Abstract
The CEPH human genome diversity cell line panel (CEPH-HGDP) of 51 globally distributed
populations was used to analyze patterns of variability in 20 core human identification
STRs. The markers typed comprised the 15 STRs of Identifiler, one of the most widely
used forensic STR multiplexes, plus five recently introduced European Standard Set
(ESS) STRs: D1S1656, D2S441, D10S1248, D12S391 and D22S1045. From the genotypes obtained
for the ESS STRs we identified rare, intermediate or off-ladder alleles that had not
been previously reported for these loci. Examples of novel ESS STR alleles found were
characterized by sequence analysis. This revealed extensive repeat structure variation
in three ESS STRs, with D12S391 showing particularly high variability for tandem runs
of AGAT and AGAC repeat units. The global geographic distribution of the CEPH panel
samples gave an opportunity to study in detail the extent of substructure shown by
the 20 STRs amongst populations and between their parent population groups. An assessment
was made of the forensic informativeness of the new ESS STRs compared to the loci
they will replace: CSF1PO, D5S818, D7S820, D13S317 and TPOX, with results showing
a clear enhancement of discrimination power using multiplexes that genotype the new
ESS loci. We also measured the ability of Identifiler and ESS STRs to infer the ancestry
of the CEPH-HGDP samples and demonstrate that forensic STRs in large multiplexes have
the potential to differentiate the major population groups but only with sufficient
reliability when used with other ancestry-informative markers such as single nucleotide
polymorphisms. Finally we checked for possible association by linkage between the
two ESS multiplex STRs closely positioned on chromosome-12: vWA and D12S391 by examining
paired genotypes from the complete CEPH data set.
Keywords
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References
ALFRED allele frequency database: http://alfred.med.yale.edu/alfred/.
- A human genome diversity cell line panel.Science. 2002; 296: 261-262
- Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives.Ann. Hum. Genet. 2006; 70: 841-847
- New multiplexes for Europe-Amendments and clarification of strategic development.Forensic Sci. Int. 2006; 163: 155-157
- A highly variable STR at the D12S391 locus.Int. J. Legal Med. 1996; 109: 134-138
- Sequence variation of a hypervariable short tandem repeat at the D1S1656 locus.Int. J. Legal Med. 1998; 111: 244-247
- The development of reduced size STR amplicons as tools for analysis of degraded DNA.J. Forensic Sci. 2003; 48: 1054-1064
- Development and validation of a next generation STR ESS-pentaplex.Forensic Sci. Int. Genet. Suppl. 2009; 2: 25-26
- SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.BMC Bioinformatics. 2008; 9: 428
- pop.STR—an online population frequency browser for established and new.Forensic Sci. Int. Genet. Suppl. 2009; 2: 361-362https://doi.org/10.1016/j.fsigss.2009.08.178
- Genetic structure of human populations.Science. 2002; 298: 2381-2385
Promega Powerstats download page: http://www.promega.com/geneticidtools/powerstats/.
- Inferring ethnic origin by means of an STR profile.Forensic Sci. Int. 2001; 119: 17-22
- Inferring ethnicity using 15 autosomal STR loci – comparisons among populations of similar and distinctly different physical traits.Forensic Sci. Int. Genet. 2009; 3: 251-254
- Measurement of admixture proportions and description of admixture structure in different U.S. populations.Hum. Mutat. 2009; 30: 1299-1309
- An evaluation of genetic distances for use with microsatellite loci.Genetics. 1995; 92: 6723-6727
- Genetic absolute dating based on microsatellites and the origin of modern humans.Proc. Natl. Acad. Sci. U.S.A. 1995; 92: 6723-6727
- Informativeness of genetic markers for inference of ancestry.Am. J. Hum. Genet. 2003; 73: 1402-1422
- Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs.Forensic Sci. Int. Genet. 2007; 1: 273-280
vWA data: http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=240641; D12 data: http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=2703.
- A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity.Genetica. 1995; 96: 3-12
- The rarity of DNA profiles.Ann. Appl. Stat. 2007; 1: 358-370
- Estimating F-statistics for the analysis of population structure.Evolution. 1984; 38: 1358-1370
- Estimating F-statistics.Ann. Rev. Genet. 2002; 36: 721-750
ALFRED population descriptions: The Karitianas make up a very small Amazonian basin population that is composed of less than 200 people (1994 est.) who live in a single village on a reservation in Brazil's Rondonia Province. The approximately 800 Rondonian Surui, or Paiter, live in several small villages scattered along the border between the Brazilian provinces of Mato Grosso and Rondonia which was in isolation from the outside world until 1969.
T. Tverdebrink, Overdispersion in allelic counts and θ-correction in forensic genetics, Ann. Appl. Stat., 2010, submitted for publication.
- Allele frequencies of the ACTBP2, D18S51, D8S1132, D12S391, D2S1360, D3S1744, D5S2500, D7S1517, D10S2325 and D21S2055 loci in a German population sample.Forensic Sci. Int. 2005; 151: 303-305
- Increased forensic efficiency of DNA fingerprints through simultaneous resolution of length and nucleotide variability by high-performance mass spectrometry.Hum. Mutat. 2008; 29: 427-432
- Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.Proc. Natl. Acad. Sci. U.S.A. 2005; 102: 15942-15947
- Worldwide human relationships inferred from genome-wide patterns of variation.Science. 2008; 319: 1100-1104
- Use of subpopulation data in Australian forensic DNA casework.Forensic Sci. Int. Genet. 2007; 1: 238-246
- How reliable is the subpopulation model in DNA testimony?.Forensic Sci. Int. 2006; 157: 144-148
- Resolving relationship tests that show ambiguous STR results using autosomal SNPs as supplementary markers.Forensic Sci. Int. Genet. 2008; 2: 198-204
Article info
Publication history
Published online: March 08, 2010
Accepted:
February 6,
2010
Received in revised form:
February 2,
2010
Received:
December 10,
2009
Identification
Copyright
© 2010 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
