Platinum-Quality Mitogenome Haplotypes from United States Populations.

A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC).

A comparison of single quadrupole mass detection and diode array ultraviolet detection interfaced to ultra-high performance supercritical chromatography for the quantitative analysis of synthetic cathinones.

A comparison of single quadruple mass spectrometry and diode array-ultraviolet (PDA-UV) detection interfaced to ultra-high performance supercritical fluid chromatography was performed for the quantitative analysis of synthetic cathinones. Synthetic cathinones, also known as "bath salts", are derived from cathinone, a component of the khat plant. For 15 controlled solutes linearity, repeatability, and limits of detection were determined using both UV and MS detection.

Correction to: Population data of 21 autosomal STR loci in the Hausa, Igbo and Yoruba people of Nigeria.

In the original paper author Alani Sulaimon Akanmu was erroneously omitted from the author list. Prof. Akanmu has now been added as 4 author.

Population data of 21 autosomal STR loci in the Hausa, Igbo and Yoruba people of Nigeria.

The three major ethnic groups of Nigerian population namely the Hausa, Igbo and Yoruba make up 29, 21 and 18% of the total population, respectively. To provide genetic information necessary for forensic analysis, this study was carried out to determine STR allele frequencies in 102 Hausa, 128 Igbo and 134 Yoruba individuals in Nigeria using 21 STR loci including the 20 CODIS (Combined DNA Index System) loci plus SE33.

Patterns of DNA Methylation Across the Leptin Core Promoter in Four Diverse Asian and North American Populations.

DNA methylation is the most widely studied of epigenetic mechanisms, with environmental effects recorded through patterned attachments of methyl groups along the DNA that are capable of modifying gene expression without altering the DNA sequencing. The degree to which these patterns of DNA methylation are heritable, the expected range of normality across populations, and the phenotypic relevance of pattern variation remain unclear. Genes regulating metabolic pathways appear to be vulnerable to ongoing nutritional programming over the life course, as dietary nutrients are significant environmental determinants of DNA methylation, supplying both the methyl groups and energy to generate the methylation process.

Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.

The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations.

Mutation rates of 15 X chromosomal short tandem repeat markers.

Though allele frequency data for a variety of X chromosomal short tandem repeat (STR) markers in a range of populations have been reported, fewer studies of mutation rates in these same markers or populations are available. In order to address possible mismatches during kinship analysis due to mutation, a robust estimate of the rate of mutation must be established. Here, mutation rates in three US populations have been determined for a total of 15 markers (DXS6789, DXS9902, DXS7132, DXS7130, DXS6795, DXS10147, DXS8378, DXS7423, HPRTB, DXS101, DXS7424, GATA31E08, GATA172D05, GATA165B12, and DXS6803).

A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population.

When an STR DNA profile obtained from crime scene evidence does not match identified suspects or profiles from available databases, further DNA analyses targeted at inferring the possible ancestral origin and phenotypic characteristics of the perpetrator could yield valuable information. Single Nucleotide Polymorphisms (SNPs), the most common form of genetic polymorphisms, have alleles associated with specific populations and/or correlated to physical characteristics. We have used single base primer extension (SBE) technology to develop a 50 SNP assay (composed of three multiplexes) designed to predict ancestry among the primary U.

Immunoglobulin allotypes in Southwest Asia: populations at the crossroads.

Southwest Asia has a long history of contact with Central Asian and with Sub-Saharan African populations. Is the genetic structure of these populations reflective of these historical facts? To study this, data was generated on the immunoglobulin heavy chain (GM) and light chain (KM) allotypes from seven Arab and three non-Arab populations in SW Asia to examine the relationship of these populations to SE European, NW Indian, Sub-Saharan African, and Central Asian populations. Like mtDNA and Y chromosome markers, the GM haplotypes are largely continent specific making them an excellent tool for the detection of gene flow whereas the KM markers are less informative.

Development of a multiplex single base extension assay for mitochondrial DNA haplogroup typing.

Aim: To provide a screening tool to reduce time and sample consumption when attempting mitochondrial DNA (mtDNA) haplogroup typing.

Methods: A single base primer extension assay was developed to enable typing, in a single reaction, of twelve mtDNA haplogroup specific polymorphisms. For validation purposes a total of 147 samples were tested including 73 samples successfully haplogroup typed using mtDNA control region (CR) sequence data, 20 samples inconclusively haplogroup typed by CR sequence data, 21 samples previously haplogroup typed using RFLP analysis, and 31 samples of known ancestral origin without previous haplogroup typing.

Evaluation of Purkait's triangle method for determining sexual dimorphism.

The identification of sex from the skeleton is an important demographic assessment in medicolegal investigations. Rama Purkait developed a method for estimating sex using measurements from a triangle defined by three points on the proximal end of the femur using skeletal material from Bhopal, India. This method was tested with measurements on 200 Indo-European and African American adult femora from the Terry collection using discriminant function analysis to determine if Purkait's method was valuable for determining sex in Americans.

Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats.

Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method.

Expanding Southwest Pacific mitochondrial haplogroups P and Q.

Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3).

Immunoglobulin allotypes among Taiwan aborigines: evidence of malarial selection could affect studies of population affinity.

The aborigines of Taiwan represent the indigenous inhabitants of the island at the time of the arrival of the Chinese from the mainland. Linguistically, the aboriginal Taiwanese are related to the Malayo-Polynesian-speaking inhabitants of Indonesia and the Philippines. Three tribes occupied lowland areas while six tribes occupied highland areas.

Phylogenetic relationships of human populations in sub-Saharan Africa.

This study utilizes the GM/KM immunoglobulin allotype system to elucidate the phylogenetic relationships of sub-Saharan Africans. The importance of understanding the relatedness of these peoples stems from the sub-Saharan region being the possible birthplace of humans. Haplotype distributions were determined for 19 populations and compared using chi-square analysis.

Application of forensic DNA testing in the legal system.

DNA technology has taken an irreplaceable position in the field of the forensic sciences. Since 1985, when Peter Gill and Alex Jeffreys first applied DNA technology to forensic problems, to the present, more than 50,000 cases worldwide have been solved through the use of DNA based technology. Although the development of DNA typing in forensic science has been extremely rapid, today we are witnessing a new era of DNA technology including automation and miniaturization.

Distribution of the 3' VNTR polymorphism in the human dopamine transporter gene in world populations.

A polymorphism with a variable number of tandem repeats (VNTR) found in the 3' untranslated region of the human dopamine transporter gene (DAT1) was scored in unrelated individuals drawn from 10 geographically widely dispersed populations in order to assess this marker's usefulness in human population genetics. The populations that were analyzed in this study included 4 indigenous groups of Siberia, natives of North and South America, as well as Caucasian and Oceanic groups, most of which represented small-scale societies. A total of 5 DAT1 alleles were seen overall, but only in one Siberian population, the Altai-Kizhi, were all 5 present, and in the Native Americans of Colombia the locus was monomorphic.

Premature termination codon in the aggrecan gene of nanomelia and its influence on mRNA transport and stability.

Aim: To analyze the influence of the premature termination codon on mRNA transport and stability

Methods: Chondrocyte mRNA was isolated from homozygous and heterozygous nanomelic 17-days old embryos and examined by RT-PCR analysis. To analyze aggrecan mRNA stability, mRNA synthesis was inhibited with DRB [5,6 dichloro-1-(-D-ribofuranosyl benzimidazole)], a specific inhibitor of RNA polymerase II. Visualization of the aggrecan alleles was performed by in situ hybridization.

Deletion polymorphism in the human COL1A2 gene: genetic evidence of a non-African population whose descendants spread to all continents.

We report the frequencies of a deletion polymorphism at the alpha 2 (1) collagen gene (COL1A2) and argue that this distribution has major implications for understanding the evolution of modern humans immediately after their exodus from sub-Saharan Africa as well as their subsequent spread to all continents. The high frequency of the deletion in non-African populations and its complete absence in sub-Saharan African groups suggest that the deletion event occurred just before or shortly after modern humans left Africa. The deletion probably arose shortly after the African exodus in a group whose descendants were among the ancestors of all contemporary populations, except for sub-Saharan Africans.