Variant alleles, triallelic patterns, and point mutations observed in nuclear short tandem repeat typing of populations in Bosnia and Serbia

Aim

To present a compendium of off-ladder alleles and other genotyping irregularities relating to rare/unexpected population genetic variation, observed in a large short tandem repeat (STR) database from Bosnia and Serbia.

Methods

DNA was extracted from blood stain cards relating to reference samples from a population of 32 800 individuals from Bosnia and Serbia, and typed using Promega’s PowerPlex®16 STR kit.

Results

There were 31 distinct off-ladder alleles were observed in 10 of the 15 STR loci amplified from the PowerPlex®16 STR kit. Of these 31 alleles, 3 have not been previously reported. Furthermore, 16 instances of triallelic patterns were observed in 9 of the 15 loci. Primer binding site mismatches that affected amplification were observed in two loci, D5S818 and D8S1179.

Conclusion

Instances of deviations from manufacturer’s allelic ladders should be expected and caution taken to properly designate the correct alleles in large DNA databases. Particular care should be taken in kinship matching or paternity cases as incorrect designation of any of these deviations from allelic ladders could lead to false exclusions.Commercial kits for forensic short tandem repeat (STR) multiplexes include allelic ladders that assist the user in allele designation by co-migrating with any commonly expected allelic variants in the population (1). In the selection of loci and other steps in the development of commercial STR kits, huge amounts of effort are put into screening population genetic variation to ensure that the locus varies in a simple and easy-to-interpret manner, and that allele frequencies are known for statistical interpretation. Allelic ladders are based on variation observed in the development process, but, inevitably, when large population samples are typed, variants are encountered that were not represented in the developmental screening. This is particularly true when the populations under testing differ from those that were studied during kit development.Practitioners of forensic STR typing need to be aware of the possibility of rare variants, so the variants can be recognized and dealt with properly in casework interpretation. If designated correctly, variant alleles can sometimes greatly increase the power of discrimination in DNA comparisons (2). In this regard, it is important that the forensic science community share information on the occurrence of these variants. In some contexts, these variants may actually occur rather commonly, and public documentation of their occurrence can save individual investigators much time and effort (3).Unexpected or “anomalous” genetic variation that can complicate STR typing takes a number of forms, with a variety of consequences on the testing results. New length variants not represented on the allelic ladder can be due to insertion/deletions of full repeat units, or to “microvariants” differing due to the insertion/deletion of single bases or partial repeats (2,4-6). In some cases, larger or smaller off-ladder alleles may fall within the allelic ladder of an adjacent locus (5,6), with the potential for significant confusion. Triallelic patterns (7-9) can be due to length mutations that occur and segregate during an individual’s development, or to localized duplication of a locus, or to chromosomal trisomy. Sequence variation, rather than length variation, can also have effects, particularly in the case of sequence differences in the amplification primer binding sites. Primer mismatches can result in complete amplification failure and cause null alleles, or can lower the peak height of affected alleles (10-18). Any of these anomalies can cause problems during interpretation of results if the analysts are not familiar with these occurrences.The International Commission on Missing Persons (ICMP) was founded in 1996 to address the issue of persons missing as a result of the conflicts that occurred during the breakup of the former Yugoslavia during the 1990s. DNA profiles are obtained from reference samples collected from living relatives which are entered into a DNA reference database (currently greater than 80 000 unique profiles). Likewise, DNA profiles generated from skeletal remains recovered from grave sites are entered into a missing persons DNA database (currently containing more than 12 000 unique profiles). Both databases are screened against each other on a daily basis, resulting in possible kinship matches.We report here a new compendium of all off-ladder variants/microvariants, primer binding site mutations, and instances of triallelic patterns that have been observed in a subset of the ICMP blood sample reference database representing ~ 32 800 individuals from Bosnia and Serbia, including Kosovo.     

Pattern of cancers in adolescent and young adults.: A 15-year retrospective study at King Fahad Hospital,Al-Madinah Al-Munawwarah,Saudi Arabia

Objectives:To evaluate the incidence and pattern of cancer in adolescents and young adults (AYAs) age group in Al-Madinah Al-Munawwarah region of Saudi Arabia.Methods:This retrospective histopathology-based study was conducted at a tertiary care center in Al-Madinah Al-Munawwarah, Saudi Arabia and comprised cases of cancers for 15 years between January 2006 and December 2020.Results:During the last 15-year period, 8,769 cases of cancers were diagnosed out of which 475 (5.4%) cases were registered in AYAs. Of these cases, 232 (48.8%) were males while 243 (51.2%) were females, with a male-to-female ratio of 0.9:1. The 3 most common cancer groups in the entire cohort were carcinomas (n=165; 34.7%), lymphomas (n=135; 28.4%), and leukemias (n=91; 19.2%). The most common sites in carcinomas were thyroid (n=60; 12.6%), breast (n=35; 7.4%), and gastrointestinal (n=18; 3.8%). The leading cancers in males were the lymphomas (n=74; 15.6%), leukemias (n=57; 12%), bone (n=21; 4.4%), and central nervous system (n=20; 4.2%), while in females, the most common cancers were the lymphomas (n=61; 12.8%), thyroid (n=40; 8.4%), breast (n=34; 7.2%), and leukemias (n=34; 7.2%).Conclusion:Our findings are in concordance with studies in national and international literature and we believe that our study provides a baseline tool for future population-targeted studies.     

Management of completely displaced extention type supracondylar fractures of humerus in children based on a new classification

Background

Paediatric supracondylar fractures are the most common childhood fractures under 8 years of age. Displaced paediatric supracondylar fractures are mostly classified on the basis of fracture geometry and none of the classification systems takes the clinical condition of the limb into consideration.

Incidence and importance of reflux in testicular veins of healthy men evaluated with color duplex sonography

PURPOSE: Reflux in the testicular veins plays a crucial role in the diagnosis of a varicocele. The aim of this study was to evaluate the incidence and the sonographic features-duration and velocity-of reflux in testicular veins of healthy men using color duplex sonography (CDS). METHODS: Healthy male volunteers, 18-45 years old, whose physical examinations and semen analyses were normal, were recruited for this study. The maximum diameters of testicular veins during both normal respiration and Valsalva's maneuver were measured by CDS using a 7.5-MHz linear-array transducer. Veins greater than 2 mm in diameter were considered to be a varicocele, and the subjects in these cases were excluded from the analysis. In cases in which reflux was present, the velocity and duration of reflux in the testicular veins during Valsalva's maneuver were measured. RESULTS: Seventy men, whose mean (+/- standard deviation) age was 27 +/- 7 years, were enrolled in this study. Fourteen of the 70 patients had a left varicocele and thus were excluded from the analysis. Of the 112 hemiscrotums in the remaining 56 patients, 61 (54%) had reflux induced by Valsalva's maneuver and 51 (46%) did not. Twenty-two (39%) of refluxes were on the right side, with a mean duration of 1.1 +/- 0.5 seconds, and a mean velocity of 4.2 +/- 2.1 cm/second; 39 (70%) of the refluxes were on the left side, with a mean duration of 1.1 +/- 0.5 seconds and a mean velocity of 4.9 +/- 2.3 cm/second. The incidence of reflux was significantly higher on the left side (p = 0.003). The duration and velocity of the reflux did not differ significantly between the right and left sides. The difference in the testicular vein diameters between the right (1.3 +/- 0.2 mm; n = 56) and left (1.6 +/- 0.2 mm; n = 56) sides was statistically significant (p < 0.001). CONCLUSIONS: Normal-sized testicular veins in healthy subjects had a remarkably high incidence of reflux induced by Valsalva's maneuver. The presence of reflux in subfertile men with normal testicular vein diameters is a diagnostic criterion, but it is necessary to quantify the reflux to prevent misdiagnosis of a varicocele and unnecessary surgery. The measurement of the duration and velocity limits of reflux in a large series of subjects may provide a reliable indicator for the diagnosis of varicocele.     

Statistical Study of Nonthermal Plasma-Assisted ZnO Coating of Cotton Fabric through Ultrasonic-Assisted Green Synthesis for Improved Self-Cleaning and Antimicrobial Properties

Nonthermal plasma processing is a dry, environment-friendly and chemical-free method of improving the wettability, adhesion, self-cleaning and dying quality of fabrics without affecting their bulk properties. This study presents a green synthesis and coating method for the immobilization of nanoparticles of ZnO on the nonthermal plasma functionalized cotton fabric. The self-cleaning activity of ZnO-coated cotton was then optimized statistically. The ultraviolet protection and antimicrobial activity of the optimized and a control sample were also elaborated in this study. Psidium guajava Linn (guava) plant extract and zinc chloride were used in the ultrasonic biosynthesis of ZnO nanoparticles and concurrent immobilization over plasma functionalized cotton. Sodium hydroxide was used as a reaction accelerator. Statistical complete composite design (CCD) based on the amount of ZnCl₂, NaOH and plasma exposure time was used to optimize the role of input parameters on the self-cleaning ability of the coated cotton. Methylene blue in water was used as a sample pollutant in the self-cleaning study. The ZnO-coated cotton showed notably high self-cleaning activity of 94% and a UV protection factor of 69.87. The antimicrobial activity against E. Coli and S. Aureus bacteria was also appreciably high compared to the control.     

The factors influencing peripapillary choroidal thickness in primary open-angle glaucoma

Purpose

To investigate whether there is a difference between primary open-angle glaucoma (POAG) patients and control group with regard to choroidal thickness (CT) and the factors influencing CT.

Methods

Ninety eyes of 90 patients who were being followed up with POAG and 72 eyes of 72 healthy subjects matched for age and gender were included. Peripapillary retinal nerve fiber layer thickness (RNFLT), peripapillary CT, lamina cribrosa thickness (LCT), and prelaminar tissue thickness (PTT) were measured with spectral-domain optical coherence tomography (SD-OCT) enhanced depth imaging (EDI) in all patients.

Results

According to multi-variable linear regression analysis results, the factors influencing CT were found as axial length (AL) (B = ?22.78, p = 0.002), intraocular pressure (IOP) (B = ?7.95, p = 0.001), age (B  = ?1.77, p = 0.009), and radial pulse rate (B  = 1.42, p = 0.015). A statistically significant relationship was not detected between CT and central corneal thickness, mean deviation value of visual field, cup/disk ratio, RNFLT, LCT, PTT. CT was found significantly thinner in glaucoma group (147.5 ± 61.2 μm) compared to control group (167.1 ± 37.3 μm). However, IOP was found significantly higher (p < 0.001) and pulse rate was found significantly lower (p = 0.021) in POAG group. IOP and pulse rate were considered to have affected CT difference between the groups. In advanced and worser stage patients, there were significant positive correlations between CT and RNFLT in inferior and superior quadrants.

Conclusions

In addition to previous studies, IOP and pulse rate were detected to be effective on CT. Further studies are required for determining the whole factors effective on CT and better understanding CT and glaucoma relationship.

     

Two cases of subacute sclerosing panencephalitis associated with brainstem involvement

The most commonly involved areas in subacute sclerosing panencephalitis (SSPE) are periventricular and subcortical white matter. The basal ganglia, cerebellum, spinal cord and corpus callosum are less commonly involved. Brainstem involvement is rare and usually accompanied by other intracranial lesions. In this article, we report two cases of SSPE associated with brainstem involvement. The first case a 9-year-old girl had the typical symptom of SSPE. Magnetic resonance imaging (MRI) of the brain revealed a focal lesion 2 x 2.5 cm a diameter in the pons. The second case was a 6-year-old girl. On admission, MRI of the brain was normal. During 6th month of follow-up, T2-weighted MRI showed a hyperintense lesion in the pons and pedincule of cerebellum. On account of these cases we would like to stress that brainstem involvement may be seen in patients with SSPE; therefore, these patients should be monitored for this disorder.