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

International Journal of Legal Medicine

Volumn 126, Issue 1, 2012, Pages 97-105

  Pereira, Rui ^a,b   Pereira, Vânia ^a,c   Gomes, Iva ^d   Tomas, Carmen ^c   Morling, Niels ^c   Amorim, António ^a   Prata, Maria João ^a   Carracedo, Ángel ^b   Gusmão, Leonor ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d UNIVERSITY HOSPITAL OF COLOGNE   (Germany)

Author keywords

Forensic genetics; Human identification; Indel; Insertion deletion polymorphism; Kinship testing; Multiplex PCR; X chromosome

Indexed keywords

ANGOLA; ARTICLE; FEMALE; FORENSIC GENETICS; GENETIC POLYMORPHISM; GENETICS; GENOTYPE; HUMAN; INDEL MUTATION; MACAO; MALE; METHODOLOGY; MOZAMBIQUE; MULTIPLEX POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; POPULATION GENETICS; PORTUGAL; SOMALIA; X CHROMOSOME;

ANGOLA; CHROMOSOMES, HUMAN, X; FEMALE; FORENSIC GENETICS; GENETICS, POPULATION; GENOTYPE; HUMANS; INDEL MUTATION; MACAU; MALE; MOZAMBIQUE; MULTIPLEX POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; PORTUGAL; SOMALIA;

EID: 84861132393     PISSN: 09379827     EISSN: 14371596     Source Type: Journal    
DOI: 10.1007/s00414-011-0593-2     Document Type: Article

References (28)

1. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, DanteM, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, ZodyMC, Linton L, Lander ES, Altshuler D (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409(6822):928-933. doi:10.1038/35057149. (Pubitemid 32165347)
2. Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G (2002) Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 71(4):854-862. doi:10.1086/342727. (Pubitemid 135750517)
3. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16 (9):1182-1190. doi:10.1101/gr.4565806. (Pubitemid 44320405)
4. Pereira R, Phillips C, Alves C, Amorim A, Carracedo A, Gusmão L (2009) A new multiplex for human identification using insertion/deletion polymorphisms. Electrophoresis 30(21):3682- 3690. doi:10.1002/elps.200900274.
5. Yang N, Li H, Criswell LA, Gregersen PK, Alarcon-Riquelme ME, Kittles R, Shigeta R, Silva G, Patel PI, Belmont JW, Seldin MF (2005) Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Hum Genet 118(3-4):382-392. doi:10.1007/s00439-005-0012-1. (Pubitemid 43101691)
6. Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet 1(6):e70. doi:10.1371/journal.pgen. 0010070.
7. Bastos-Rodrigues L, Pimenta JR, Pena SD (2006) The genetic structure of human populations studied through short insertion- deletion polymorphisms. Ann Hum Genet 70(Pt 5):658-665. doi:10.1111/j.1469-1809.2006.00287.x. (Pubitemid 44173374)
8. Ribeiro-Rodrigues EM, Santos NP, Ribeiro-dos-Santos AK, Pereira R, Amorim A, Gusmão L, Zago MA, Santos SE (2009) Assessing interethnic admixture using an X-linked insertion- deletion multiplex. Am J Hum Biol 21(5):707-709. doi:10.1002/ajhb.20950.
9. Edelmann J, Hering S, Augustin C, Szibor R (2009) Indel polymorphisms-An additional set of markers on the Xchromosome. Forensic Sci Int Genet Supplement Series 2 (1):510-512. doi:10.1016/j.fsigss.2009.08.148.
10. Santos NP, Ribeiro-Rodrigues EM, Ribeiro-dos-Santos AK, Pereira R, Gusmão L, Amorim A, Guerreiro JF, Zago MA, Matte C, Hutz MH, Santos SE (2010) Assessing individual interethnic admixture and population substructure using a 48-insertion- deletion (INDEL) ancestry-informative marker (AIM) panel. Hum Mutat 31(2):184-190. doi:10.1002/humu.21159.
11. Schaffner SF (2004) The X chromosome in population genetics. Nat Rev Genet 5(1):43-51. doi:10.1038/nrg1247. (Pubitemid 38055335)
12. Casto AM, Li JZ, Absher D, Myers R, Ramachandran S, Feldman MW (2010) Characterization of X-linked SNP genotypic variation in globally distributed human populations. Genome Biol 11(1): R10. doi:10.1186/gb-2010-11-1-r10.
13. Szibor R, Krawczak M, Hering S, Edelmann J, Kuhlisch E, Krause D (2003) Use of X-linked markers for forensic purposes. Int J Legal Med 117(2):67-74. doi:10.1007/s00414-002-0352-5. (Pubitemid 36717446)
14. Szibor R, Plate I, Edelmann J, Hering S, Kuhlisch E, Michael M, Krause D (2003) Chromosome X haplotyping in deficiency paternity testing principles and case report. Int Congr Ser 1239:815-820. doi:10.1016/s0531-5131(02)00569-1.
15. Szibor R (2007) X-chromosomal markers: past, present and future. Forensic Sci Int Genet 1(2):93-99. doi:10.1016/j.fsigen.2007.03.003. (Pubitemid 46760407)
16. Gomes I, Prinz M, Pereira R, Meyers C, Mikulasovich RS, Amorim A, Carracedo A, Gusmão L (2007) Genetic analysis of three US population groups using an X-chromosomal STR decaplex. Int J Legal Med 121(3):198-203. doi:10.1007/s00414- 006-0146-2. (Pubitemid 46866576)
17. Tomas C, Sanchez JJ, Barbaro A, Brandt-Casadevall C, Hernandez A, Ben DhiabM, RamonM, Morling N (2008) X-chromosome SNP analyses in 11 humanMediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans). BMC Evol Biol 8:75. doi:10.1186/1471-2148-8- 75. (Pubitemid 351550360)
18. Freitas NS, Resque RL, Ribeiro-Rodrigues EM, Guerreiro JF, Santos NP, Ribeiro-dos-Santos AK, Santos SE (2010) X-linked insertion/deletion polymorphisms: forensic applications of a 33- markers panel. Int J Legal Med 124(6):589-593. doi:10.1007/s00414-010-0441-9.
19. Tomas C, Sanchez JJ, Castro JA, Borsting C, Morling N (2010) Forensic usefulness of a 25 X-chromosome single-nucleotide polymorphism marker set. Transfusion (Paris) 50(10):2258-2265. doi:10.1111/j.1537-2995.2010.02696.x.
20. Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of nontemplated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. Biotechniques 20 (6):1004-1006, 1008-1010.
21. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564-567. doi:10.1111/j.1755-0998.2010.02847.x.
22. Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L (1998) Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci 43(5):1046-1049. (Pubitemid 28397189)
23. Pereira R, Gomes I, Amorim A, Gusmão L (2007) Genetic diversity of 10 X chromosome STRs in northern Portugal. Int J Legal Med 121(3):192-197. doi:10.1007/s00414-006-0144-4. (Pubitemid 46866575)
24. Gomes I, Alves C, Maxzud K, Pereira R, Prata MJ, Sánchez-Diz P, Carracedo A, Amorim A, Gusmão L (2007) Analysis of 10 XSTRs in three African populations. Forensic Sci Int Genet 1 (2):208-211. doi:10.1016/j.fsigen. 2007.01.001. (Pubitemid 46760385)
25. Gusmão L, Sánchez-Diz P, Alves C, Gomes I, Zarrabeitia MT, Abovich M, Atmetlla I, Bobillo C, Bravo L, Builes J, Caine L, Calvo R, Carvalho E, Carvalho M, Cicarelli R, Catelli L, Corach D, Espinoza M, Garcia O, Malaghini M, Martins J, Pinheiro F, Joao Porto M, Raimondi E, Riancho JA, Rodriguez A, Rodriguez Cardozo B, Schneider V, Silva S, Tavares C, Toscanini U, Vullo C, Whittle M, Yurrebaso I, Carracedo A, Amorim A (2009) A GEPISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations. Int J Legal Med 123(3):227-234. doi:10.1007/s00414-008- 0309-4.
26. Phillips C, Fondevila M, Garcia-Magarinos M, Rodriguez A, Salas A, Carracedo A, Lareu MV (2008) Resolving relationship tests that show ambiguous STR results using autosomal SNPs as supplementary markers. Forensic Sci Int Genet 2(3):198-204. doi:10.1016/j.fsigen.2008.02.002.
27. Pereira R, Phillips C, Alves C, Amorim A, Carracedo A, Gusmão L (2009) Insertion/deletion polymorphisms: a multiplex assay and forensic applications. Forensic Sci Int Genet Suppl Ser 2(1):513- 515. doi:10.1016/j.fsigss.2009.09.005.
28. Weir BS (1992) Independence of VNTR alleles defined as fixed bins. Genetics 130(4):873-887.