Silent Witness - Volume 4, Number 3, 1999
Y Chromosome DNA Typing - A New Forensic Tool on the Horizon
by Kim Herd, Program Manager and Adrianne Day, Legal Intern, APRI's DNA Legal Assistance Unit
Introduction
Y chromosome DNA typing received international notice after an article published in Nature concluded that Thomas Jefferson fathered a child with Sally Hemings, one of his slaves [1] This controversial story was debated by Jeffersonian historians for years.[2] After the article's publication, a vigorous scientific debate ensued regarding the validity of its conclusions. Nature published a follow-up article which disputed these findings.[3] Other articles involving Y chromosome technology also recently suggested that modern man is traceable to a single African male who lived less than 200,000 years ago.[4]
In addition, the law enforcement community is beginning to use Y chromosome typing. Since October 1998, the Chief Medical Examiner's Office in New York City has performed Y chromosome testing on 143 forensic samples in 80 different cases.[5] Some of these results will soon be presented in court for the first time. Given its ability to assist in deciphering mixed evidence samples often found in sexual assault cases, prosecutors will find Y chromosome typing to be an exciting new forensic technology.
Y chromosome typing is also being used for forensic casework outside of the United States. Dr. Peter de Knijff of the Forensic Laboratory for DNA Research at The Netherlands' Leiden University, and a co-author of the first Nature article about Thomas Jefferson, has successfully used Y chromosome markers for identification cases. These were ultimately not heard in court. He also helped a Japanese professor solve a 20-year-old rape case using Y chromosome technology. Although few forensic laboratories are currently using this technology in their casework, inevitably, a commercial kit will be developed[6] and Y chromosome typing will take its place in the array of forensic tools. Before this happens, prosecutors should familiarize themselves with the basics of Y chromosome typing.
Y Chromosome Basics
DNA, the human genetic material, is a long sequence of four basic units that translate into approximately 100,000 genes. Some genes determine physical characteristics, while others determine such things as an individual's predisposition to develop certain diseases. In between these "functional" genes, are sequences of DNA that are not known to code for anything. These are referred to as "nonfunctional" genes or “non-coding” sequences. A massive effort is currently underway (known as the Human Genome Project) to locate all functional and nonfunctional genes and to place them on a genetic map. The position a gene occupies on this map is called a locus (“loci” for plural).
The genes and non-functional sequences that comprise DNA are packaged on chromosomes. The nuclei of most human cells contain forty six chromosomes organized into twenty-three pairs. During fertilization, one half of the pair is contributed by the mother and the other half by the father. The mother's egg and the father's sperm each contain twenty-two chromosomes called "autosomes," carrying a broad range of genetic information. The additional chromosome in the egg and sperm are the sex chromosomes, which contain genes that code for sex determination. The egg always contains an "X", but the sperm can contain either an "X" or a "Y".[7] An XX combination will produce a female and an XY combination will produce a male. Therefore, the father's contribution always decides the sex of the child. So far, genetic research has determined that much of the DNA on the Y chromosome codes for testes differentiation and sperm formation.
The Y chromosome is unique for several reasons. First, since it determines the sex of the child, the Y chromosome is passed only from fathers to sons. Second, unlike the X chromosome and the autosomes, most of the information on the Y chromosome is not exchanged during cell division. Consequently, the Y chromosome generally retains its genetic makeup.[8] As a result of these two factors, when a father passes a Y chromosome to his son, it is virtually identical to his own. Then, when the son has a male child, he passes that same Y chromosome to his own son. Furthermore, when a father passes a Y chromosome to multiple sons, each son will share a Y chromosome virtually identical to their father’s. As long as the biological parentage is not in question, grandfathers, fathers, sons, brothers, and uncles will have virtually identical Y chromosomes. This enables scientists to trace a Y chromosome backwards through the male ancestral lineage. In addition to its intergenerational consistency, the Y chromosome has unique structural properties. It is notably smaller and shaped differently than the X chromosome. Some scientists consider the Y chromosome to be a former X chromosome that developed separately, with its own unique properties.[9]
Like the X chromosome, the Y chromosome contains short tandem repeats (STRs) and other variable genetic sites (known as polymorphisms) used for DNA typing. STRs are repeating blocks of a certain sequence of two to five base pairs that are differentiated by the number of repetitions. STRs interspersed throughout most chromosomes in immense numbers. Many forensic laboratories are currently using STRs located on autosomal chromosomes for forensic casework. Y chromosome STRs can be typed in the same manner as autosomal STRs with a few minor differences.
Forensic Applications of Y Chromosome Technology
Dr. Mechthild Prinz, Ph.D. of the New York City Chief Medical Examiner's Office performed a two-year study on Y chromosome typing of semen and other biological evidence pursuant to TWGDAM recommendations in order to determine the validity of this technology for forensic casework.[10] Dr. Prinz and others feel the true potential for Y chromosome typing is in deciphering “mixtures” in rape cases. Mixtures are evidence samples containing a combination of female and male DNA, or DNA from multiple donors. The current method for separating mixtures -- differential lysis -- endeavors to remove the female cells from the mixture, leaving only the sperm portion to be typed. For various reasons, however, differential lysis is not always successful in separating the cells. Dr. Prinz suggests that differential lysis may be inhibited when samples have insufficient sperm DNA, or when a small sperm fraction is overpowered by a large female DNA background. With small or degraded samples, differential lysis can inadvertently result in a loss of sperm DNA. Furthermore, mixtures of autosomal cells, such as victim/suspect blood or saliva, can not be differentiated at all because they contain the same types of cells. Therefore, the technician is left with the often difficult task of subtracting the victim's type from the mixture's type to see if the suspect's type remains.
Y chromosome testing significantly increases the likelihood of obtaining a perpetrator’s profile from male/female mixtures because Y chromosome "primers" (chemical agents that recognize pre-designated sequences of DNA) do not amplify X chromosome or autosome DNA sequences. Therefore, in a rape situation where a vaginal swab contains the victim's cells and the rapist's sperm (or epithelial cells), Y chromosome testing can sift through all the female DNA to locate the male DNA, and could thus include a suspect as a possible contributor. In certain instances, Y chromosome testing can sometimes detect the DNA type of different male contributors to a mixture.
Presently, Dr. Prinz is using four Y STR loci with a discrimination rate of 46-54%, and is planning validation studies for four new loci that would bring the overall discrimination rate up to an estimated 91-97%. Dr. John Hartmann of the Orange County, CA Sheriff-Coroner's Department is also in the process of validating Y STRs for forensic casework. Dr. Hartmann also believes that this technology will be focused on female/male mixtures, perhaps in mass screening of rape kits. In addition, Dr. Hartmann envisions that Y chromosome testing will eventually combine more Y STRs and new, highly promising DNA typing methodologies currently being developed.[11] With the inclusion of these additional loci, Dr. Hartmann envisions highly discriminating results from Y chromosome testing.
Conclusion
Regardless of the exact form Y chromosome typing takes, it is certain to make a pronounced appearance in American courtrooms in the near future. Like PCR technology in the mid-90s, the use of Y chromosome typing will likely increase until it is a mainstay of forensic evidence. Prosecutors can avoid the rush to learn later by building a solid base of understanding today.
Michigan Murder Case Illustrates the Durability of DNA
By Assistant Prosecuting Attorney David Wallace, Calhoun County, MI
A 1996 murder case in Michigan illustrates how DNA technology, specifically PCR typing, can prevail over the physical elements of nature and help solve crimes.
Robert Rogers, an 80 year-old Michigan man, was found murdered at his home on April 26, 1996. An autopsy revealed that Rogers died after being repeatedly struck in the head with a blunt instrument. On May 13, 1996, police divers located a section of pipe submerged in a pond behind the victim’s house. Testing by the Michigan State Police Crime Laboratory confirmed the presence of human blood on the pipe. The blood from the pipe and a sample of the victim’s blood were sent to LabCorp for DNA testing. Using PCR typing techniques, LabCorp analyzed the two samples at ten genetic markers and declared a match. The statistics for the Caucasian population were one in 1,450,000,000 that a randomly selected, unrelated individual would match the DNA found on the pipe. The match of the victim’s blood to the blood on the pipe helped prove that the pipe was the murder weapon. Based on this and other evidence, Sharon Zachary, the victim’s neighbor and care giver was convicted of armed robbery and first degree murder.
The pipe was likely underwater for seventeen days from the day of the murder to the day it was discovered. Despite the passage of so many days, usable DNA evidence was located on the pipe and proved to be a crucial piece of evidence.
See Eugene A. Foster, et al., Jefferson Fathered Slave's Last Child, 396 Nature 27 (1998); Eric S. Lander & Joseph J. Ellis, Founding Father, 396 Nature 13 (1998).
See The Hemings-Jefferson Controversy: A Brief Account <<http://www.monticello.org/Matters/people/hemings-jefferson_contro.html>> (last modified Nov. 2, 1998).
See David M. Abbey, The Thomas Jefferson Paternity Case, 397 Nature 32 (1998); Gary Davis, The Thomas Jefferson Paternity Case, 397 Nature 32 (1998); Eugene A. Foster, et al., The Thomas Jefferson Paternity Case, 397 Nature 32 (1998).
See Steve Sternberg, Modern Man Traced to Mutant DNA << http://www.detnews.com/1997/discover/9711/ 11/11100031.htm>> (last updated Nov. 10, 1997); Deborah M. Ketterer, M.S., Why, Oh Why Study the Y? The Origin of Man (as opposed to Woman) <<http:// www.asri.edu/genetics/brochure/agh/news/jan96/y.html>>.
See Mechthild Prinz, et al., Validation and Casework Application of a Y Chromosome Specific STR Multiplex at 11 (submitted).
Interview, Dr. John Hartmann, Orange County Sheriff-Coroner Department, Santa Ana, California (Jan. 9, 1999); Interview, Dr. Mechthild Prinz, Ph.D., Chief Medical Examiner's Office, New York, NY, (Jan. 16, 1999).
There are exceptions to this general rule such as additional or missing sex chromosomes that impact appearance and fertility.
Changes can occur through gradual mutations.
See UNSW Embryology: Sex Determination Molecular Development <<http://anatomy.med.unsw.edu.au/cbl/ embryo/MolDev/Sex.htm>>.
Technical Working Group on DNA Analysis Methods - a group of forensic scientists that recommends standards for forensic DNA testing.
Such as SNPs or Single Nucleotide Repeats.
|
