title: Characterization of 114 insertion/deletion (INDEL) polymorphisms, and selection for a global INDEL panel for human identification.
abstract: Bi-Allelic Insertions and Deletions (INDELs) are a powerful set of genetic markers for Human Identification (HID). They have certain desirable features, such as low mutation rates, no stutter, and potentially small amplicon sizes that could prove effective in some circumstances. In this study, we analyzed the distribution of 114 INDELs in four North American populations (Caucasian, African American, Southwest Hispanic, and Asian) to estimate their distribution in major global populations. Of the 114 INDELs a primary panel of 38 candidate markers was selected that met the criteria of (1) a minimum allele frequency of greater than 0.20 across the populations studied; (2) general concordance with Hardy-Weinberg equilibrium (HWE) expectations; (3) relatively low FST based on the major populations; (4) physical distance between markers greater than 40 Mbp; and (5) a lack of linkage disequilibria between syntenic markers. Additionally, another 11 supplemental markers were selected for an expanded panel of 49 markers which met the above criteria, with the exception that they are separated at least by 20 Mbp. The resulting panels had Random Match Probabilities that were at least 10(-16) and 10(-19), respectively, and combined FST values of approximately 0.02. Given these findings, these INDELs should be useful for HID.
authors.affiliation: Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Forth Worth, Texas 76107, USA. Electronic address: Bobby.larue@unthsc.edu.
authors.forename: Bobby L
authors.initials: BL
authors.lastname: LaRue
authors.affiliation: Life Technologies, 850 Lincoln Centre Drive, Foster City, California 94404, USA. Electronic address: Robert.lagace@lifetech.com.
authors.forename: Robert
authors.initials: R
authors.lastname: Lagacé
authors.affiliation: Life Technologies, 850 Lincoln Centre Drive, Foster City, California 94404, USA. Electronic address: Chien-wei.chang@lifetech.com.
authors.forename: Chien-Wei
authors.initials: CW
authors.lastname: Chang
authors.affiliation: Life Technologies, 850 Lincoln Centre Drive, Foster City, California 94404, USA. Electronic address: Allison.holt@lifetech.com.
authors.forename: Allison
authors.initials: A
authors.lastname: Holt
authors.affiliation: Life Technologies, 850 Lincoln Centre Drive, Foster City, California 94404, USA. Electronic address: Lori.hennesy@lifetech.com.
authors.forename: Lori
authors.initials: L
authors.lastname: Hennessy
authors.affiliation: Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Forth Worth, Texas 76107, USA. Electronic address: Jianye.ge@unthsc.edu.
authors.forename: Jianye
authors.initials: J
authors.lastname: Ge
authors.affiliation: Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Forth Worth, Texas 76107, USA. Electronic address: Jonathan.king@unthsc.edu.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: King
authors.affiliation: Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Forth Worth, Texas 76107, USA. Electronic address: Ranajit.chakraborty@unthsc.edu.
authors.forename: Ranajit
authors.initials: R
authors.lastname: Chakraborty
authors.affiliation: Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Forth Worth, Texas 76107, USA; Center of Excellence in Genomic Medicine (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia. Electronic address: Bruce.budowle@unthsc.edu.
authors.forename: Bruce
authors.initials: B
authors.lastname: Budowle
mesh_terms: D044466:Asian People / Q000235:genetics; D005819:Genetic Markers; D005828:Genetics, Population; D060005:Genotyping Techniques; D006801:Humans; D054643:INDEL Mutation; D009656:North America; D011110:Polymorphism, Genetic / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers
keywords: Degraded DNA; Human genotyping; INDEL; Identity testing; Population genetics; SNP; STR