A repository of 14 PCR-loci Italian gene frequencies in the World Wide Web

A collection of 6830 typing results produced by the Immunohematology Laboratory at the UCSC, pertaining to 11 STRs (FES/FPS, vWA31, HUMTH01, F13A1, MBP, D21S11, D7S460, D18S51, CD4, TPOX, CSF1PO) and 3 AmpFLPs (D1S80, APO-B, COL2A1), is publicly available as an electronic archive at a website.     

Genetic data on nine STRs (CSF1PO, TPOX, THO1, F13AO1, FESFPS, vWA, D16S539, D7S820 and D13S317) and two VNTRs (D1S80 and D17S5) in Rosario population, Santa Fe Argentine

Allele frequencies for nine short tandem repeats (STRs) loci (CSF1PO, TPOX, THO1, F13AO1, FES/FPS, vWA, D16S539, D7S820 and D13S317) and two variable number tandem repeats (VNTRs) were obtained from a sample of 270 unrelated individuals born in the Rosario city, Santa Fe province of Argentina.     

Genetic data on 11 STRs (CSF1PO,TPOX, TH01, F13A01, FESFPS,vWA, D16S539, D7S820, D13S317, F13B,LPL) in an Argentine northeast population

Allele frequencies for 11 short tandem repeats (STRs) loci (CSF1PO, TPOX, TH01, F13A01, FESFPS, vWA, D16S539, D7S820, D13S317, F13B and LPL) were obtained from a sample of 225 unrelated individuals born in the Entre Ríos state of Argentina.     

Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel

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.     

The Slovenian population data on the PCR based loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80

Allele frequencies for the loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80 were determined for a sample population of unrelated individuals from Slovenia. All loci meet Hardy-Weinberg expectations, except the loci GYPA (p = 0.041) and D1S80 (p = 0.009). There is little evidence for association of alleles among the seven loci. Only one out of 21 pairwise comparisons demonstrated departures from independence (HLA-DQA1/HBGG, p = 0.008). The allelic frequency data generally are similar to that of U.S. Caucasians.     

Population data of nine STRs of Mexican-Mestizos from Mexico City

One hundred and thirteen individuals were PCR-typed for nine STR loci with the AmpFlSTR Profiler Plus PCR amplification kit, including the following autosomal STRs: D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820. Allele frequencies for each STR were estimated, and they were compared to other populations. Genotype distribution by locus and by two-loci combination was in agreement with Hardy-Weinberg expectations for all nine STRs. For this region of Mexico, the combined probability of exclusion (PE) and power of discrimination (PD) were estimated: PE=99.964% and PD>99.999%.     

Observation of tri-allelic patterns in autosomal STRs during routine casework

We report three cases of tri-allelic patterns observed during routine forensic casework on 5964 Belgian residents. These individuals had been typed for the following 15 autosomal STRs: CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, vWA, FGA, TH01, TPOX, D2S1338 and D19S433.The first example of a tri-allelic pattern had the genotype 13;15;16 for the D8S1179 locus. In the second observation there was 16;21;22 pattern for the D18S51 locus. The third case had the alleles 10;11;13 also for D18S51.All cases belonged to the Type I tri-allelic pattern, with three uneven peaks, the sum of the heights of both smaller peaks equalling the height of the tallest peak.Three cases in 5964 typed individuals is a frequency for tri-allelic patterns in autosomal STRs of 0.05%.     

Genetic data on eight STRs (D5S818, D7S820, F13B,LPL, TH01, TPOX,VWA31, CSF1PO) from a Colombian population

Allele frequencies for eight short tandem repeats (STRs) (D5S818, D7S820, F13B, LPL, TH01, TPOX, VWA31 and CSF1PO) were estimated from a sample of 155 unrelated individuals living in different departments of the southwest of Colombia, Caquetá, Cauca, Huila, Nari?o, Putumayo and Cauca Valley.     

13 STR loci frequencies in the population from Paraíba, Northeast Brazil

As part of a long-term project on Northeastern Brazilians, population genetic data were obtained from 323 unrelated individuals from the state of Paraíba. The loci studied were CSF1P0, TPOX, TH01, vWA, D16S539, D7S820, D13S317, D18S51, D21S11, D8S1179, F13A01, F13B and LPL. Their distributions are in Hardy-Weinberg equilibrium. Forensic parameters were calculated and a comparison was made with geographically nearby populations.     

World population data for the HLA-DQA1, PM and D1S80 loci with least and most common profile frequencies for combinations of loci estimated following NRC II guidelines

All published and unpublished gene frequency data for the PCR-based loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80 that could be located are presented in summary tables. These gene frequencies provide the data necessary for estimating probabilities of chance match according to NRC II guidelines for any DNA profile that includes any combination of these loci for any of the populations. To illustrate the range of polymorphism for combined locus profiles, least and most common profile frequencies were estimated following NRC II guidelines for: the PM loci for all populations for which PM data were available; and for combinations of HLA-DQA1/PM, HLA-DQA1/D1S80, PM/D1S80, and HLA-DQA1/ PM/D1S80 for populations for which data were available for the relevant combinations. The profile frequencies were calculated at theta values of zero and 0.01. Minimum allele frequencies (MAF) were calculated, and are shown, for each data set for which the MAF was greater than the lowest observed allele frequency. Least common profile frequencies were calculated using MAF in those cases to illustrate a conservative estimate. The effect of using MAF versus lowest observed allele frequency in estimating least common profile frequencies is briefly illustrated as well. We finally show that aggregate U.S. gene frequency data for the classical MN and GC polymorphisms for both Caucasian and African-American populations is fully in accord with the DNA-based gene frequency data obtained from PM reverse dot-blot strips for GYPA and GC, respectively.     

Evaluation of reliability of STR typing in human colon carcinomas tissues used for identification purpose

The short tandem repeats (STRs) have become an important and widely used tool in forensic casework. Clinical tissue samples are not usually employed in forensic casework, but sometimes, malignant tissue samples may be the only source of biological material for forensic investigations. However, in use of such samples, uncertainties due to microsatellite instability (MSI) and loss of heterozygosity (LOH) may be encountered. In our study of 77 human colon carcinomas tissue with the AmpFlSTR Identifiler Kit comprising 15 STR loci and the amelogenin gene, we detected four kinds of changes between normal tissue and tumor tissue including pLOH, LOH, occurrence of an additional allele (Add) and occurrence of a new allele (New) instead of that found in normal tissue. The overall variation detectable rate was 11.28%, of which pLOH was 79.1%, LOH was 7.9%, Add was 7.9% and New was 5%. Of the above four changes, the incidence rate of pLOH, LOH, Add and New was respectively 8.93%, 0.89%, 0.89% and 0.57%. The STRs mostly affected were D18S51, D5S818, FGA and D19S433. Only pLOH was found at five loci including vWA, TPOX, TH01, D13S317 and amelogenin gene. Our results demonstrate that great care should be taken in the evaluation of typing results obtained from clinical tissue specimens, in particular when no reference samples are available, because genetic instability is a very common event observed in different tumors and the STRs used for individual identification could sometimes be affected.     

Population data on the PCR-based loci LDLR,GYPA, HBGG,D7S8, Gc,HLA-DQA1, and D1S80 from Arabs from Dubai

Population data were generated for the loci LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, and D1S80 from 180 Arabs from Dubai. Except for D7S8 (P = 0.003), the genotype frequency distributions for the loci do not deviate from Hardy Weinberg expectations. There was no evidence for departures from expectations of independence between the loci. Using a test for homogeneity, the loci LDLR, GYPA, D7S8, and Gc were similar between the Dubaian Arab population sample and an Arab population sample from Palestine and the occupied territories, while the loci HBGG (P = 0.003), DQA1 (P < 10⁻³), and D1S80 (P = 0.020) were statistically different.     

Analysis of STR loci in Cartagena, a Caribbean city of Colombia

Allele frequencies, together with some parameters of forensic interest were estimated for nine STRs included in the AmpF/STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA) in a sample of 215 unrelated individuals from Cartagena (Colombia). For all loci, no significant deviations from Hardy-Weinberg equilibrium were observed. Comparative analysis results between our data and those from other Colombian and African population samples revealed significant differences, except with two Colombian Caribbean Coast sub-regions.     

Analysis of STR loci in Cartagena, a Caribbean city of Colombia

Allele frequencies, together with some parameters of forensic interest were estimated for nine STRs included in the AmpF/STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA) in a sample of 215 unrelated individuals from Cartagena (Colombia). For all loci, no significant deviations from Hardy-Weinberg equilibrium were observed. Comparative analysis results between our data and those from other Colombian and African population samples revealed significant differences, except with two Colombian Caribbean Coast sub-regions.     

Chorionic villus sampling prior to pregnancy termination, a tool for forensic paternity testing.

Chorionic villus sampling (CVS), prior to pregnancy termination (pre-termination CVS), is suggested as a tool for forensic paternity testing. Unlike the abortion material, which consists of ruptured tissues of fetal and maternal origin, extra-embryonic membranes obtained through CVS can provide an uncontaminated source of fetal tissue for genotyping. We discuss the possibility of confined placental mosaicism (CPM) and its implications on the polymerase chain reaction (PCR) based analyses of short tandem repeats (STRs) and the D1S80 loci.     

Population data on nine STRs from Cantabria, a mountainous region in northern Spain.

Allele frequencies for nine STRs loci included in the AmpFlTR Profiler Plus kit (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) were obtained from a sample of 158 unrelated individuals living in Cantabria, a region in northern Spain.     

STR data for the AmpFlSTR Profiler Plus and COfiler loci from the Maghreb (North Africa)

Allele frequencies for 13 STRs (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, THO1, TPOX, CSF1PO and D16S539) included in the AmpFlSTR Profiler Plus and COfiler kits were determined for a population sample from the Maghreb (Northern Africa).     

STR data for the AmpFlSTR SGM Plus from Marmara region of Turkey

Allele frequencies of the 10 STRs loci (D16S539, D2S1338, D3S1358, vWA, D18S51, D21S11, D8S1179, D19S433, FGA, THO1) included in the AmpFlSTR SGM Plus kit (PE Applied Biosystems) were obtained from a sample of 173 unrelated individuals in Marmara region of Turkey.     

Allele distribution of 15 STR loci used for human identity purposes in the Greek Cypriot population of the island of Cyprus

Allele frequencies for 15 STRs (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, THO1, Penta E, D16S539, CSF1PO, Penta D and TPOX) in the PowerPlex-16 System (Promega Corporation) were derived from a sample of 1475 unrelated Greek Cypriot individuals from the island of Cyprus.     

STR data for the AmpFlSTR SGM Plus from Aegean region of Turkey

Allele frequencies of the 10 STRs loci (D16S539, D2S1338, D3S1358, vWA, D18S51, D21S11, D8S1179, D19S433, FGA, THO1) included in the AmpFlSTR SGM Plus Kit (PE Applied Biosystems) were obtained from a sample of 166 unrelated individuals in Aegean region of Turkey.