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A new forensics technique called proteomics analyzes proteins to infer DNA sequences.

DNA evidence has revolutionized forensic science in the past few years, cracking open cold cases and bringing both convictions and exonerations. The same techniques help archaeologists and anthropologists studying remains from ancient peoples or human ancestors.

But DNA is a relatively fragile molecule that breaks down easily. That’s where proteomics comes in. By reading the sequence of amino acids from fragments of protein, scientists can work backwards to infer the sequence of DNA that produced the protein.

“It’s reading DNA when you don’t have any DNA to read,” says Glendon Parker, adjunct associate professor in the department of environmental toxicology and graduate group in forensic science at the University of California, Davis. “Protein is much more stable than DNA, and protein detection technology is much better now.”

Proteomics technology could be useful when samples are old or degraded, and to back up results from DNA analysis, Parker says. Like genomics—the study of entire genomes and large amounts of DNA—it’s a new field that rapid advances in protein sequencing technology and computing make possible.

How proteomics works

Proteins are made up of chains of units called amino acids. There are 20 naturally occurring amino acids that are encoded by DNA. A three-letter sequence of DNA corresponds to a specific amino acid, so reading the sequence of DNA can give you the amino acid sequence of the corresponding protein. The DNA sequence can also be deduced by reading the amino acid sequence and comparing it against databases of known proteins and genes.

The instruments like those at the UC Davis Proteomics Core Facility can work with vanishingly small amounts of protein, as little as 50 nanograms. An inch of human hair contains 100 micrograms of protein.

Hair is often found at crime scenes. Hair has very little DNA, but more than enough protein (mostly keratin) for analysis. By looking at variant amino acids in keratin, researchers can identify single-nucleotide polymorphisms, or SNPs, in the underlying DNA. That information can be used for both personal identification and to get information on ancestry.

Hairs vary somewhat depending on where on the body they come from, but a recent paper led by graduate student Zachary Goecker from Parker’s team shows that the differences between scalp, beard, armpit, and pubic hair are not great enough to affect identification. Changes such as graying, dyeing, and peroxide treatments had no effect on the identifying information from peptides, Parker says. The study appeared in March in Forensic Science International: Genetics.

One tooth can reveal a person’s sex

For anthropologists, bones and teeth are a window to people of the past, but DNA may be in a very poor state. Working with anthropology professor Jelmer Eerkens, graduate student Julia Yip of Parker’s laboratory developed a method to determine the biological sex of an individual based on a single tooth.

That’s possible because teeth contain a protein called amelogenin, which happens to be located on the X and Y chromosomes that determine biological sex. If a tooth has amelogenin-Y, then it must have come from an individual with XY chromosomes and therefore most likely a biological male.

In side-by-side tests, the tooth protein analysis was more sensitive and reliable for sex determination than either DNA or looking at the anatomy of skeletons. The work appeared last year in the Journal of Archaeological Science and continues.

In a paper published in May 2019 in Forensic Science International: Genetics, the team has also shown that it is possible to get enough protein for personal identification from a fingermark. The issue is in finding and collecting the sample rather than the sensitivity of the machine, Parker says.

Closed cases

Parker hopes that forensic proteomics can move out of the laboratory and into some real-world cases. The technique needs to be thoroughly validated before going into wide use, Parker says, but he expects those “boxes to be checked” within about a year. One possible starting point would be working on “cold case” sexual assault kits that are also being tested for DNA and other evidence.

“We’re trying to get the interest of the forensics community in getting us involved in some of these cases,” Parker says.

Support for parts of the work have come from the National Institute of Justice, the National Institutes of Health, and the National Science Foundation.

Source: UC Davis