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PubMed1997

Multiplex DNA typing of short-tandem-repeat loci on the Y chromosome.

To facilitate evolutionary and forensic studies of DNA polymorphisms on the Y chromosome, we devised a multiplex amplification procedure for short-tandem-repeat (STR) loci. Four tetranucleotide STR loci (DYS19, DYS390, DYS391, and DYS393) were simultaneously amplified with FAM-labeled primers and genotypes were determined with an automated DNA sequencer. We typed 162 males from three U.S. populations (African-Americans, European-Americans and Hispanics) and found that the haplotype diversities range from 0.920 to 0.969. This quadruplex system provides a facile means of genotyping these Y chromosome STRs, and should be useful in population genetic and forensic applications.

Adult↗

PubMed2005

Analysis of artificially degraded DNA using STRs and SNPs--results of a collaborative European (EDNAP) exercise.

Recently, there has been much debate about what kinds of genetic markers should be implemented as new core loci that constitute national DNA databases. The choices lie between conventional STRs, ranging in size from 100 to 450 bp; mini-STRs, with amplicon sizes less than 200 bp; and single nucleotide polymorphisms (SNPs). There is general agreement by the European DNA Profiling Group (EDNAP) and the European Network of Forensic Science Institutes (ENFSI) that the reason to implement new markers is to increase the chance of amplifying highly degraded DNA rather than to increase the discriminating power of the current techniques. A collaborative study between nine European and US laboratories was organised under the auspices of EDNAP. Each laboratory was supplied with a SNP multiplex kit (Foren-SNPs) provided by the Forensic Science Service, two mini-STR kits provided by the National Institute of Standards and Technology (NIST) and a set of degraded DNA stains (blood and saliva). Laboratories tested all three multiplex kits, along with their own existing DNA profiling technique, on the same sets of degraded samples. Results were collated and analysed and, in general, mini-STR systems were shown to be the most effective. Accordingly, the EDNAP and ENFSI working groups have recommended that existing STR loci are reengineered to provide smaller amplicons, and the adoption of three new European core loci has been agreed.

Analysis of Variance↗

PubMed2002

Genetic variation at 15 autosomal microsatellite loci in the three highly endogamous tribal populations of Orissa, India.

Although microsatellite diversity in autosomal chromosomes has been extensively described for many of the Indian populations, there is still a lacuna left on information about the genetic diversity of tribal populations. This paper reports the genetic data on the three tribal populations belonging to the Austroloid ethnic group from Orissa (Juang, Paroja and Saora). The 15 STR (D3S1358, THO1, D21S11, D18S51, PentaE, D5S818, D13S317, D7S820, D16S539, CSF1PO, PentaD, vWA, D8S1179, TPOX, FGA) polymorphism would help to accentuate the STR database for better understanding of population genetics and forensic applications. The microsatellites included in the system are found to be highly polymorphic, with the combined power of exclusion being greater than 0.999, in all the three investigated populations.

Ethnicity↗

PubMed2003

[Studying the polymorphism at DYF155S1 locus in Chinese Han population by MVR-PCR marked with fluorescence].

The simple and useful genotyping methods of DYF155S1 locus by silver staining and fluorescence detection have been established. The blood samples from 155 unrelated males in Chinese Han population were typed by these two methods respectively and the same results were obtained. Among the 155 samples 66 alleles were found, out of them 38 were observed once only. The most frequent alleles named 18 or 22, which frequency was 0.065, the size of their first DNA fragments was 180 bp and the number of fragments was 16 or 17. The gene diversity (h) was 0.9789. Out of the 155 samples, 25 samples had one or two bands lost (null repeat) among the successive bands. It was demonstrated by sequencing that the position of the lost bands corresponded to type 3 repeats. Our results indicated that the method, which revealed the 5' end diversity of DYF155S1 locus, was a technique that could obtain the most Y-specific polymorphic information only by one PCR reaction. The allele frequencies of DYF155S1 locus in Chinese Han population provided the basic data for the study of population genetics and forensic practices.

Alleles↗

PubMed2003

[Genetic polymorphism of six short tandem repeat loci in the Han population in Hebei province of China].

OBJECTIVE: This article reports a population genetic study on six short tandem repeat(STR) loci, D7S820, D19S253, D12S391, D5S818, D16S539 and D8S1179, in a sample of unrelated Chinese Han individuals(n=122-173) living in Hebei province. METHODS: DNA extraction from blood samples (200 in number) and multiplex amplification of the above six loci were carried out. Using denaturing polyacrylamide gel electrophoresis and silver stain, the authors investigated the distribution of allele frequencies of the six loci in Han population in Hebei province. RESULTS: The STR polymorphisms at all of the six loci were observed in Chinese Han population in Hebei province. The observed heterozygosities of D7S820, D19S253, D12S391, D5S818, D16S539 and D8S1179 were 0.828, 0.757, 0.769, 0.837, 0.785 and 0.852, respectively. The measured values of the power of discrimination (PD) were 0.914, 0.919, 0.940, 0.909, 0.917, 0.944; of the mean exclusion chance(MEC) 0.618, 0.740, 0.801, 0.557, 0.655, 0.696 and of the polymorphism information content (PIC) in Chinese 0.771, 0.760, 0.762, 0.708, 0.776 and 0.794, respectively. CONCLUSION: The genotype distributions of the six STR were in accordance with Hardy-Weinberg equilibrium. The numerical values of the PD and MEC are relatively high in Hebei province, and thus can be of significant application in population genetics and forensic medicine.

Asian People↗

PubMed2005

[Genetic polymorphism of 6 short-tandem repeat loci in Miao minority group of Rongshui county in Guangxi province].

OBJECTIVE: To investigate the distributions of six short-tandem repeat (STR) loci, namely D7S820, D13S317, D16S539, HUMCSF1PO, HUMTPOX and HUMTH01, in Miao minority group at Rongshui county in Guangxi province and construct the relevant genetic database. METHODS: Sodium-citrated blood specimens were collected from 208 healthy unrelated Miao individuals in Rongshui county. The DNAs from the specimens were extracted with phenol-chloroform method; AmplFSTR Identifier PCR Amplification Kit was used to amplify the extracted DNAs, and 3100 Genetic Analyzer was used to analyze and screen the amplified products. RESULTS: In this study, 7, 8, 6, 7, 5, 7 alleles were observed at the 6 STR loci respectively. The expected distribution of genotype accorded with Hardy-Weinbery equilibrium. The total discrimination power, cumulative paternity exclusion power and total polymorphism information were 0.999995, 0.9959 and 0.9987 respectively. CONCLUSION: The results demonstrate that these 6 STR loci are of high polymorphism and hereditary stability and are in accord with Mendel's law. The data obtained are valuable in population genetics research, forensic application, and individual identifications.

Adolescent↗

PubMed2004

Population-specific alleles: the polymorphism (K121Q) of the human glycoprotein PC-1 gene is strongly associated with race but not with insulin resistance in black and white children.

The K121Q polymorphism of the glycoprotein PC-1 gene was recently reported to associate with insulin resistance (IR) in an all-Caucasian, Sicilian population. Given black-white differences in plasma insulin and IR, we compared the prevalence of the KK, KQ, and QQ genotypes and their associations with insulin and IR in 2 large, biracial pediatric samples: 1 hospital-based (n = 301, 137 blacks and 164 whites) and 1 school-based (n = 639, 344 blacks and 295 whites). The Q allele frequencies in the hospital-based and school-based cohorts in black children were 0.80 and 0.77 and in the white children, 0.15 and 0.13. The K allele frequencies in the hospital-based and school-based cohorts in black children were 0.20 and 0.23 and in the white children, 0.85 and 0.87. Differences in allelic frequencies were highly significant (chi square test, P <.0001) for both the hospital-based cohort and the school-based cohort. Both cohorts were in Hardy-Weinberg equilibrium. Within race, after covariance adjusting for age and body mass index (BMI), there were no significant differences (P >/=.10) among the 3 PC-1 genotypes for insulin, glucose, or homeostasis model assessment (HOMA) IR. After covariance adjusting for age and BMI, black girls had higher insulin (P =.0007) and higher HOMA IR (P =.0002) than white girls. The K121Q polymorphism was not associated with insulin, glucose, or HOMA IR measures in black or white children. However, the QQ genotype was population-specific, encompassing most black children versus 1% to 3% of white children. As such, K121Q genotyping should be useful in epidemiology, population genetics, and forensic anthropology.

Adolescent↗

PubMed2002

Comprehensive human genome amplification using multiple displacement amplification.

Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4-6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20-30 microg product from as few as 1-10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.

Blotting, Southern↗

PubMed2004

Heterologous mitochondrial DNA recombination in human cells.

Inter-molecular heterologous mitochondrial DNA (mtDNA) recombination is known to occur in yeast and plants. Nevertheless, its occurrence in human cells is still controversial. To address this issue we have fused two human cytoplasmic hybrid cell lines, each containing a distinct pathogenic mtDNA mutation and specific sets of genetic markers. In this hybrid model, we found direct evidence of recombination between these two mtDNA haplotypes. Recombinant mtDNA molecules in the hybrid cells were identified using three independent experimental approaches. First, recombinant molecules containing genetic markers from both parental alleles were demonstrated with restriction fragment length polymorphism of polymerase chain reaction products, by measuring the relative frequencies of each marker. Second, fragments of recombinant mtDNA were cloned and sequenced to identify the regions involved in the recombination events. Finally, recombinant molecules were demonstrated directly by Southern blot using appropriate combinations of polymorphic restriction sites and probes. This combined approach confirmed the existence of heterogeneous species of recombinant mtDNA molecules in the hybrid cells. These findings have important implications for mtDNA-related diseases, the interpretation of human evolution and population genetics and forensic analyses based on mtDNA genotyping.

Blotting, Southern↗

PubMed2004

Genetic data of 15 STR forensic loci in eastern Chinese population.

Allele frequencies for the 15 short tandem repeats (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TH01, D16S539, D2S1338, TPOX D19S433 (AmpFLSTR Identifiler) were determined in a population sample of unrelated individuals living in eastern China.

China↗

PubMed2025

Uncovering new lineages in the Sunda pangolin (Manis javanica) with museum mitogenomics.

Accurately identifying evolutionarily significant units (ESUs) is crucial for conservation planning, especially for species like pangolins threatened by overhunting and habitat loss. ESUs help categorize different pangolin populations, aiding in understanding their genetic diversity and distribution, which is vital for targeted conservation efforts. This research generated mitochondrial genomes from historical museum specimens of Sunda pangolins (Manis javanica) from underrepresented locations, uncovering a new evolutionary lineage from the Mentawai Islands that diverged from Indochina and west Sundaland populations around 760 000 years ago. This population thereby represents a divergent ESU with a small distribution, important for conservation planning. The novel sequences provide resources for forensic labs tracing the origin of confiscated scales and shed light into the potential distribution of the 'mysterious pangolin'. Additionally, this research confirmed the presence of the two major M. javanica lineages in Java and extended the known distribution of the eastern clade to Bali and East Kalimantan. Our findings potentially suggest a recent bottleneck and postglacial expansion of pangolins across Indochina and west Sundaland. Further investigation with genomic and morphological evidence, contact area sampling and type sequencing will be required to evaluate the taxonomic status of different M. javanica lineages and M. culionensis.

Genomics↗

PubMed2003

Validation of the multiplex kit genRESMPX-2 for forensic casework analysis.

Validation studies were carried out using the commercially available PCR multiplex system genRESMPX-2. In addition to amelogenin, this system comprises the complete set of eight STR systems which are components of the German DNA database established in 1998 by the Federal Criminal Office of Germany (BKA). The minimum amount of template DNA which gave a complete DNA pattern ranged between 100 pg and 200 pg. Mixed samples could clearly be assigned from ratios between 1:5 (ACTBP2) and 1:20 (VWA, FGA). Experimental investigations with different forensic materials, environmental studies, reproducibility and precision data as well as practical casework analysis revealed that the genRESMPX-2 kit can be regarded as a sensitive, reliable and robust multiplex system even in the case of samples containing limited amounts or degraded DNA.

Animals↗

PubMed2003

[Genetic polymorphism of 8 STR loci on short arm of chromosome 3].

OBJECTIVE: To get the genotype and allele frequency distributions of 8 short tandem repeat (STR) loci on chromosome 3p (D3S1297, D3S1489, D3S1266, D3S1568, D3S1289, D3S1300, D3S1285 and D3S3681) in Chinese Han population in Hunan area. METHODS: Blood samples were collected from the random Han individuals in Hunan and the whole genomic DNA was extracted. STR loci were amplified by multiplex-PCR technique and genotyped by ABI 377 sequencer. RESULTS: Ninety-one alleles were detected, with frequencies ranging from 0.002 to 0.431, and these alleles constituted 312 genotypes. All the 8 loci met Hardy-Weinberg equilibrium. The statistical analysis of 8 STR loci showed the heterozygosity (H) >or= 0.729, the discrimination power (DP) >or= 0.725, the probabilities of paternity exclusion (PPE) >or= 0.596, and the polymorphic information content (PIC >or= 0.682). The result indicated that there was a significant difference between Han ethnic group and the white and the black. CONCLUSION: These results could serve as valuable data to enrich the Chinese genetic database and play an important role in Chinese population genetic and forensic medical application.

Adult↗

PubMed2003

Extraction and analysis of human nuclear and mitochondrial DNA from electron beam irradiated envelopes.

The United States Postal Service is considering methods such as electron beam irradiation to neutralize biological agents sent through the mail. While this is proven to reduce/eliminate pathogenic organisms, it may also degrade human genomic DNA and therefore hinder the ability to garner forensically informative genetic profiles. To determine the effects of electron beam irradiation on DNA typing, 16 white, standard letter-sized envelopes were licked. Half of the envelopes served as nonirradiated controls while the other half underwent irradiation at dosages sufficient to kill anthrax spores (29.3 and 51.6 kGy). Total cellular DNA was extracted from all envelopes; nuclear short tandem repeat loci, as well as the hypervariable region I from mitochondrial DNA, were amplified by means of the polymerase chain reaction. Short tandem repeat profiles and mitochondrial DNA sequence haplotypes were acquired on an ABI Prism 310 Genetic Analyzer platform. Analysis of data from irradiated samples revealed evidence of DNA degradation; however, the ability to construct full genetic profiles from both nuclear and mitochondrial DNA remained largely unaffected. The use of the polymerase chain reaction, coupled with florescent fragment analysis and mitochondrial DNA sequencing, should be considered to profile biological material from evidence enduring irradiation to inactivate infectious agents.

Complementarity Determining Regions↗

PubMed1995

[Application of AmpliType PM kit to forensic sciences].

Five genetic loci, low density lipoprotein (LDLR), glycophorin A (GYPA), hemoglobin G gammaglobin (HBGG), D7S8 and group specific component (GC), can be identified in a single step by the AmpliType PM kit. The kit uses multiplex PCR amplification and hybridization by a reverse dot blot method. To introduce the new marker system in forensic caseworks in Japan, a relevant Japanese population database must be established. In this context, the allele frequencies of the 5 genetic loci were determined for 246 unrelated Japanese. The allele frequencies were LDLR*A 0.173, LDLR*B 0.827, GYPA*A 0.528, GYPA*B 0.472, HBGG*A 0.352, HBGG*B 0.648, HBGG*C 0.000, D7S8*A 0.612, D7S8*B 0.388, GC*A 0.258, GC*B 0.504 and GC*C 0.238, respectively. In all 5 systems, the genotype frequencies are in good accordance with the Hardy-Weinberg expectations. The power of discrimination (PD) of LDLR, GYPA, HBGG, D7S8 and GC were 0.449, 0.624, 0.600, 0.612 and 0.788, respectively, resulting in a combined PD of 0.993, while these 5 DNA types could be determined from slaiva and semen. And the GYPA or GC genotypes were observed to have good relations with the MN and serum Gc phenotypes. The AmpliType PM kit was confirmed to be a reliable DNA typing system which was well suited for use in forensic sciences.

Alleles↗

PubMed2002

Determining sequence length or content in zero, one, and two dimensions.

High-throughput assays are essential for the practical application of mutation detection in medicine and research. Moreover, such assays should produce informative data of high quality that have a low-error rate and a low cost. Unfortunately, this is not currently the case. Instead, we typically witness legions of people reviewing imperfect data at astronomical expense yielding uncertain results. To address this problem, for the past decade we have been developing methods that exploit the inherent quantitative nature of DNA experiments. By generating high-quality data, careful DNA-signal quantification permits robust analysis for determining true alleles and certainty measures. We will explore several assays and methods. In a one-dimensional readout, short tandem repeat (STR) data display interesting artifacts. Even with high-quality data, PCR artifacts such as stutter and relative amplification can confound correct or automated scoring. However, by appropriate mathematical analysis, these artifacts can be essentially removed from the data. The result is fully automated data scoring, quality assessment, and new types of DNA analysis. These approaches enable the accurate analysis of pooled DNA samples, for both genetic and forensic applications. On a two-dimensional surface (comprised of zero-dimensional spots) one can perform assays of extremely high-throughput at low cost. The question is how to determine DNA sequence length or content from nonelectrophoretic intensity data. Here again, mathematical analysis of highly quantitative data provides a solution. We will discuss new lab assays that can produce data containing such information; mathematical transformation then determines DNA length or content.

Artifacts↗

PubMed1995

An infrared fluorescent dATP for labeling DNA.

Near-infrared fluorescence provides a nonradioactive method of detection with high sensitivity and low background. An infrared fluorophore has been attached covalently to the nucleotide deoxyadenosine triphosphate (dATP) to provide a reagent for enzymatic labeling of various types of DNA molecules and for facilitating their detection with an automated DNA sequencing and analysis system. DNA sequencing reaction products can be labeled internally by performing limited polymerization utilizing infrared-labeled dATP (IR-dATP) as the sole source of adenine deoxynucleotide prior to a dideoxy-specific termination reaction. PCR products can be labeled fluorescently by the addition of limited quantities of IR-dATP to the amplification reaction. This latter strategy has been utilized for detection of short tandem repeat polymorphisms (STRPs) which are useful for gene mapping, genetic diagnostics, forensic analysis, and paternity testing. Restriction fragments can be labeled also by fill-in reactions of appropriate 5' overhangs. Diminutive amounts of such fluorescently labeled DNA molecules can be visualized rapidly and conveniently using infrared detection technology.

Adenosine Triphosphate↗

PubMed2024

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes.

BACKGROUND: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. RESULTS: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. CONCLUSIONS: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

Animals↗