Paternity Index

In paternity testing, Paternity Index (PI) is a calculated value generated for a single genetic marker or locus (chromosomal location or site of DNA sequence of interest) and is associated with the statistical strength or weight of that locus in favor of or against parentage given the phenotypes of the tested participants and the inheritance scenario. Phenotype typically refers to physical characteristics such as body plan, color, behavior, etc. in organisms. However, the term used in the area of DNA paternity testing refers to what is observed directly in the laboratory. Laboratories involved in parentage testing and other fields of human identity employ genetic testing panels that contain a battery of loci (plural for locus) each of which is selected due to extensive allelic variations within and between populations. These genetic variations are not assumed to bestow physical and/or behavioral attributes to the person carrying the allelic arrangement(s) and therefore are not subject to selective pressure and follow Hardy Weinberg inheritance patterns.

The product of the individual PIs is the CPI (Combined Paternity Index) which is ultimately used to calculate the Probability of Paternity seen on paternity test reports. Minimum Probability of Paternity value requirements for state cases differ between states but the AABB requires in their Standards for Relationship Testing Laboratories (currently in the 9th edition)[1] a minimum of 99.0% be reported where the tested man is ‘not excluded’ as the biological father of the child in question. U.S. Department of State requires a minimum Probability of Paternity of 99.5% for all immigration cases.[2]

PI calculations utilize allele frequencies generated from established population databases[3] most commonly using Short Tandem Repeats.[3]

Because allele frequencies can be either generated in-house or published, PI’s can differ between companies. This is an understood phenomenon and justifiable amongst members of the testing community.

Calculations

The PI is a likelihood ratio[4] that is generated by comparing two probabilities where PI = X / Y:

  1. Numerator (“X”) – The probability that we observe the phenotypes of the tested participants in the inheritance scenario given that the tested man is the true biological father. More simply, the probability that some event will occur given a certain set of circumstances or conditions. This calculation assumes that the individuals tested are a “true trio/duo” (which is explained two paragraphs down) or in other words, the parent(s) tested are the true biological parents.
  2. Denominator (“Y”) – The probability that we observe the phenotypes of the tested participants in the inheritance scenario given that a random man is the true biological father. More simply, the probability that some event will occur given a different set of circumstances or conditions. This calculation assumes that the individuals tested are a “false trio/duo” or in other words, the parent(s) tested are not the true biological parents.

In general, X / Y can be translated as: It is X / Y times more likely to see the observed phenotypes if the tested man is the true biological father than if an untested, unrelated randomly selected man from the same racial population was the true biological father.

There are 14 possible trio paternity combinations and 5 possible duo paternity combinations.[5]

gollark: Repeaters? You use rednet? Why?
gollark: What?
gollark: Or store a list of valid keys/levels on pastebin, and have each door controller download those.
gollark: Or use my idea.
gollark: Or... you could have them communicate with a central thing over a **wired** network?

See also

References
  1. Guidance for Standards for Relationship Testing Laboratories (9th ed.). ISBN 978-1-56395-293-7.
  2. "DNA Relationship Testing Procedures". Bureau of Consular Affairs.
  3. Budowle, B; Shea, B; Niezgoda, S; Chakraborty, R (2001). "CODIS STR loci data from 41 sample populations". Journal of Forensic Sciences. 46 (3): 453–89. doi:10.1520/JFS14996J. PMID 11372982.
  4. Baur, MP; Elston, RC; Gürtler, H; Henningsen, K; Hummel, K; Matsumoto, H; Mayr, W; Moris, JW; et al. (1986). "No fallacies in the formulation of the paternity index". American Journal of Human Genetics. 39 (4): 528–36. PMC 1683973. PMID 3766545.
  5. http://dna-view.com/patform.htm

Further reading
  • Budowle, B; Monson, KL; Chakraborty, R (1996). "Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci". International Journal of Legal Medicine. 108 (4): 173–6. doi:10.1007/BF01369786. PMID 8652419.
  • Budowle, B; Sprecher, CJ (2001). "Concordance study on population database samples using the PowerPlex 16 kit and AmpFlSTR Profiler Plus kit and AmpFlSTR COfiler kit". Journal of Forensic Sciences. 46 (3): 637–41. doi:10.1520/JFS15016J. PMID 11373002.
  • Budowle, Bruce; Collins, Patrick J.; Dimsoski, Pero; Ganong, Constance K.; Hennessy, Lori K.; Leibelt, Craig S.; Rao-Coticone, Sulekha; Shadravan, Farideh; Reeder, Dennis J. (2001). "Population Data on the STR Loci D2S1338 and D19S433". Forensic Science Communications. 3 (3).
  • Levadokou, EN; Freeman, DA; Budzynski, MJ; Early, BE; McElfresh, KC; Schumm, JW; Amin, AS; Kim, YK; et al. (2001). "Allele frequencies for fourteen STR loci of the PowerPlex 1.1 and 2.1 multiplex systems and Penta D locus in Caucasians, African-Americans, Hispanics, and other populations of the United States of America and Brazil". Journal of Forensic Sciences. 46 (3): 736–61. PMID 11373021.
  • Butler, JM; Decker, AE; Vallone, PM; Kline, MC (2006). "Allele frequencies for 27 Y-STR loci with U.S. Caucasian, African American, and Hispanic samples". Forensic Science International. 156 (2–3): 250–60. doi:10.1016/j.forsciint.2005.02.011. PMID 16410169.
  • Butler, JM; Schoske, R; Vallone, PM; Redman, JW; Kline, MC (2003). "Allele frequencies for 15 autosomal STR loci on U.S. Caucasian, African American, and Hispanic populations". Journal of Forensic Sciences. 48 (4): 908–11. doi:10.1520/JFS2003045. PMID 12877323.
  • Vallone, PM; Decker, AE; Butler, JM (2005). "Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African-American, and Hispanic samples". Forensic Science International. 149 (2–3): 279–86. doi:10.1016/j.forsciint.2004.07.014. PMID 15749374.
  • Brenner CH (1999) Kinship Analysis by DNA When There Are Many Possibilities, Progress in Forensic Genetics 8, Eds G Sensabaugh et al. ISBN 978-0-444-50303-9
  • Que, TZ; Yan, PH; Lin, Y; Liu, Y; Li, L (2009). "The evaluation of Identifiler system in paternity testing". Fa Yi Xue Za Zhi. 25 (3): 184–6. PMID 19697775.
  • Thomson, JA; Pilotti, V; Stevens, P; Ayres, KL; Debenham, PG (1999). "Validation of short tandem repeat analysis for the investigation of cases of disputed paternity". Forensic Science International. 100 (1–2): 1–16. doi:10.1016/S0379-0738(98)00199-6. PMID 10356771.
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