A compilation of tri-allelic SNPs from 1000 Genomes and use of the most polymorphic loci for a large-scale human identification panel.

In a directed search of 1000 Genomes Phase III variation data, 271,934 tri-allelic single nucleotide polymorphisms (SNPs) were identified amongst the genotypes of 2,504 individuals from 26 populations. The majority of tri-allelic SNPs have three nucleotide substitution-based alleles at the same position, while a much smaller proportion, which we did not compile, have a nucleotide insertion/deletion plus substitution alleles. SNPs with three alleles have higher discrimination power than binary loci but keep the same characteristic of optimum amplification of the fragmented DNA found in highly degraded forensic samples. Although most of the tri-allelic SNPs identified had one or two alleles at low frequencies, often single observations, we present a full compilation of the genome positions, rs-numbers and genotypes of all tri-allelic SNPs detected by the 1000 Genomes project from the more detailed analyses it applied to Phase III sequence data. A total of 8,705 tri-allelic SNPs had overall heterozygosities (averaged across all 1000 Genomes populations) higher than the binary SNP maximum value of 0.5. Of these, 1,637 displayed the highest average heterozygosity values of 0.6-0.666. The most informative tri-allelic SNPs we identified were used to construct a large-scale human identification panel for massively parallel sequencing, designed for the identification of missing persons. The large-scale MPS identification panel comprised: 1,241 autosomal tri-allelic SNPs and 29 X tri-allelic SNPs (plus 46 microhaplotypes adapted for genotyping from reduced length sequences). Allele frequency estimates are detailed for African, European, South Asian and East Asian population groups plus the Peruvian population sampled by 1000 Genomes for the 1,270 tri-allelic SNPs of the final MPS panel. We describe the selection criteria, kinship simulation experiments and genomic analyses used to select the tri-allelic SNP components of the panel. Approximately 5 % of the tri-allelic SNPs selected for the large-scale MPS identification panel gave three-genotype patterns in single individual samples or discordant genotypes for genomic control DNAs. A likely explanation for some of these unreliably genotyped loci is that they map to multiple sites in the genome - highlighting the need for caution and detailed scrutiny of multiple-allele variant data when designing future forensic SNP panels, as such patterns can arise from common structural variation in the genome, such as segmental duplications.

Recent time trends in levels of self-reported anxiety, mental health service use and suicidal behaviour in Stockholm.

OBJECTIVE: To investigate recent time trends in several indicators of mental ill-health and the patterning of these indicators between genders and younger vs. older individuals in Stockholm County. METHOD: Several indicators were used; self-reported anxiety from the Swedish Survey of Living Conditions, information on psychiatric in-patient and out-patient care, attempted and completed suicides from national and regional registers. Gender- and age-specific trends were compared for the time period of 1997-2006. RESULTS: Self-reported anxiety and psychiatric service use increased among young individuals of both genders, while attempted suicides increased only among young women. By contrast, these indicators decreased or remained stable in the older age group from year 2001 and onwards. CONCLUSION: Our data indicate a rising, and highly prevalent, mental ill-health among the young in Stockholm County, a region representative of urbanized, secular Western societies.

Nutritional effects of the siege on new-born babies in Sarajevo.

OBJECTIVE: To investigate the influence of maternal nutrition on perinatal mortality, morbidity, malformations and low birth weight (< 2500 grams). DESIGN: All mothers and their babies born in Kosevo Hospital during three different time periods were sampled: September 1992 to February 1993 (pilot study), May 1993 to February 1994 (main study) and statistics compiled in 1991 (pre-war). SETTING: Data were collected at the gynaecology and obstetric clinic, Kosevo hospital, city of Sarajevo. SUBJECTS: A total of 920 babies were included in the pilot study, 1225 mothers of 1237 babies participated in the main study and birth data from 8676 babies born in 1991 were used as baseline data. INTERVENTIONS: Birth outcome data were compiled for all three time periods. In the main study, a questionnaire was administered on arrival at the clinic in which mothers were asked to estimate their weight prior to pregnancy. Information on energy and protein intake was collected for all women by estimating weekly food intake during pregnancy. Mothers were weighed and had their heights measured within 12 hours of delivery. Women were divided into three groups based on their body mass index (BMI) using self-reported prepregnancy weight (underweight BMI < 21.5; normal weight BMI 21.5-25.6; overweight BMI > 25.6). Four groups were defined according to dietary intake during pregnancy (daily energy intake < 2755 kcal and 2755 + kcal; protein intake < 80 and 80 + grams). RESULTS: Weight gain during pregnancy was low in overweight women (3.2 kg) compared with normal weight (10.4 kg) and underweight (11.7 kg) women. Underweight women had babies with the lowest mean birthweight (3072 grams) and the highest percentage of low birth weight babies (13.0%). Perinatal mortality increased from 15.8/1000 live births in 1991 (pre-war) to 36/1000 in May 1993-February 1994. Morbidity among babies increased from 3.4% to 8.2% in the same time period. There was a significant increase in babies born with malformations from 0.4% in the pre-war period to 3.0% in May 1993 to February 1994. CONCLUSIONS: It is concluded that the war has had a deleterious effect on birth outcomes in Sarajevo.

[Frequency of induced abortions in mid-pregnancy at the Gynecology and Obstetrics Clinic in Sarajevo 1993-1994]. / Ucestalost prekida visokih trudnoca na Klinici za ginekologiju i akuserstvo u Sarajevu, u periodu 1993-1994. godine.

During the two war years, higher pregnancies were interrupted by 133 patients either for medical, social or ethical causes. To induce abortions, 15 methyl prostaglandin F2 was used. In advance, portions had been prepared (softened) with cervical application of prepidil gel in dose of 0.5 g. Starting eight to ten hours later Prostin 15 M was applied every 3 hours in dose of 250 mg. An average period from gel application to expulsion of ovulum was 30 hours by nullipara and 21 hours by patients who have delivered a child before. Due to strong uterotonic activity of these medicaments side effects like nausea, vomiting, diarrhoea and prostration occurred several times. Serious complications were registered in 4 patients. Three of them suffered cervix rupture due either to insufficient preparation or external orifitium spasm. The fourth one had profuse bleeding due to secondary atonia. Ruptures were sutured and bleeding stopped with standard uterotonic and blood transfusion.

[Preoperative priming with Prepidil gel and laminaria in the first trimester of pregnancy]. / Preoperativni priming Prepidil gelom i laminarijama kod gravida u prvom trimestru trudnoce.

To study possibilities of prevention of late sequelae of first trimester dilatation and curettage, such as cervical incompetence, spontaneous abortions and premature deliveries in aftercoming pregnancies, we used cervical preoperative priming with Prepidil gel and laminariae. The study included 60 primigravidas who were 6-10 weeks pregnant. Six hours included preoperatively one subgroup was treated with laminariae intracervically. Success of cervical priming was compared with so called ideal cervical score. In relation to such criteria the success in Prepidil group was 88%, and in laminaria group 82%. This difference was not significant. It could be concluded that preoperatively undertaken cervical priming with prostaglandins and laminariae successfully increased cervical score, cervical resistance being reduced in that way. In this gestational period such priming makes abortion less dangerous procedure and it lessens the possibility of different early and late complications of first trimester dilatation and curettage.

[Urinary infections during pregnancy and methods of prevention]. / Urinarne infekcije u trudnoci i mjere prevencije.

Urinary tract infections in pregnant women develop owing to the short urethra in women, mechanical pressure of the uterus onto atonic urethra during pregnancy, atony of the urinary bladder caused by the level of progesterone, iatrogenic factors (catheterization), some metabolic disorders, anemia, obstipation etc. These are frequent reasons why pregnant women over the pregnancy period develop infections of urinary tract, where a significant number of them have bacteriuria showing no symptoms of acute infection whatsoever. The research covered unselectively 4,850 urine samples of pregnant women. The results obtained by classical methods--taking urinoculture and doing antibiogramme--have shown that in this sample there is a large number of asymptomatic bacteria (13%), which is complicated by an increased incidence of pyelonephritis gestoses in the second half of the pregnancy. In our sample, the commonest cause of urinary infections has been E. Coli, then the second trimester of risk gestation period; the risk group with regard to parity are primiparas, while the risk age is between 20 and 29.