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DNA phenotyping

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Not to be confused with DNA profiling.
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DNA phenotyping (fee-no-type-ing) is the process of predicting an organism’s phenotype using only genetic information collected from genotyping or DNA sequencing. This term, also known as molecular photofitting, is primarily used to refer to the prediction of a person’s physical appearance and/or biogeographic ancestry for forensic purposes.

DNA phenotyping uses many of the same scientific methods as those being used for genetically-informed personalized medicine, in which drug responsiveness (pharmacogenomics) and medical outcomes are predicted from a patient’s genetic information. Significant genetic variants associated with a particular trait are discovered using a genome-wide association study (GWAS) approach, in which hundreds of thousands or millions of single-nucleotide polymorphisms (SNPs) are tested for their association with each trait of interest. Predictive modeling is then used to build a mathematical model for making trait predictions about new subjects.

Predicted phenotypes

Biogeographic ancestry determination methods have been highly developed within the genetics community, as it is a key GWAS quality control step.[1] These approaches typically use genome-wide human genetic clustering and/or principal component analysis to compare new subjects to curated individuals with known ancestry, such as the International HapMap Project or the 1000 Genomes Project. Another approach is to assay ancestry informative markers (AIMs), SNPs that vary in frequency between the major human populations.[2]

Beginning in 2009, academic groups developed and reported on predictive models for eye color and, more recently, hair color in the European population.[3] More recently, companies such as Parabon NanoLabs and Identitas have begun offering forensic DNA phenotyping services for U.S. and international law enforcement.

Differences between DNA profiling and DNA phenotyping

Traditional DNA profiling, sometimes referred to as DNA fingerprinting, uses DNA as a biometric identifier. Like an iris scan or fingerprint, a DNA profile can uniquely identify an individual with very high accuracy. For forensic purposes, this means that investigators must have already identified and obtained DNA from a potentially matching individual. DNA phenotyping is used when investigators need to narrow the pool of possible individuals or identify unknown remains by learning about the person’s ancestry and appearance. When the suspected individual is identified, traditional DNA profiling can be used to prove a match, provided there is a reference sample that can be used for comparison.

An early and successful use of forensic DNA phenotyping - the Baton Rouge serial killer

From the late 1990s to the early 2000s, a series of murders were committed in Louisiana. Eyewitness statements and FBI profiling indicated the perpetrator was likely a Caucasian male. After investigators tested DNA samples from thousands of Caucasian males and found no matches with DNA from the crime scenes, DNA phenotyping was performed on a crime scene DNA sample by DNAPrint Genomics. This testing indicated the ancestry of the suspect was 85% sub-Saharan African and 15% Caucasian, pointing to an African-American individual and changing the direction of the investigation. Within two months, police arrested Derrick Todd Lee, who was later convicted for two of these murders.

Published DNA phenotyping composites

  • On 9 January 2015, the fourth anniversary of the murders of Candra Alston and her three-year-old daughter Malaysia Boykin, police in Columbia, South Carolina, issued a press release containing what is thought to be the first composite image in forensic history to be published entirely on the basis of a DNA sample.[4][5] The image, produced by Parabon NanoLabs with the company's Snapshot DNA Phenotyping System, consists of a digital mesh of predicted face morphology overlaid with textures representing predicted eye color, hair color and skin color.
  • On 30 June 2015, NBC Nightly News featured a DNA phenotyping composite, also produced by Parabon, of a suspect in the 1988 murder of April Tinsley near Fort Wayne, Indiana.[6] The television segment also included a composite of national news correspondent Kate Snow, which was produced using DNA extracted from the rim of a water bottle that the network submitted to Parabon for a blinded test of the company’s Snapshot™ DNA Phenotyping Service. Snow’s identity and her use of the bottle were revealed only after the composite had been produced.
  • Sheriff Tony Mancuso of the Calcasieu Parish Sheriff's Office in Lake Charles, Louisiana, held a press conference on 1 September 2015 to announce the release of a Parabon Snapshot composite for a suspect in the 2009 murder of Sierra Bouzigard in Moss Bluff, Louisiana.[7] The investigation had previously focused on a group of Hispanic males with whom Bouzigard was last seen. Snapshot analysis indicates the suspect is predominantly European, with fair skin, green or possibly blue eyes and brown or black hair. Sheriff Mancuso told the media, “This totally redirects our whole investigation and will move this case in a new direction.”[8]
  • Florida police chiefs from Miami Beach, Miami, Coral Gables and Miami-Dade jointly released a Snapshot composite of the “Serial Creeper” on 10 September 2015.[9] For more than a year, the perpetrator has been spying on and sexually terrorizing women, and police believe he is connected to at least 15 crimes, possibly as many as 40. In a Miami Beach attack on 18 August 2015, which was first reported to the public on 23 September 2015, the perpetrator spoke in Spanish and told his victim he was from Cuba.[10] Consistent with this claim, Snapshot had previously determined that the subject is Latino, with European, Native American, and African ancestry, an admixture most similar to that found in Latino individuals from the Caribbean and Northern South America.
  • On 2 February 2016, the Anne Arundel County Maryland Police Department released what is believed to be the first published composite created by combining DNA phenotyping and forensic facial reconstruction from a victim’s skull.[11] The victim’s body was found on 23 April 1985 in a metal trash container at the construction site of the Marley Station Mall in Glen Burnie, MD. Police estimate the homicide occurred approximately five months before the body was discovered. Thom Shaw, an IAI-certified forensic artist at Parabon NanoLabs, performed the physical facial reconstruction and the digital adaptation of a Snapshot composite to reflect details gleaned from the victim’s facial morphology.
  • Police in Tacoma, Washington, disclosed Parabon Snapshot reports to the public on 6 April 2016 for two male suspects believed to be individually responsible for the deaths of Michella Welch (age 12) and Jennifer Bastian (age 13), both abducted from Tacoma’s North End area in 1986, just four months apart.[12] Investigators long believed one person committed both crimes because of their many similarities; however, recent DNA testing proved two individuals were separately involved, one in each case. Snapshot descriptions of the two killers were released to aid the public in generating new leads for the investigations.
  • Also on 6 April 2016, police in Athens Ohio released a Snapshot composite of an active sexual predator linked to at least three attacks, the most recent in December 2015 near Ohio University.[13]
  • On 15 April 2016, the Hallandale Beach Florida Police Department released a Snapshot composite of a suspect believed to be responsible for the murders of Toronto residents David “Donny” Pichosky and Rochelle Wise. It was the first time a Snapshot composite of a female was released to the public.[14]
  • On 21 April 2016, police in Windsor, Canada, released a Snapshot composite of the suspect responsible for the abduction and murder of Ljubica Topic in 1971.[15] It was the first public release of a Snapshot composite outside of the United States and, at the time, the oldest case to which the technology had been applied.
  • On 11 May, the Loudoun County Sheriff’s Office in Virginia released a Snapshot composite of a suspect responsible for abducting and sexually assaulting a 9-year-old girl in 1987.[16]
  • On 16 May 2016, eve of the third anniversary of veteran John “Jack” Fay’s murder, the Warwick Rhode Island Police Department released a Snapshot composite produced using DNA taken from a hammer found near the crime scene.[17] Police hope the composite will generate fresh leads in a case that may involve multiple assailants.

See also

References

  1. ^ Tian, C.; Gregersen, P. K.; Seldin, M. F. (208). "Accounting for ancestry: population substructure and genome-wide association studies". Human Molecular Genetics. 17 (R2): R143-50. doi:10.1093/hmg/ddn268.
  2. ^ Shriver, M. D.; Smith, M. W.; Jin, L.; Marcini, A.; Akey, J. M.; Deka, R.; Ferrell, R. E. (1997). "Ethnic-affiliation estimation by use of population-specific DNA markers". American Journal of Human Genetics. 60: 957–964. PMID 9106543. {{cite journal}}: Unknown parameter |last-author-amp= ignored (|name-list-style= suggested) (help)
  3. ^ Liu, F.; van Duijn, K.; Vingerling, J. R.; Hofman, A.; Uitterlinden, A. G.; Janssens, A. C. J. W.; Kayser, M. (2009). "Eye color and the prediction of complex phenotypes from genotypes". Current Biology. 19 (5): R192-3. doi:10.1016/j.cub.2009.01.027. PMID 19278628.
  4. ^ Allocca, Sean (15 January 2015). "First DNA-Phenotyped Image of 'Person of Interest' in Double Homicide". Forensic Magazine.
  5. ^ Cookson, Clive (30 January 2015). "DNA: the next frontier in forensics". Financial Times.
  6. ^ Snow, Kate (30 June 2015). "Putting a Face to DNA: How New Tech Gives Hope in Cold Cases". NBC Nightly News.
  7. ^ Manning, Johnathan (1 September 2015). "CPSO releases sketch based on DNA sample from cold-case murder". KPLC News.
  8. ^ Full article on this in National Geographic, July 2016, page 34.
  9. ^ DeFede, Jim (10 September 2015). "Revolutionary DNA Tech Used to Create 'Serial Creeper' Sketch". CBS Miami.
  10. ^ Rabin, Charles (23 September 2015). "DNA links 'The Creeper' to sex attack on Miami Beach". Miami Herald.
  11. ^ Dacey, Kim (3 February 2016). "Police hope composite image can help close cold case". WBAL.
  12. ^ Glenn, Stacia (6 April 2016). "Tacoma police release composite images of suspects in 1986 slayings". Tacoma News Tribune.
  13. ^ DeWitt, David (6 April 2016). "Police sharpen image of uptown Athens serial rapist, ask public for help identifying". The Athens News.
  14. ^ Robinson, Michael (15 April 2016). "New DNA technique could lead to a break in snowbird murder case". The Star.
  15. ^ Bezaire, Christie (21 April 2016). "Windsor police hope DNA composite profile will help solve 45-year-old murder". CTV News Windsor.
  16. ^ Culver, David (11 May 2016). "Loudoun County Turns to Composite Image Based on DNA to Crack Cold Case". NBC4 News Washington.
  17. ^ Towne, Shaun (16 May 2016). "Police release composite of suspect in unsolved Warwick murder". WPRI 12 News.
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