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A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR

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Abstract

Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility of being analysed using short amplicon strategies, which increases the ease of analysis, contributing to justify their interest in population and forensic genetics. After the advent of autosomal and uniparental genomes (mtDNA and Y chromosome), these fields of research are also focusing on the X chromosome, given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian population samples and revealed high forensic efficiency, as measured by the accumulated power of discrimination (0.9999990 was the lowest value in males and 0.999999999998 was the highest in females) and mean exclusion chance varied between 0.998 and 0.9996 in duos and between 0.99997 and 0.999998 in trios. Finally, a segregation analysis was performed using trio constellations of father–mother–daughters in order to address the transmission pattern and assess mutation rates of this type of markers.

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Acknowledgements

This work was partially supported through PhD grants to R.P. (SFRH/BD/30039/2006) and V.P. (SFRH/BD/70881/2010) awarded by the Portuguese Foundation for Science and Technology (FCT) and co-financed by the European Social Fund (Human Potential Thematic Operational Programme). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by FCT. The assistance of Fundación Botín is also acknowledged with appreciation.

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Author notes

  1. Iva Gomes

    Present address: Institute of Legal Medicine, University Hospital, University of Cologne, Cologne, Germany

Authors and Affiliations

  1. IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal

    Rui Pereira, Vânia Pereira, Iva Gomes, António Amorim, Maria João Prata & Leonor Gusmão

  2. Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain

    Rui Pereira & Ángel Carracedo

  3. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark

    Vânia Pereira, Carmen Tomas & Niels Morling

  4. Faculty of Sciences of the University of Porto, Porto, Portugal

    Vânia Pereira, António Amorim & Maria João Prata

  5. Genomic Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain

    Ángel Carracedo

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  1. Rui Pereira
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Correspondence to Leonor Gusmão.

Electronic supplementary material

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Table SM1

Haplotype frequencies for MID357-MID356 and MID3690-MID3719-MID2089 (PDF 60 kb)

Table SM2

Statistical parameters indicative of forensic efficiency obtained for the 32 X-Indel set: Power of Discrimination (PD) and Mean Exclusion Chance (MEC) (PDF 107 kb)

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Pereira, R., Pereira, V., Gomes, I. et al. A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR. Int J Legal Med 126, 97–105 (2012). https://doi.org/10.1007/s00414-011-0593-2

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  • DOI: https://doi.org/10.1007/s00414-011-0593-2

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