Y chromosome analysis

DEFINITION: DNA (deoxyribonucleic acid) analysis technique that focuses on the Y chromosome, which determines male sex in human beings.

SIGNIFICANCE: Analyses of Y chromosome markers and mitochondrial (maternally inherited) DNA are important for forensic, genealogical, archaeological, and anthropological studies because they can be conducted even with very small or degraded samples of genetic material.

The Y and the X chromosomes are sex chromosomes. Within the twenty-three pairs of human chromosomes, one pair in a female human has two X chromosomes, and one pair in a male human has an X and a Y chromosome. The Y chromosome is the smallest human chromosome in terms of the number of genes it contains, about fifty-nine million base pairs, or 2 percent of the total DNA (deoxyribonucleic acid) in cells.

Two small regions (called the pseudoautosomal regions) at the tips of the X and Y chromosomes are homologous. The pseudoautosomal regions of the X and Y chromosomes pair during meiosis. The rest of the Y chromosome (about 95 percent) is present in just one copy (is haploid) and does not have a homologous copy with which to pair, so there is no genetic recombination for the majority of the Y chromosome. Because no genetic recombination occurs in most of the Y chromosome, the Y markers can be tracked through generations.

The nonrecombining portion of the Y chromosome has been shown to have different kinds of polymorphisms that mutate at different rates. Short tandem repeats (STRs) on the Y chromosome are such polymorphic markers. These short sequences are typically one to six base pairs long and are repeated a variable number of times in different individuals. Polymerase chain reaction (PCR), a DNA amplification method, is used to amplify the particular Y-STR through the use of primers specific for that STR. A large number of different STRs are amplified in a single reaction through the use of primers specific to each STR (multiplex PCR). The amplified DNA is sized using electrophoresis (often capillary electrophoresis) to enable the identification of which allele (copy of a gene) of the Y-STR an individual has. Single nucleotide polymorphisms (SNPs) are also used. Kits to PCR-amplify Y-STRs are commercially available, and numerous Y-STR profiles have been collected for comparisons in the Y Chromosome Haplotype Reference Database. In 2023, the complete human Y chromosome sequence was published.

Y-STRs are important to extract male-specific information from a sample when sperm are not present. Such a sample from a crime scene may take the form of a mixture of blood from a male perpetrator and a female victim or male saliva on a female victim. Y chromosome markers are also used in paternal lineage testing, including some paternity cases and in missing persons investigations. Further, the lack of recombination of most of the Y chromosomes makes Y markers useful in human migration and evolutionary studies comparing male humans over lengthy periods.

Because PCR can amplify a small amount of DNA, small and degraded samples can be analyzed for Y-STRs. One disadvantage of Y chromosome analysis is that loci are not independent of one another, so haplotypes (the alleles at all the tested loci) must be examined. Also, unless a mutation has occurred, paternal lineages often have the same Y-STR haplotype, so fathers, sons, brothers, uncles, and paternal cousins cannot usually be distinguished from each other by Y-STR analysis. However, studies show that rapidly mutating (RM) Y-STR markers improve the discrimination of closely related males, addressing a key limitation of traditional Y-STR analysis in forensic and kinship investigations.

Accordingly, forensic Y-STR kits are increasingly incorporating RM loci, enhancing the statistical power of male lineage analysis in applications such as missing persons cases and paternal kinship testing.

Bibliography

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Haarkötter, Christian, et al. “Evaluating the Efficacy of Three Y-STRs Commercial Kits in Degraded Skeletal Remains.” Science & Justice, vol. 64, no. 5, Sept. 2024, pp. 543–48, doi:10.1016/j.scijus.2024.07.007. Accessed 3 Feb. 2026.

Hanson, Erin K., and Jack Ballantyne. “Comprehensive Annotated STR Physical Map of Human Y Chromosome: Forensic Implications.” Legal Medicine, vol. 8, Mar. 2006, pp. 110–20.

Kobilinsky, Lawrence F., et al. Forensic DNA Analysis. Chelsea House, 2007.

Ndomondo, Sunganani, et al. “Forensic Applications of Rapidly Mutating Y-STR Markers: Current Status and Future Perspectives.” Forensic Science, Medicine and Pathology, 28 Oct. 2025, doi:10.1007/s12024-025-01120-6. Accessed 3 Feb. 2026.

Rhie, Arang, et al. “The Complete Sequence of a Human Y Chromosome.” Nature, vol. 621, 2023, pp. 344–54, doi:10.1038/s41586-023-06457-y. Accessed 3 Feb. 2026.

“What Are Y-DNA STRs?” Genebase Support, support.genebase.com/hc/en-us/articles/5604119595661-What-are-Y-DNA-STRs. Accessed 3 Feb. 2026.

Willuweit, Sascha, and Lutz Roewer. “Y Chromosome Haplotype Reference Database (YHRD): Update.” Forensic Science International: Genetics, vol. 1, no. 2, 2006, pp. 83–87.

“Y Chromosome.” MedlinePlus Genetics, National Library of Medicine, U.S. National Institutes of Health, 3 Feb. 2026, medlineplus.gov/genetics/chromosome/y/. Accessed 3 Feb. 2026.