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Published in: International Journal of Legal Medicine 3/2017

01-05-2017 | Population Data

Study of InDel genetic markers with forensic and ancestry informative interest in PALOP’s immigrant populations in Lisboa

Authors: Ana Inácio, Heloísa Afonso Costa, Cláudia Vieira da Silva, Teresa Ribeiro, Maria João Porto, Jorge Costa Santos, Gilberto Igrejas, António Amorim

Published in: International Journal of Legal Medicine | Issue 3/2017

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Abstract

The migratory phenomenon in Portugal has become one of the main factors for the genetic variability. In the last few years, a new class of autosomal insertion/deletion markers—InDel—has attracted interest in forensic genetics. Since there is no data for InDel markers of Portuguese-speaking African countries (PALOP) immigrants living in Lisboa, our aim is the characterization of those groups of individuals by typing them with at least 30 InDel markers and to compare different groups of individuals/populations. We studied 454 bloodstain samples belonging to immigrant individuals from Angola, Guinea-Bissau, and Mozambique. DNA extraction was performed with the Chelex® 100 method. After extraction, all samples were typed with the Investigator® DIPplex method. Through the obtained results, allelic frequencies show that all markers are at Hardy-Weinberg equilibrium, and we can confirm that those populations show significant genetic distances between themselves, between them, and the host Lisboa population. Because of this, they introduce genetic variability in Lisboa population.
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Literature
1.
go back to reference Morais P, Amorim A, Vieira da Silva C, Ribeiro T, Costa Santos J, Afonso Costa H (2015) Genetic portrait of Lisboa immigrant population from Cabo Verde with mitochondrial DNA analysis. J Genet 94(3):509–512CrossRefPubMed Morais P, Amorim A, Vieira da Silva C, Ribeiro T, Costa Santos J, Afonso Costa H (2015) Genetic portrait of Lisboa immigrant population from Cabo Verde with mitochondrial DNA analysis. J Genet 94(3):509–512CrossRefPubMed
3.
go back to reference Afonso Costa H, Morais P, Vieira da Silva C, Matos S, Marques Santos R, Espinheira R, Costa Santos J, Amorim A (2014) X-Chromosome STR markers data in a Cabo Verde immigrant population of Lisboa. Mol Biol Rep 41:2559–2569. doi:10.1007/s11033-014-3114-9 CrossRefPubMed Afonso Costa H, Morais P, Vieira da Silva C, Matos S, Marques Santos R, Espinheira R, Costa Santos J, Amorim A (2014) X-Chromosome STR markers data in a Cabo Verde immigrant population of Lisboa. Mol Biol Rep 41:2559–2569. doi:10.​1007/​s11033-014-3114-9 CrossRefPubMed
4.
go back to reference Marques dos Santos R, Vieira da Silva C, Afonso Costa H, Ferreira Gomes P, Sanches S, Espinheira R, Costa Santos J, Amorim A (2012) Genetic portrait of an immigrant population from Angola living in Lisboa. Forensic Sci Int Genet 6:170–173. doi:10.1016/j.fsigen.2012.05.010 CrossRef Marques dos Santos R, Vieira da Silva C, Afonso Costa H, Ferreira Gomes P, Sanches S, Espinheira R, Costa Santos J, Amorim A (2012) Genetic portrait of an immigrant population from Angola living in Lisboa. Forensic Sci Int Genet 6:170–173. doi:10.​1016/​j.​fsigen.​2012.​05.​010 CrossRef
5.
go back to reference Amorim A, Marques dos Santos R, Vieira da Silva C, Afonso Costa H, Espinheira R, Ferreira Gomes P, Costa Santos J (2012) Genetic portrait of a native population of Cabo Verde living in Lisboa. Forensic Sci Int Genet 6:166–169. doi:10.1016/j.fsigen.2012.05.006 CrossRef Amorim A, Marques dos Santos R, Vieira da Silva C, Afonso Costa H, Espinheira R, Ferreira Gomes P, Costa Santos J (2012) Genetic portrait of a native population of Cabo Verde living in Lisboa. Forensic Sci Int Genet 6:166–169. doi:10.​1016/​j.​fsigen.​2012.​05.​006 CrossRef
7.
go back to reference Amorim A, Vieira da Silva C, Afonso Costa H, Sanches S, Espinheira R, Costa Santos J (2011) Allele frequencies of all CODIS and four non-CODIS STR loci of an immigrant Brazilian population living in Lisbon—preliminary results. Forensic Sci Int Genet Suppl Ser 3:127–128. doi:10.1016/j.fsigss.2011.08.063 CrossRef Amorim A, Vieira da Silva C, Afonso Costa H, Sanches S, Espinheira R, Costa Santos J (2011) Allele frequencies of all CODIS and four non-CODIS STR loci of an immigrant Brazilian population living in Lisbon—preliminary results. Forensic Sci Int Genet Suppl Ser 3:127–128. doi:10.​1016/​j.​fsigss.​2011.​08.​063 CrossRef
9.
go back to reference Meng H-T, Zhang Y-D, Shen C-M, Yuan G-L, Yang C-H, Jin R, Yan J-W, Wang H-D, Liu W-J, Jing H, Zhu B-F (2015) Genetic polymorphism analyses of 30 InDels in Chinese Xibe ethnic group and its population genetic differentiations with other groups. Sci Rep 5:8260. doi:10.1038/srep08260 CrossRefPubMedPubMedCentral Meng H-T, Zhang Y-D, Shen C-M, Yuan G-L, Yang C-H, Jin R, Yan J-W, Wang H-D, Liu W-J, Jing H, Zhu B-F (2015) Genetic polymorphism analyses of 30 InDels in Chinese Xibe ethnic group and its population genetic differentiations with other groups. Sci Rep 5:8260. doi:10.​1038/​srep08260 CrossRefPubMedPubMedCentral
10.
go back to reference LaRue BL, Lagacé R, Chang CW, Holt A, Hennessy L, Ge J, King JL, Chakraborty R, Budowle B (2014) Characterization of 114 insertion/deletion (INDEL) polymorphisms, and selection for a global INDEL panel for human identification. Leg Med 16:26–32. doi:10.1016/j.legalmed.2013.10.006 CrossRef LaRue BL, Lagacé R, Chang CW, Holt A, Hennessy L, Ge J, King JL, Chakraborty R, Budowle B (2014) Characterization of 114 insertion/deletion (INDEL) polymorphisms, and selection for a global INDEL panel for human identification. Leg Med 16:26–32. doi:10.​1016/​j.​legalmed.​2013.​10.​006 CrossRef
11.
go back to reference Zidkova A, Horinek A, Kebrdlova V, Korabecna M (2013) Application of the new insertion-deletion polymorphism kit for forensic identification and parentage testing on the Czech population. Int J Legal Med 127:7–10. doi:10.1007/s00414-011-0649-3 CrossRefPubMed Zidkova A, Horinek A, Kebrdlova V, Korabecna M (2013) Application of the new insertion-deletion polymorphism kit for forensic identification and parentage testing on the Czech population. Int J Legal Med 127:7–10. doi:10.​1007/​s00414-011-0649-3 CrossRefPubMed
13.
go back to reference Pereira R, Phillips C, Pinto N, Santos C, dos Santos SEB, Amorim A, Carracedo Á, Gusmão L (2012) Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One 7:1–10. doi:10.1371/journal.pone.0029684 CrossRef Pereira R, Phillips C, Pinto N, Santos C, dos Santos SEB, Amorim A, Carracedo Á, Gusmão L (2012) Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One 7:1–10. doi:10.​1371/​journal.​pone.​0029684 CrossRef
16.
go back to reference Ferreira Palha TDJB, Ribeiro Rodrigues EM, Cavalcante GC, Marrero A, de Souza IR, Seki Uehara CJ, Silveira da Motta CHA, Koshikene D, da Silva DA, de Carvalho EF, Chemale G, Freitas JM, Alexandre L, Paranaiba RTF, Soler MP, Santos S (2015) Population genetic analysis of insertion–deletion polymorphisms in a Brazilian population using the Investigator DIPplex kit. Forensic Sci Int Genet 19:10–14. doi:10.1016/j.fsigen.2015.03.015 CrossRef Ferreira Palha TDJB, Ribeiro Rodrigues EM, Cavalcante GC, Marrero A, de Souza IR, Seki Uehara CJ, Silveira da Motta CHA, Koshikene D, da Silva DA, de Carvalho EF, Chemale G, Freitas JM, Alexandre L, Paranaiba RTF, Soler MP, Santos S (2015) Population genetic analysis of insertion–deletion polymorphisms in a Brazilian population using the Investigator DIPplex kit. Forensic Sci Int Genet 19:10–14. doi:10.​1016/​j.​fsigen.​2015.​03.​015 CrossRef
22.
go back to reference Friis SL, Børsting C, Rockenbauer E, Poulsen L, Fredslund SF, Tomas C, Morling N (2012) Typing of 30 insertion/deletions in Danes using the first commercial indel kit - Mentype® DIPplex. Forensic Sci Int Genet 6:72–74. doi:10.1016/j.fsigen.2011.08.002 CrossRef Friis SL, Børsting C, Rockenbauer E, Poulsen L, Fredslund SF, Tomas C, Morling N (2012) Typing of 30 insertion/deletions in Danes using the first commercial indel kit - Mentype® DIPplex. Forensic Sci Int Genet 6:72–74. doi:10.​1016/​j.​fsigen.​2011.​08.​002 CrossRef
23.
go back to reference Kis Z, Zalán A, Volgyi A, Kozma Z, Domján L, Pamjav H (2012) Genome deletion and insertion polymorphisms (DIPs) in the Hungarian population. Forensic Sci Int Genet 6:125–126CrossRef Kis Z, Zalán A, Volgyi A, Kozma Z, Domján L, Pamjav H (2012) Genome deletion and insertion polymorphisms (DIPs) in the Hungarian population. Forensic Sci Int Genet 6:125–126CrossRef
25.
go back to reference Walsh P, Metzger D, Higuchi R (1991) Chelex 100 as a médium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506–513PubMed Walsh P, Metzger D, Higuchi R (1991) Chelex 100 as a médium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506–513PubMed
26.
go back to reference Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50 Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50
28.
29.
go back to reference Reis RA, InDel e SNP (2014) Caracterização Genética das Populações Imigrantes de Cabo Verde e Guiné-Bissau a residir na Região de Lisboa, Escola Superior de Saúde Egas Moniz Reis RA, InDel e SNP (2014) Caracterização Genética das Populações Imigrantes de Cabo Verde e Guiné-Bissau a residir na Região de Lisboa, Escola Superior de Saúde Egas Moniz
30.
go back to reference Felsenstein J (1989) PHYLIP—Phylogeny Inference Package (Version 3.2). Cladistics 5:164–166 Felsenstein J (1989) PHYLIP—Phylogeny Inference Package (Version 3.2). Cladistics 5:164–166
31.
go back to reference Pereira L, Gusmão L, Alves C, Amorim A, Prata MJ (2002) Bantu and European Y-lineages in Sub-Saharan Africa. Ann Hum Genet 66:369–378CrossRefPubMed Pereira L, Gusmão L, Alves C, Amorim A, Prata MJ (2002) Bantu and European Y-lineages in Sub-Saharan Africa. Ann Hum Genet 66:369–378CrossRefPubMed
32.
go back to reference Carracedo A, Butler JM, Gusmão L, Linacre A, Parson W, Roewer L, Schneider PM (2014) Update of guidelines for the publication of genetic population data. Forensic Sci Int Genet 10:A1–A2CrossRefPubMed Carracedo A, Butler JM, Gusmão L, Linacre A, Parson W, Roewer L, Schneider PM (2014) Update of guidelines for the publication of genetic population data. Forensic Sci Int Genet 10:A1–A2CrossRefPubMed
Metadata
Title
Study of InDel genetic markers with forensic and ancestry informative interest in PALOP’s immigrant populations in Lisboa
Authors
Ana Inácio
Heloísa Afonso Costa
Cláudia Vieira da Silva
Teresa Ribeiro
Maria João Porto
Jorge Costa Santos
Gilberto Igrejas
António Amorim
Publication date
01-05-2017
Publisher
Springer Berlin Heidelberg
Published in
International Journal of Legal Medicine / Issue 3/2017
Print ISSN: 0937-9827
Electronic ISSN: 1437-1596
DOI
https://doi.org/10.1007/s00414-016-1484-3

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