Y chromosome analysis
Y chromosome analysis is a DNA analysis technique that focuses on the Y chromosome, which plays a crucial role in determining male sex in humans. This method is significant for various fields, including forensics, genealogy, archaeology, and anthropology, as it allows for the examination of genetic material, even from small or degraded samples. The Y chromosome, the smallest human chromosome, is roughly 50 million base pairs long and comprises about 2 percent of total DNA. Notably, it does not undergo genetic recombination in the majority of its length, which enables researchers to track specific genetic markers, such as short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), through generations.
These Y-STR markers are particularly valuable in forensic investigations, as they can extract male-specific information from mixed samples, like blood or saliva. They are also instrumental in paternity testing and tracing male lineage over time. While Y chromosome analysis has its advantages, such as the ability to analyze small DNA amounts using techniques like polymerase chain reaction (PCR), it also has limitations. For example, since paternal lineages share the same Y-STR haplotype unless mutations occur, distinguishing between close male relatives can be challenging. Overall, Y chromosome analysis serves as a powerful tool for understanding human genetics and history.
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Y chromosome analysis
DEFINITION: DNA 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—about fifty 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 (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, 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 three to five nucleotides long and are repeated a variable number of times (five to thirty 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 gel 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 sequences 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 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 paternity testing and in missing persons investigations. Further, the lack of recombination 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 have the same Y-STR haplotype, so fathers, sons, brothers, uncles, and paternal cousins cannot be distinguished from each other by Y-STR analysis.
Bibliography
Gusmão, Leonor, et al. “DNA Commission of the International Society of Forensic Genetics (ISFG): An Update of Recommendations on Use of Y-STRs in Forensic Analysis.” Forensic Science International 157 (2006): 187-197.
Hanson, Erin K., and Jack Ballantyne. “Comprehensive Annotated STR Physical Map of Human Y Chromosome: Forensic Implications.” Legal Medicine (Tokyo) 8 (March, 2006): 110-120.
Kobilinsky, Lawrence F., Louis Levine, and Henrietta Margolis-Nunno. Forensic DNA Analysis. New York: Chelsea House, 2007.
Rhie, Arang, et al. "The Complete Sequence of a Human Y Chromosome." Nature, vol. 621, 2023, pp. 344-354, doi.org/10.1038/s41586-023-06457-y. Accessed 19 Aug. 2024.
Willuweit, Sascha, and Lutz Roewer. “Y Chromosome Haplotype Reference Database (YHRD): Update.” Forensic Science International: Genetics 1, no. 2 (2006): 83-87.