Forensic performance of two insertion-deletion marker assays

International Journal of Legal Medicine

Volumn 126, Issue 5, 2012, Pages 725-737

  Fondevila, M ^a,d   Phillips, C ^a   Santos, C ^a   Pereira, R ^b   Gusmao L ^b,c   Carracedo, A ^a   Butler, J M ^d   Lareu, M V ^a   Vallone, P M ^d  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^b UNIVERSITY OF PORTO   (Portugal)

^c Federal Do Para University   (Brazil)

^d NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

InDel; Insertion deletion polymorphisms; Population variation; Short amplicon binary markers

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ARTICLE; COMPARATIVE STUDY; DNA SEQUENCE; ETHNIC GROUP; FORENSIC GENETICS; FOUNDER EFFECT; GENE FREQUENCY; GENETIC MARKER; GENETICS; GENOTYPE; HETEROZYGOTE DETECTION; HUMAN; INDEL MUTATION; METHODOLOGY; MULTIPLEX POLYMERASE CHAIN REACTION; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; ETHNIC GROUPS; FORENSIC GENETICS; FOUNDER EFFECT; GENE FREQUENCY; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPE; HETEROZYGOTE DETECTION; HUMANS; INDEL MUTATION; MICROSATELLITE REPEATS; MULTIPLEX POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84867020823     PISSN: 09379827     EISSN: 14371596     Source Type: Journal    
DOI: 10.1007/s00414-012-0721-7     Document Type: Article

References (31)

1. Pereira R, Phillips C, Alves C, Amorim A, Carracedo A, Gusmão L (2009) A new multiplex for human identification using insertion/ deletion polymorphisms. Electrophoresis 30:3682-3690
2. Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G (2002) Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 71:854-862
3. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, PittardWS, Devine SE (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16:1182-1190
4. Mullaney JM, Mills RE, Pittard WS, Devine SE (2010) Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 19(R2):131-136
5. Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS et al (2011) Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res 21:830-839
6. Väli U, Brandström M, Johansson M, Ellegren H (2008) Insertiondeletion polymorphisms (InDels) as genetic markers in natural populations. BMC Genet 9:8
7. Romanini C, Catelli ML, Borosky A, Pereira R, Romero M, Salado Puerto M, Phillips C, FondevilaMet al (2011) Typing short amplicon binary polymorphisms: supplementary SNP and InDel genetic information in the analysis of highly degraded skeletal remains. Forensic Sci Int Genet. doi:10.1016/j.fsigen.2011.10. 006
8. Zidkova A, Horinek A, Kebrdlova V, Korabecna M (2011) Application of the new insertion-deletion polymorphism kit for forensic identification and parentage testing on the Czech population. Int J Legal Med. doi:10.1007/s00414- 011-0649-3
9. Larue BL, Ge J, King JL, Budowle B (2012) A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification. Int J Legal Med (in press)
10. Friis SL, Børsting C, Rockenbauer E, Poulsen L, Fredslund SF, Tomas C, Morling N (2011) Typing of 30 insertion/deletions in Danes using the first commercial InDel kit-Mentype® DIPplex. Forensic Sci Int Genet. doi:10.1016/j.fsigen.2011.08.002
11. FondevilaM, Pereira R, Gusmao L, Phillips C, Lareu MV, Carracedo A, Butler JM, Vallone PM(2011) Forensic performance of insertion-deletion marker systems. Forensic Sci Int Genet Suppl Ser 3:e443-e444
12. Golenberg E, Bickel A, Weihs P (1996) Effect of highly fragmented DNA on PCR. Nucleic Acids Research Nucleic Acids Res 24:5026-5033
13. Sikorsky JA, Primerano DA, Fenger TW, Denvir J (2007) DNA damage reduces Taq DNA polymerase fidelity and PCR amplification efficiency. Biochem Biophys Res Commun 355:431-437
14. Fondevila M, Phillips C, Naverán N, Fernandez L, Cerezo M, Salas A, Carracedo A, Lareu MV (2008) Case report: identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur. Forensic Sci Int Genet 2:212-218
15. Investigator DIPplex Kit. http://www.qiagen.com/products/ investigatordipplexkit.aspx
16. Phillips C, Fondevila M, García-Magariños 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 2:198-204
17. Phillips C, Ballard D, Gill P, Syndercombe Court D, Carracedo A, Lareu MV (2012) The recombination landscape around forensic STRs: accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data. Forensic Sci Int Genet 6:354-365
18. Schneider S, Roessli D, Excoffier L (2000) Arlequin: a software for population genetics data analysis User manual ver 2.00. Genetics and Biometry Lab, Dept. of Anthropology, University of Geneva; Geneva
19. Kline MC, Butts ELR, Hill CR, Coble MD, Duewer DL, Butler JM (2011) The new Standard Reference Material 2391c: PCR-based DNA profiling standard. Forensic Sci Int Genet Suppl Ser 3:e355-e356
20. Eschelbach JW, Zhuome D, Grady B, Goetzinger W (2011) Characterization of short-term temperature, exposure, and solubilization effects on library compound quality. J Biomol Screen 16:1112-1118
21. Kline MC, Hill CR, Decker AE, Butler JM (2011) STR sequence analysis for characterizing normal, variant, and null alleles. Forensic Sci Int Genet 5:329-332
22. Coble MD, Butler JM (2005) Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples. J Forensic Sci 50:43-53
23. Hill CR, Kline MC, Coble MD, Butler JM (2008) Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples. J Forensic Sci 53:73-80
24. Kosambi DD (1943) The estimation of map distances from recombination value. Ann Eugen 12:172-175
25. Phillips C, Fondevila M, Vallone PM, Santos C, Freire-Aradas A, Butler JB, Lareu MV, Carracedo A (2011) Characterization of U.S. population samples using a 34plex ancestry informative SNP multiplex. Forensic Sci Int Genet. Suppl Ser 3 (2011) e182-e183
26. Lao O, Vallone PM, Coble MD, Diegoli TM, van Oven M, van der Gaag KJ, Pijpe J, de Knijff P et al (2010) Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA. Hum Mutat 12:1875-1893
27. Ryckman K, Williams SM (2008) Calculation and use of the Hardy-Weinberg model in association studies. Curr Protoc Hum Genet 1:1.18
28. Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E et al (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27:1713-1724
29. Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, Calaza M, Casares de Cal M, Ballard D, Lareu MV, Carracedo A (2007) The SNPforID Consortium, Inferring ancestral origin using a single multiplex assay of ancestryinformative marker SNPs. Forensic Sci Int Genet 1:273-280
30. Pereira R, Phillips C, Pinto N, Santos C, dos Santos SEB, Amorim A, Carracedo A, Gusmão L (2012) Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One 7:e29684
31. Fondevila M, Santos C, Phillips C, Carracedo A, Butler JM, Lareu MV, Vallone PM (2011) An assesment of linkage between forensic markers: core STRs, mini-STRs and InDels. Proccedings of 22nd International Symposium of Human Identification, Washington.https://www.promega.com/?/media/files/resources/ conference%20-proceedings/ishi%2022/oral%20presentations/fondevila.ashx?la0en. Accessed 1 February 2012