Genomic analyses inform on migration events during the peopling of Eurasia.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets.

A Novel Mutation in a Kazakh Family with X-Linked Alport Syndrome.

Alport syndrome is a genetic condition that results in hematuria, progressive renal impairment, hearing loss, and occasionally lenticonus and retinopathy. Approximately 80% of Alport syndrome cases are caused by X-linked mutations in the COL4A5 gene encoding type IV collagen. The objective of this study was to define the SNP profiles for COL4A5 in patients with hereditary nephritis and hematuria.

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck.

Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in inhabitants of Astana, the capital city of Kazakhstan.

Background: Kazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations.

Methodology/principal Findings: A total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci.

Behçet's disease in HLA-B*51 negative Germans and Turks shows association with HLA-Bw4-80I.

Introduction: Behçet's disease (BD) as systemic vasculitis of unknown etiology is associated with HLA-B*51 in European and Asian populations. HLA-A*26 was claimed as an additional BD susceptibility marker in Japanese and Greek patients. This study was performed to test for HLA associations in HLA-B*51 negative German and Turkish BD populations.

Estrogen Receptor Gene (ESR1) PVUII and XBAI Polymorphisms and Bone Mineral Density in Kazakh Women.

Introduction: Osteoporosis is a common age-related disease that is strongly influenced by genetics. Polymorphisms of the estrogen receptor gene alpha (ESR1) are consistently been associated with bone mineral density (BMD) and fracture.The purpose of this investigation was to evaluate potential association of single nucleotide polymorphism (SNP) variants of the ESR1 gene and bone mineral density (BMD) of the lumbar spine in Kazakh women.

The need for standardized biobanks in Kazakhstan.

Biobanks are an important tool for clinical and research studies conducted on biomarkers of genetic therapy, diagnostic tests and new drugs; however, most biobanks remain incomplete and are often used without uniform standards and criteria. There is also a a lack of high-quality biological samples and many bioethical problems are often overlooked. Currently, Kazakhstan has no standard requirements and protocols for biomedical organizations.

Vitamin D Receptor Gene Polymorphisms and Breast Cancer Risk in Kazakhstan.

Introduction: The steroid hormone 1,25-dihydroxyvitamin D3 is thought to protect against breast cancer. The activity of 1,25-dihydroxyvitamin D3 is mediated via the vitamin D receptor (VDR), and a number of polymorphisms in the gene have been identified. These result in distinct genotypes, some of which may alter susceptibility to breast cancer.

Pharmacogenetic research in Kazakhstan.

Introduction: Pharmacogenomics is an emerging field of medicine that combines genetics and pharmacology. Pharmacogenomic research is relatively new in Kazahkstan, but, in recent years, significant progress has been made in this field. The National Scientific Laboratory for Biotechnology has launched several government-funded research projects focused on finding genetic markers that determine susceptibility to various drugs.

Frequency of NAT2 and GSTP1 polymorphisms in the Kazakh population.

Introduction: Phase II xenobiotic biotransformation enzymes perform detoxification of hydrophilic and often toxic Phase I products through glutathionetransferase (GST), UDP-glucuronosyltransferase (UDF), N-acetyltransferase (NAT) families and other enzymes. GST protein families metabolize a large number of electrophilic xenobiotics, by conjugating fusing them with glutathione. Arylamine-N-acetyltransferase (NAT) catalyzes the acetylation of the aromatic and heterocyclic amines.

Draft Genome Sequence of the Live Vaccine Strain Brucella abortus 82.

Vaccination is a crucial part of the brucellosis eradication programs worldwide. A live vaccine strain of Brucella abortus 82 has been successfully used for the vaccination of cattle against brucellosis in the former Soviet republics for the last 39 years. Here, we report the genome sequence of Brucella abortus 82.

Draft Genome Sequence of Rhodococcus erythropolis DN1, a Crude Oil Biodegrader.

We report the 6,548-Mb genome sequence of Rhodococcus erythropolis strain DN1, isolated from the oil-contaminated soil in the Karagandy region of Kazakhstan. The draft genome sequence of strain DN1 might provide new insights into the genetic mechanisms of crude oil biodegradation.

Genetic profile and determinants of homocysteine levels in Kazakhstan patients with breast cancer.

Aim: To analyze associations between homocysteine level, MTHFR and FTO rs1477196 polymorphisms and folate status in patients with breast cancer (BC) in order to clarify determinants of hyperhomocysteinemia.

Patients And Methods: The study included 315 BC cases and 604 controls.

Results: The MTHFRC677T genotype was associated with an increased incidence of BC [Odds ratio (OR)=1.

Complete Genome Sequences of Helicobacter pylori Rifampin-Resistant Strains.

Here we present the complete genome sequences of two Helicobacter pylori rifampin-resistant (Rif(r)) strains (Rif1 and Rif2). Rif(r) strains were obtained by in vitro selection of H. pylori 26695 on agar plates with 20 µg/ml rifampin.

and Gene Mutations Screening In Sporadic Breast Cancer Patients In Kazakhstan.

Background: A large number of distinct mutations in the and genes have been reported worldwide, but little is known regarding the role of these inherited susceptibility genes in breast cancer risk among Kazakhstan women.

Aim: To evaluate the role of BRCA1/2 mutations in Kazakhstan women presenting with sporadic breast cancer.

Methods: We investigated the distribution and nature of polymorphisms in and entire coding regions in 156 Kazakhstan sporadic breast cancer cases and 112 age-matched controls using automatic direct sequencing.

Molecular characterization of rifampicin- and isoniazid-resistant Mycobacterium tuberculosis strains isolated in Kazakhstan.

Kazakhstan is one of the 14 countries with a high rate of morbidity due to multidrug-resistant tuberculosis (MDR TB) in WHO European region. The aim of our study was to characterize mutations associated with drug resistance to rifampicin and isoniazid in Mycobacterium tuberculosis isolates from Kazakhstan. M.

Application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the study of Helicobacter pylori.

The characteristics of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry based investigation of extremely variable bacteria such as Helicobacter pylori were studied. H. pylori possesses a very high natural variability.

Functional divergence of Helicobacter pylori related to early gastric cancer.

Helicobacter pylori is an extra macro- and microdiverse bacterial species, but where and when diversity arises is not well-understood. To test whether a new environment accelerates H. pylori genetic changes for quick adaptation, we have examined the genetic and phenotypic changes in H.

Phenylethynylpyrene excimer forming hybridization probes for fluorescence SNP detection.

Excimer formation is a unique feature of some fluorescent dyes (e.g., pyrene) which can be used for probing the proximity of biomolecules.

Comparative genome analysis of Ureaplasma parvum clinical isolates.

Ureaplasma parvum colonizes human mucosal surfaces, primarily in the respiratory and urogenital tracts, causing a wide spectrum of diseases, from non-gonococcal urethritis to pneumonitis in immunocompromised hosts. Although the basis for these diverse clinical outcomes is not yet understood, more severe disease may be associated with strains harboring a certain set of strain-specific genes. To investigate this, whole genome DNA macroarrays were constructed and used to assess genomic diversity in 10 U.

Coexpressionfinder: a new algorithm for finding groups of coexpressed genes.

Results: A new algorithm is developed which is intended to find groups of genes whose expression values change in a concordant manner in a series of experiments with DNA arrays. This algorithm is named as CoexpressionFinder. It can find more complete and internally coordinated groups of gene expression vectors than hierarchical clustering.

Phenylethynylpyrene-labeled oligonucleotide probes for excimer fluorescence SNP analysis of 23S rRNA gene in clarithromycin-resistant Helicobacter pylori strains.

The use of phenylethynylpyrene excimer forming pair in the design of specific fluorescent probes for determination of A2144G (A2143G and/or A2143C) mutations in 23S rRNA gene of Helicobacter pylori is described. Analysis of fluorescence spectra of model duplexes revealed optimal positions of fluorophore residues in the probe sequences for maximum efficiency of SNP detection. Application of excimer forming probes for analysis of DNA samples isolated from natural bacterial strains of H.