title: Completion of a worldwide reference panel of samples for an ancestry informative Indel assay.
abstract: The use of ancestry informative markers (AIMs) in forensic analysis is of considerable utility since ancestry inference can progress an investigation when no identification has been made of DNA from the crime-scene. Short-amplicon markers, including insertion deletion polymorphisms, are particularly useful in forensic analysis due to their mutational stability, capacity to amplify degraded samples and straightforward amplification technique. In this study we report the completion of H952 HGDP-CEPH panel genotyping with a set of 46 AIM-Indels. The study adds Central South Asian and Middle Eastern population data, allowing a comparison of patterns of variation in Eurasia for these markers, in order to enhance their use in forensic analyses, particularly when combined with sets of ancestry informative SNPs. Ancestry analysis using principal component analysis and Bayesian methods indicates that a proportion of classification error occurs with European-Middle East population comparisons, but the 46 AIM-Indels have the capability to differentiate six major population groups when European-Central South Asian comparisons are made. These findings have relevance for forensic ancestry analyses in countries where South Asians form much of the demographic profile, including the UK, USA and South Africa. A novel third allele detected in MID-548 was characterized - despite a low frequency in the HGDP-CEPH panel samples, it appears confined to Central South Asian populations, increasing the ability to differentiate this population group. The H952 data set was implemented in a new open access SPSmart frequency browser - forInDel: Forensic Indel browser.
authors.affiliation: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain. Electronic address: carla.arcanjo.santos@gmail.com.
authors.forename: Carla
authors.initials: C
authors.lastname: Santos
authors.affiliation: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.
authors.forename: Christopher
authors.initials: C
authors.lastname: Phillips
authors.affiliation: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.
authors.forename: Fabio
authors.initials: F
authors.lastname: Oldoni
authors.affiliation: Galician Foundation of Genomic Medicine (SERGAS), CIBERER (University of Santiago de Compostela), Sanatiago de Compostela, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Amigo
authors.affiliation: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Fondevila
authors.affiliation: IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
authors.forename: Rui
authors.initials: R
authors.lastname: Pereira
authors.affiliation: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain; Galician Foundation of Genomic Medicine (SERGAS), CIBERER (University of Santiago de Compostela), Sanatiago de Compostela, Spain.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Carracedo
authors.affiliation: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.
authors.forename: Maria Victoria
authors.initials: MV
authors.lastname: Lareu
mesh_terms: D000483:Alleles; D030541:Databases, Genetic / Q000592:standards; D066264:Datasets as Topic / Q000592:standards; D005006:Ethnicity / Q000235:genetics; D053803:Forensic Genetics / Q000379:methods* / Q000592:standards; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods* / Q000592:standards; D060005:Genotyping Techniques / Q000379:methods / Q000592:standards; D006801:Humans; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction; D044469:Racial Groups / Q000235:genetics; D012016:Reference Values
keywords: AIM-Indels; Central South Asia; HGDP–CEPH; Middle East