria to address locus assignment
2.1.2. Allele Designation:
The laboratory should designate alleles in concordance with the
recommendations of the DNA Commission of the International Society
of Forensic Genetics.
184.108.40.206. Whenever possible,
allele designation should be based operationally on the number of
repeat units contained within the allele and by comparison to an
220.127.116.11. The designation
of alleles containing an incomplete repeat motif (i.e., an off-ladder
allele falling within the range spanned by the ladder alleles) should
include the number of complete repeats and, separated by a decimal
point, the number of base pairs in the incomplete repeat (e.g.,
DYS385 15.2 allele).
18.104.22.168. If an allele
falls above the largest or below the smallest allele of the allelic
ladder, the allele should be designated as either greater than (>)
or less than (<) the respective ladder allele, or when appropriate,
extrapolation can be used.
22.214.171.124. For some duplicated
loci, the alleles cannot be assigned unequivocally to a defined
genetic locus. In concordance with recommendations of the DNA Commission
of the International Society of Forensic Genetics, the results should
be treated as a genotype (e.g., DYS385 11–14).
2.2. Artifacts can
occur and should be noted. These may include, but are not limited
to, the following: pull-up, stutter, incomplete nontemplate nucleotide
addition, and nonspecific female DNA amplification.
Interpretation of Results
3.1. The interpretation
guidelines should include criteria to determine if an observed peak
is a true allele as outlined in Section 2.1. The laboratory should
define conditions in which the data would lead to the conclusion
that the source of the male DNA is from either an apparent single
male or two or more males of different paternal lineages. This may
be accomplished by an examination of the number of alleles at each
locus and the peak-height (or band-intensity) ratios at those loci
that exhibit locus duplication such as DYS385.
Single Male Contributor: A sample may be considered to represent
a single male haplotype when the observed number of alleles at each
locus is one and the signal intensity ratio of alleles at a duplicated
locus is consistent with a profile from a single contributor. All
loci should be evaluated in making this determination. It should
be noted that individuals have been typed who exhibit multiple locus
duplications at loci other than DYS385.
with Major/Minor Male Contributors: A sample may be considered
to consist of a mixture of major and minor male contributors if
a distinct contrast in signal intensity exists among the alleles.
All loci should be evaluated in making this determination.
with a Known Male Contributor(s): In some cases, when one of
the male contributors (e.g., the victim) is known, the genetic profile
of the unknown male contributor may be inferred. Depending on the
profiles in the specific instance, this can be accomplished by subtracting
the contribution of the known male donor from the mixed profile.
with Indistinguishable Male Contributors: When major or minor
male contributors cannot be distinguished because of similarity
in signal intensities or the presence of shared or masked alleles,
individual males may still be included or excluded as possible contributors.
3.2. The laboratory
should have guidelines for the interpretation of partial profiles
(i.e., profiles with fewer loci than tested) that may arise from
degraded or limited-quantity DNA or from the presence of polymerase
chain reaction (PCR) inhibitors. Occasionally, deletion of a portion
of the Y-chromosome or a primer-binding site mutation can result
in the failure to detect one or more Y-STR loci.
Conclusions and Reporting
4.1. The laboratory
should prepare guidelines for formulating conclusions resulting
from comparisons of evidentiary samples and known reference samples.
4.1.1. General categories
of conclusions are inclusion or match, exclusion
or nonmatch, inconclusive or uninterpretable, and no
4.1.2. Comparison of
haplotypes cannot distinguish between males from the same paternal
lineage; therefore, inclusions need to be qualified.
5.1. Y-STR loci are
located on the nonrecombining part of the Y-chromosome and, therefore,
should be considered linked as a single locus. A Y-STR database
must consist of haplotype frequencies rather than allele frequencies.
The source of the population database(s) used should be documented.
Relevant population(s) for which the frequency will be estimated
should be identified. A consolidated U.S. Y-STR database (http://usystrdatabase.org)
has been established and should be used for population frequency
estimation. A number of other Y-STR haplotype frequency databases
exist online. (See available listing on the NIST [National Institute
of Standards and Technology] STRBase Web site at http://www.cstl.nist.gov/biotech/strbase/y_strs.htm.)
5.2. In reporting matches,
haplotype searches of the population database should be conducted
using all loci for which results were obtained from the evidentiary
sample. In cases where less information is obtained from the known
sample, only those loci for which results were obtained from both
the known and evidentiary samples should be used in the population
5.3. The basis for
the haplotype frequency estimation is the counting method. The application
of a confidence interval corrects for database size and sampling
variation. Reporting a haplotype count without a confidence interval
is acceptable as a factual statement regarding observations in the
5.3.1. If a confidence
interval is applied, the following example calculation could be
126.96.36.199. The haplotype
has not been previously observed in the database:
The formula for calculating the upper
95 percent confidence limit in this case would be
1 – (0.05)1/n
where n is the size of the database.
188.8.131.52. The haplotype
has been observed in the database:
The formula for calculating the upper 95 percent confidence limit
in this case would be
where p is x/n, n = database size, and x = the
number of observations of the haplotype in the database.
5.4. For Y-STR mixtures
that cannot be deconvoluted, calculations may be performed for the
probability of exclusion and likelihood ratios.
5.5. If both autosomal
and Y-STR data are collected on a sample, the product rule may be
used to combine the autosomal STR genotype match probability and
Y-STR haplotype frequency information.
5.6. It is recognized
that population substructure exists for Y-STR haplotypes. Studies
with current population databases have shown that the FST values
are very small for most populations. Thus the use of the counting
method that incorporates the upper-bound estimate of the count proportion
offers an appropriate and conservative statistical approach to evaluating
the probative value of a match.
Balding, D. J. Weight-of-Evidence for Forensic DNA Profiles.
John Wiley & Sons, Hoboken, New Jersey, 2005, pp. 99–101.
Ballantyne, J., Fatolitis, L., and Roewer, L. Creating and managing
effective Y-STR databases, Profiles in DNA (2006) 9(2)10–13.
Also available: http://www.promega.com/profiles/902/ProfilesinDNA_902_10.pdf.
Buckleton, J., Walsh, S., and Harbison, S. Nonautosomal forensic
markers. In: Forensic DNA Evidence Interpretation. J. Buckleton,
C. M. Triggs, and S. J. Walsh, Eds. CRC Press, Boca Raton, Florida,
2004, pp. 299–331.
Budowle, B., Adamowicz, M., Aranda, X. G. et al. Twelve short tandem
repeat loci Y chromosome haplotypes: Genetic analysis of populations
residing in North America, Forensic Science International
Budowle, B., Jianye, G., and Chakraborty, R. Basic principles for
estimating the rarity of Y-STR haplotypes derived from forensic
evidence. In: Proceedings of the Eighteenth International Symposium
on Human Identification, 2007. Available: http://www.promega.com/geneticidproc/ussymp18proc/oralpresentations/Budowle.pdf.
Budowle, B., Sinha, S. K., Lee, H. S., and Chakraborty, R. Utility
of Y-chromosome short tandem repeat haplotypes in forensic applications,
Forensic Science Review (2003) 15:153–162.
Butler, J. M. Recent developments in Y-short tandem repeat and
Y-single nucleotide polymorphism analysis, Forensic Science
Review (2003) 15:91–111. Available: http://www.cstl.nist.gov/biotech/strbase/pub_pres/Butler2003b.pdf.
Butler, J. M. Y Chromosome DNA Testing. In: Forensic DNA Typing:
Biology, Technology, and Genetics of STR Markers. 2nd ed. J.
M. Butler, Ed. Elsevier Academic Press, New York, 2005, pp. 201–239.
Butler, J. M., Decker, A. E., Kline, M. C., and Vallone, P. M.
Chromosomal duplications along the Y-chromosome and their potential
impact on Y-STR interpretation, Journal of Forensic Sciences
(2005) 50:853–859. Available: http://www.cstl.nist.gov/strbase/pub_pres/ButlerJFS_Y-STRduplication.pdf.
DNA Advisory Board. Quality assurance standards for forensic DNA
typing laboratories, Forensic Science Communications [Online].
(July 2000). Available: http://www.fbi.gov/hq/lab/fsc/backissu/july2000/codis2a.htm.
Dupuy, B. M., Stenersen, M., Egeland, T., and Olaisen, B. Y-chromosomal
microsatellite mutation rates: Differences in mutation rate between
and within loci, Human Mutation (2004) 23:117–124.
Gill, P., Brenner, C., Brinkmann, B. et al. DNA Commission of the
International Society of Forensic Genetics: Recommendations on forensic
analysis using Y-chromosome STRs, International Journal of Legal
Medicine (2001) 114:305–9 and Forensic Science International (2001) 124:5–10.
Gusmão, L., Butler, J. M., Carracedo, A. et al. DNA Commission
of the International Society of Forensic Genetics (ISFG): An update
of the recommendations on the use of Y-STRs in forensic analysis,
Forensic Science International (2006) 157:187–197
and International Journal of Legal Medicine (2006) 120:191–200.
Gusmão, L., Sánchez-Diz, P., Calafell, F. et al.
Mutation rates at Y chromosome specific microsatellites, Human
Mutation (2005) 26:520–528.
Hammer, M. F., Chamberlain, V. F., Stover, D. et al. Population
structure of Y chromosome SNP haplogroups in the United States and
forensic implications for constructing Y chromosome STR databases,
Forensic Science International (2006) 164:45–55.
Kayser, M., Brauer, S., Schädlich, H. et al. Y chromosome
STR haplotypes and the genetic structure of U.S. populations of
African, European and Hispanic ancestry, Genome Research
Kayser M., Cagliá, A., Corach, D. et al. Evaluation of Y
chromosomal STRs: A multicenter study, International Journal
of Legal Medicine (1997) 110:125–133, 141–149.
Krenke, B. E., Viculis, L., Richard, M. et al. Validation of a
male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex,
Forensic Science International (2005) 148:1–14.
Mulero, J. J., Chang, C. W., Calandro, L. M. et al. Development
and validation of the AmpFSTR® Yfiler™ PCR amplification
kit: A male specific, single amplification 17 Y-STR multiplex system,
Journal of Forensic Sciences (2006) 51:64–75.
National Research Council, Committee on DNA Forensic Science. The
Evaluation of Forensic DNA Evidence. 2nd ed. National Academies
Press, Washington, D.C., 1996.
Prinz, M., Ishii, A., Coleman, A., Baum, H. J., and Shaler R. C.
Validation and casework application of a Y chromosome specific STR
multiplex, Forensic Science International (2001) 120:177–188.
Schoske, R., Vallone, P. M., Kline, M. C., Redman, J. W., and Butler,
J. M. High-throughput Y-STR typing of U.S. populations with 27 regions
of the Y chromosome using two multiplex PCR assays, Forensic
Science International (2004) 139:107–121. Available:
Scientific Working Group on DNA Analysis Methods (SWGDAM). Short
Tandem Repeat (STR) Interpretation Guidelines, Forensic Science
Communications [Online]. (July 2000). Available: http://www.fbi.gov/hq/lab/fsc/backissu/july2000/strig.htm.
Sinha, S. K., Budowle, B., Chakraborty, R. et al. Utility of the
Y-STR typing systems Y-PLEX™ 6 and Y-PLEX™ 5 in forensic
casework and 11 Y-STR haplotype database for three major population
groups in the United States, Journal of Forensic Sciences
Walsh, B., Redd, A. J., Hammer, M. F. Joint match probabilities
for Y chromosomal and autosomal markers, Forensic Science International