A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures

Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture’s genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.

Association of BglII Polymorphism in ITGA2 and (894G/T and −786T/C) Polymorphisms in eNOS Gene With Stroke Susceptibility in Tunisian Patients α2 Gene Polymorphism in α2β1 Integrin and eNOS Gene Variants and Stroke

Background: This study investigated the association of BglII polymorphism in α2β1 integrin gene ( ITGA2) and eNOS (894G/T and –786T/C) polymorphisms with ischemic stroke (IS) in Tunisian patients. Methods: The study comprised 210 patients with IS and 208 controls. The genotypes of the BglII polymorphism in ITGA2 and eNOS (894G/T and –786T/C) polymorphisms were determined using the PCR-RFLP. The χ2 test was used and the genotype data comparison included heterozygous groups. Haplotype estimation and multiple logistic regression analysis were performed to analyze the significance of polymorphisms. Results: The genotype distribution of the BglII polymorphism was significantly different between cases and controls ( p < 0.004). This polymorphism was associated with the risk of IS ( OR = 3.38, p < 0.001) for the BglII(+/+) genotype. Likewise, the genotype distributions of eNOS (894G/T and –786T/C) polymorphisms were significantly different between the two groups ( p < 0.005 and p < 0.01, respectively). The 894G/T polymorphism increased the risk of IS for the TT genotype ( OR = 2.23, p < 0.008) and the GT genotype ( OR = 1.74, p < 0.009). In addition, the –786T/C variant in the eNOS gene was a risk factor for IS for CC homozygous ( OR = 2.52, p < 0.005). T-C Haplotype ( OR = 3.06) from combination of the eNOS (894G/T and –786T/C) and T-C- BglII(+) haplotype ( OR = 2.76) from combination of eNOS and ITGA2 polymorphisms represented high risks for IS. Conclusions: This study suggests that the BglII variant in ITGA2 is associated with IS susceptibility. Furthermore, the 894G/T and –786T/C polymorphisms in the eNOS gene may be considered as genetic risk factors for IS in the Tunisian population.

Association of multiple nucleotide variations in the pituitary glutaminyl cyclase gene QPC with low radial BMD in adult women.

Correlation between 13 genetic variations of the glutaminyl-peptide cyclotransferase gene andadjusted aBMD was tested among 384 adult women. Among 13 variations with strong linkage disequilibrium,R54W showed a prominent association (p ? 0.0003), which was more striking when examined among 309 eldersubjects (&gt;50 years; p ? 0.0001). Contribution for postmenopausal bone loss was suggested.Introduction: Alterations in homeostatic regulation of estrogen through the hypothalamus-pituitary-gonadal axis(HPG axis) importantly affect the pathogenesis of osteoporosis. Osteoporosis-susceptibility genes have beenproposed in this hormonal axis, such as estrogen receptor genes and the gonadotropin-releasing hormone gene(GnRH). Here we report another example of genes: glutaminyl-peptide cyclotransferase gene (QPCT), an essentialmodifier of pituitary peptide hormones, including GnRH.Materials and Methods: Analyses of association of 13 single nucleotide polymorphisms (SNPs) at the QPCT locuswith adjusted areal BMD (adj-aBMD) were carried out among 384 adult women. Linkage disequilibrium (LD) wasanalyzed by haplotype estimation and calculation of D? and r2. Multiple regression analysis was applied forevaluating the combined effects of the variations.Results and Conclusions: LD analysis indicated strong linkage disequilibrium within the entire 30-kb region of theQPCT gene. Significant correlations were observed between the genotypes of the six SNPs and the radial adj-aBMD,among which R54W (nt ? 160C?T) presented the most prominent association (p ? 0.0003). Striking associationwas observed for these SNPs among the 309 subjects ?50 years of age (R54W, p ? 0.0001; ?1095T?C, p ?0.0002; ?1844C?T, p ? 0.0002). Multiple regression analyses indicated that multiple SNPs in the gene might actin combination to determine the radial adj-aBMD. These results indicate that genetic variations in QPCT are theimportant factors affecting the BMD of adult women that contribute to susceptibility for osteoporosis. The datashould provide new insight into the etiology of the disease and may suggest a new target to be considered duringtreatment.J Bone Miner

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

Background The allele and haplotype frequencies of HLA loci are various in the populations. Most of the data for HLA alleles and haplotypes were at low resolution or two fields resolution. Here, the data for HLA alleles and haplotypes at three fields resolution was reported in Chinese Han population. Methods All samples were come from the Zhejiang Cord Blood Bank, China after information consent. HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci was genotyped using next generation sequencing (NGS) method. The allele frequencies of HLA loci were analyzed at three fields resolution. The haplotype estimation and linkage disequilibrium analysis was used Arlequin software 3.5.2.2. Result The top three frequent alleles of HLA-A, -B, -C, -DRB1, -DQB1 loci were A*11:01:01 (25.81%), A*24:02:01 (16.70%), A*02:01:01 (10.61%); B*40:01:02 (15.97%), B*46:01:01 (11.48%), B*58:01:01 (7.96%); C*07:02:01 (19.03%), C*01:02:01 (17.65%), C*03:04:01 (10.41%); DRB1*09:01:02 (17.96%), DRB1*12:02:01 (9.57%), DRB1*08:03:02 (9.54%); DQB1*03:01:01(21.05%), DQB1*03:03:02 (19.15%), DQB1*06:01:01 (12.08%); DRB4*01:03:01(25.72%), DRB3*02:02:01(20.27%), DRB5*01:01:01(10.96%) respectively. A total of 1542 distinct A-B-C-DRB1-DQB1-DRB3/4/5 haplotypes were identified. The alleles of HLA loci were showed strong linkage disequilibrium. Conclusion The data of allele and haplotype of HLA-A, -B, -C, -DRB1, -DQB1 and -DRB3/4/5 loci at three fields resolution level was obtained, which will help to analyze the HLA ploymorphism in the populations.

Accurate, scalable and integrative haplotype estimation

The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.