Oliver Stojkovic

Y-STR profiling in two Afghanistan populations.

Afghanistans unique geostrategic position in Eurasia has historically attracted commerce, conflict and conquest to the region. It was also an important stop along the Silk Road, connecting the far eastern civilizations with the western world. Nevertheless, limited genetic studies have been performed in Afghan populations. In this study, 17 Y-chromosomal short tandem repeat (Y-STR) loci were typed to evaluate their forensic and population genetic applications in 189 unrelated Afghan males geographically partitioned along the Hindu Kush Mountain range into north (N=44) and south (N=145) populations. North Afghanistan (0.9734, 0.9905) exhibits higher haplotype diversity than south Afghanistan (0.9408, 0.9813) at both the minimal 9-loci and 17-loci Yfiler haplotypes, respectively. The overall haplotype diversity for both Afghan populations at 17 Y-STR loci is 0.9850 and the corresponding value for the minimal 9-loci haplotypes is 0.9487. A query using of the most frequent Afghan Yfiler haplotype (7.98%) against the worldwide Y-STR haplotype reference database (YHRD) returned no profile match, indicating a high power of discrimination with 17 Y-STR loci. A median-joining network based on 15 Y-STR loci displays limited haplotype sharing between the two Afghan populations, possibly due to the Hindu Kush Mountain range serving as a natural barrier to gene flow between the two regions.

Human Y-Chromosome Short Tandem Repeats: A Tale of Acculturation and Migrations as Mechanisms for the Diffusion of Agriculture in the Balkan Peninsula

Southeastern Europe and, particularly, the Balkan Peninsula are especially useful when studying the mechanisms responsible for generating the current distribution of Paleolithic and Neolithic genetic signals observed throughout Europe. In this study, 404 individuals from Montenegro and 179 individuals from Serbia were typed for 17 Y-STR loci and compared across 9 Y-STR loci to geographically targeted previously published collections to ascertain the phylogenetic relationships of populations within the Balkan Peninsula and beyond. We aim to provide information on whether groups in the region represent an amalgamation of Paleolithic and Neolithic genetic substrata, or whether acculturation has played a critical role in the spread of agriculture. We have found genetic markers of Middle Eastern, south Asian and European descent in the area, however, admixture analyses indicate that over 80% of the Balkan gene pool is of European descent. Altogether, our data support the view that the diffusion of agriculture into the Balkan region was mostly a cultural phenomenon although some genetic infiltration from Africa, the Levant, the Caucasus, and the Near East has occurred.

CTG repeat polymorphism in DMPK gene in healthy Yugoslav population.

Objectives– Myotonic dystrophy type 1 (DM1) is caused by large expansions of cytosine‐thymine‐guanine (CTG)‐repeats in myotonic dystrophy protein kinase (DMPK)‐gene. This gene is highly polymorphic in healthy individuals. It has been proposed that expanded alleles originated from the group of large sized normal alleles. If this is correct, one should expect a positive correlation between the frequency of large sized normal alleles and a prevalence of this disorder in a population. In this paper we determined the distribution of alleles of DMPK gene in healthy Yugoslav population. Material and methods– A sample of 235 healthy individuals of Yugoslav origin have been genotyped for the alleles of DMPK locus. Results– We found 22 different alleles, ranging in size from 5 to 29 repeats. Among 470 chromosomes studied, 41 chromosomes had more than 18 repeats (8.72%). Conclusions– Relatively high frequency of large sized normal alleles found in our population, suggest that prevalence of DM1 in Yugoslavia should not be different from the prevalence in other European populations.

Y-STR diversity in the Himalayas

Linguistic and ethnic diversity throughout the Himalayas suggests that this mountain range played an important role in shaping the genetic landscapes of the region. Previous Y-chromosome work revealed that the Himalayas acted as a biased bidirectional barrier to gene flow across the cordillera. In the present study, 17 Y-chromosomal short tandem repeat (Y-STR) loci included in the AmpFlSTR® Yfiler kit were analyzed in 344 unrelated males from three Nepalese populations (Tamang, Newar, and Kathmandu) and a general collection from Tibet. The latter displays the highest haplotype diversity (0.9990) followed by Kathmandu (0.9977), Newar (0.9570), and Tamang (0.9545). The overall haplotype diversity for the Himalayan populations at 17 Y-STR loci was 0.9973, and the corresponding values for the extended (11 loci) and minimal (nine loci) haplotypes were 0.9955 and 0.9942, respectively. No Y-STR profiles are shared across the four Himalayan collections at the 17-, 11-, and nine-locus resolutions considered, indicating a lack of recent gene flow among them. Phylogenetic analyses support our previous findings that Kathmandu, and to some extent Newar, received significant genetic influence from India while Tamang and Tibet exhibit limited or no gene flow from the subcontinent. A median-joining network of haplogroup O3a3c-M134 based on 15 Y-STR loci from our four Himalayan populations suggests either a male founder effect in Tamang, possibly from Tibet, or a recent bottleneck following their arrival south of the Himalayas from Tibet leading to their highly reduced Y single-nucleotide polymorphism and Y-STR diversity. The genetic uniqueness of the four Himalayan populations examined in this study merits the creation of separate databases for individual identification, parentage analysis, and population genetic studies.

Y-chromosomal microsatellite diversity in three culturally defined regions of historical Tibet

In the present study, we analyzed 17 Y-STR loci in 350 Tibetan males from three culturally defined regions of historical Tibet: Amdo (88), Kham (109) and U-Tsang (153). A total of 299 haplotypes were observed, 272 (90.9%) of which were unique. Only one Y-STR profile is shared across the three Tibetan groups and, incidentally, is also the most frequent haplotype (4.0%), represented by two, five and seven individuals from U-Tsang, Kham and Amdo, respectively. The overall haplotype diversity for the three Tibetan populations at 17 Y-STR loci was 0.9978 and the corresponding values for the extended (11-loci) and minimal (9-loci) haplotypes were 0.9935 and 0.9909, respectively. Both neighbor-joining and Rst pairwise analyses suggest a close genetic relationship between the Amdo and Kham populations, while U-Tsang is genetically distinct from the aforementioned groups. The results demonstrate that the 17 Y-STR loci analyzed are highly polymorphic in all three Tibetan populations examined and hence useful for forensic cases, paternity testing and population genetic studies.

Divergent patrilineal signals in three Roma populations.

Previous studies have revealed that the European Roma share close genetic, linguistic and cultural similarities with Indian populations despite their disparate geographical locations and divergent demographic histories. In this study, we report for the first time Y-chromosome distributions in three Roma collections residing in Belgrade, Vojvodina and Kosovo. Eighty-eight Y-chromosomes were typed for 14 SNPs and 17 STRs. The data were subsequently utilized for phylogenetic comparisons to pertinent reference collections available from the literature. Our results illustrate that the most notable difference among the three Roma populations is in their opposing distributions of haplogroups H and E. Although the Kosovo and Belgrade samples exhibit elevated levels of the Indian-specific haplogroup H-M69, the Vojvodina collection is characterized almost exclusively by haplogroup E-M35 derivatives, most likely the result of subsequent admixture events with surrounding European populations. Overall, the available data from Romani groups points to different levels of gene flow from local populations.

Correlation between triplet repeat expansion and computed tomography measures of caudate nuclei atrophy in Huntington’s disease

Abstract Huntington’s disease (HD) is an autosomal dominant, progressive disorder characterized by choreic movements, cognitive decline, and psychiatric manifestations. Eleven patients with HD were retrospectively selected from a larger group of 42 patients based on the similar, early onset of the disease (between 21 and 30 years) and the same duration of HD at the moment of computed tomography (CT) examination (5 years). A significant correlation between the number of CAG trinucleotides and the bicaudate index or the frontal horn index, two indices of caudate atrophy, was found in this group of patients. Our results, although in a small number of patients, suggest that the striatal degeneration, assessed by CT measures, is primarily regulated by the size of expanded CAG repeats.

PREVALENCE OF THE FRAGILE X SYNDROME IN YUGOSLAV PATIENTS WITH NON-SPECIFIC MENTAL RETARDATION

Mutations at two fragile sites, FRAXAand FRAXE, loci are caused by an expansion of a CGG/GCC trinucleotide repeat and are characterized by mental retardation. Here we report molecular screening survey of 97 unrelated individuals diagnosed with non-specific mental retardation (MR), which produced positive test for FRAXAin two boys and none positive for the FRAXEmutation. In addition, we studied allelic frequency distribution for the FRAXAlocus in this group of mentally retarded patients, as well as in the 99 healthy subjects of Yugoslav population. The distribution of FMR1CGG repeat size in both groups was similar: the most common allele contained 29 repeats (32.86% in the healthy population and 54.54% in MR population), followed by the allele with 28 CGG repeats (21.43% in the healthy and 12.2% in MR population). Premutation alleles with more than 45 repeats were not found in control nor in the MR group.

The Status of SCA1, MJD/SCA3, FRDA, DRPLA and MD Triplet Containing Genes in Patients with Huntington Disease and Healthy Controls

A number of human hereditary neuromuscular and neurodegenerative disorders are caused by the expansion of trinucleotide repeats within certain genes. Here we report the results of the analysis of five trinucleotide repeats containing genes (SCA1, MJD/SCA3, DRPLA, FRDA and MD) in HD patients and in a group of healthy controls. Allelic frequency distributions for SCA1 and FRDA genes were shifted toward larger alleles in the group of unrelated HD patients, compared to healthy controls. This linkage disequilibrium suggests a possible existance of a common mechanism of trinucleotide repeats expansion in these loci.

Prediction of autosomal STR typing success in ancient and Second World War bone samples

Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is concluded that STR typing of old bones after quantification with the PowerQuant should be performed only when both Auto and Deg targets are detected simultaneously with no respect to [Auto]/[Deg] ratio. Prediction of STR typing success could be made according to successful amplification of Deg fragment. The PowerQuant kit is capable of identifying bone DNA samples that will not yield useful STR profiles using the NGM kit, and it can be used as a predictor of autosomal STR typing success of bone extracts obtained from ancient and WWII skeletal remains.