Optimized variant calling for estimating kinship

One of the fundamental goals of forensic genetics is sample attribution, i.e., whether an item of evidence can be associated with some person or persons. The most common scenario involves a direct comparison, e.g., between DNA profiles from an evidentiary item and a sample collected from a person of interest. Less common is an indirect comparison in which kinship is used to potentially identify the source of the evidence. Because of the sheer amount of information lost in the hereditary process for comparison purposes, sampling a limited set of loci may not provide enough resolution to accurately resolve a relationship. Instead, whole genome techniques can sample the entirety of the genome or a sufficiently large portion of the genome and as such they may effect better relationship determinations. While relatively common in other areas of study, whole genome techniques have only begun to be explored in the forensic sciences. As such, bioinformatic pipelines are introduced for estimating kinship by massively parallel sequencing of whole genomes using approaches adapted from the medical and population genomic literature. The pipelines are designed to characterize a person’s entire genome, not just some set of targeted markers. Two different variant callers are considered, contrasting a classical variant calling algorithm (BCFtools) to a more modern deep convolution neural network (DeepVariant). Two different bioinformatic pipelines specific to each variant caller are introduced and evaluated in a titration series. Filters and thresholds are then optimized specifically for the purposes of estimating kinship as determined by the KING-robust algorithm. With the appropriate filtering and thresholds in place both tools perform similarly, with DeepVariant tending to produce more accurate genotypes, though the resultant types of inaccuracies tended to produce slightly less accurate overall estimates of relatedness     

Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection

Y-chromosomal haplogroups determined by Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal biogeographic ancestry inference, which has attracted a lot of interest in the forensic community. Recently, a comprehensive Y-SNP tool with dominant markers targeting haplogroups in R, E and I branches has been reported, which allows the inference of 640 Y haplogroups. It had a very good performance and could provide a high level of Y haplogroup resolution in most populations. However, the predominant haplogroups in the Chinese populations are O, C and N, suggesting that more Y-SNPs under these clades are needed to achieve the population-specific high resolution. Herein, aiming at the Chinese population, we presented a largely improved custom Y-SNP MPS panel that contains 256 carefully ascertained Y-SNPs based on our previous studies, and evaluated this panel via a series of tests, including the tests for concordance, repeatability, sensitivity, specificity, and stability, as well as the mixture, degraded and case-type sample analysis. The preliminary developmental validation demonstrated that this panel was highly reliable, sensitive, specific, and robust. In the sensitivity test, even when the DNA input was reduced to as low as 0.5 ng, the sample could still be assigned to the correct Y haplogroup. For mixture analysis, even the 1:99 (Male: Female) mixtures had no effects on the assignation of the Y haplogroup of the male contributor. In summary, this assay has provided a high-resolution Y-chromosomal haplogrouping workflow to determine a male’s paternal lineage and/or paternal biogeographic ancestry and could be widely used for Chinese Y-chromosomal haplogroups dissection.     

Paternal genetic structure of the Qiang ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs

The Qiang population mainly lived in Beichuan Qiang Autonomous County of Sichuan Province. It is one of the nomads in China, distributed along the Minjiang River. The Qiang population was assumed to have great affinity with the Han, the largest ethnic group in China, when it refers to the genetic origin. Whereas, it is deeply understudied, especially from the Y chromosome. Here in this study, we used validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) panels to study the Qiang ethnic group to unravel their paternal genetic, forensic and phylogenetic characteristics. A total of 422 male samples of the Qiang ethnic group were genotyped by 233 Y-SNPs and 29 Y-STRs. Haplogroup O-M175 (N = 312) was the most predominant haplogroup in the Qiang ethnic group, followed by D-M174 (N = 32) and C-M130 (N = 32), N-M231 (N = 27), and Q-M242 (N = 15). After further subdivision, O2a-M324 (N = 213) accounted for the majority of haplogroup O. Haplogroup C2b-Z1338 (N = 29), D1a-CTS11577 (N = 30). O2a2b1a1a1-F42 (N = 48), O2a1b1a1a1a-F11 (N = 35), and O2a2b1a1-M117 (N = 21) represented other large terminal haplogroups. The results unveiled that Qiang ethnic group was a population with a high percentage of haplogroup O2a2b1a1a1-F42 (48/422) and O2a1b1a1a1a-F11 (35/422), and O2a2b1a1-M117 (21/422), which has never been reported. Its haplogroup distribution pattern was different from any of the Han populations, implying that the Qiang ethnic group had its unique genetic pattern. Mismatch analysis indicated that the biggest mismatch number in haplogroup O2a2b1a1a1-F42 was 21, while that of haplogroup O2a1b1a1a1a-F11 was 20. The haplotype diversity of the Qiang ethnic group equaled 0.999788, with 392 haplotypes observed, of which 367 haplotypes were unique. The haplogroup diversity of the Qiang ethnic group reached 0.9767, and 53 terminal haplogroups were observed (The haplogroup diversity of the Qiang ethnic group was the highest among Qiang and all Han subgroups, indicating the larger genetic diversity of the Qiang ethnic group.). Haplogroup O2a2b1a1a1-F42 was the most predominant haplogroup, including 11.37 % of the Qiang individuals. Median-joining trees showed gene flow between the Qiang and Han individuals. Our results indicated that 1) the highest genetic diversity was observed in the Qiang ethnic group compared to any of the former studied Chinese population, suggesting that the Qiang might be an older paternal branch; 2) the haplogroup D-M174 individuals of Qiang, Tibetans and Japanese distributed in three different subclades, which was unable to identify through low-resolution Y-SNP panel; and 3) the Qiang had lower proportion of haplogroup D compared to Yi and Tibetan ethnic groups, showing that the Qiang had less genetic communication with them than with Han Chinese.     

参泽舒肝胶囊联合多烯磷脂酰胆碱胶囊治疗非酒精性脂肪肝的临床研究

目的 研究参泽舒肝胶囊联合多烯磷脂酰胆碱胶囊治疗非酒精性脂肪肝的疗效。方法 将南方医科大学珠江医院2017年12月-2019年12月收治的非酒精性脂肪肝患者184例纳入本次研究,并以随机数表法将其分为试验组与对照组,每组92例。予以对照组患者多烯磷脂酰胆碱胶囊治疗,予以试验组患者多烯磷脂酰胆碱胶囊＋参泽舒肝胶囊治疗。比较两组患者治疗后临床疗效、治疗前后肝功能指标及血脂水平、血清学指标水平变化、肝脏B超评分与肝脾CT比值指标、用药不良反应情况等指标。结果 治疗后,试验组患者临床有效率（95.65%）高于对照组（86.96%）（P<0.05）;治疗前,两组患者谷丙转氨酶(aLanine aminotransferase,ALT)、谷草转氨酶(aspartate transaminase,AST)、高密度脂蛋白胆固醇（high density liptein cholesterol,HDL-C）、谷氨酰转肽酶(glutamyl transpeptidase,GGT)、总胆固醇(totalCholesterol,TC)、甘油三酯(triGlyceride,TG)、血清超氧化物歧化酶(superOxide dismutase,SOD)、丙二醛(malondialdehyde ,MDA)和肿瘤坏死因子-α(tumor necrosis factor-α,TNF-α)、B超评分与肝脾CT比值等指标比较,差异无统计学意义（P>0.05）;治疗后,两组患者ALT、AST、GGT水平降低,且试验组降低较明显（P<0.05）;两组TC及TG水平降低,HDL-C水平升高（P<0.05）;且试验组改善较明显（P<0.05）;两组患者SOD升高,MDA和TNF-α水平降低（P<0.05）;且试验组改善较明显（P<0.05）;两组患者治疗后B超评分均下降,肝脾CT比值均提升,试验组治疗后B超评分低于对照组,肝脾CT比值高于对照组（P<0.05）。两组患者均无不良反应。结论 参泽舒肝胶囊联合多烯磷脂酰胆碱胶囊治疗非酒精性脂肪肝疗效显著,且安全可行。     

不完全射频消融对兔VX2肝癌MMP-9表达的影响

目的研究不完全射频消融（RFA）治疗对兔VX2肝癌模MMP-9蛋白表达的影响。 方法建立新西兰白兔的VX2肝癌模型,将30只兔VX2肝癌模型分为2组,即对照组和实验组,每组15只,对照组只做开关腹,而不进行RFA;实验组进行开腹消融,消融范围为肿瘤组织的75%;在实验组中设立RFA后快速进展亚组,定义为实验结束时肿瘤的倍增率大于对照组。对比其RFA后的VX2肝癌的体积变化、残留VX2肝癌基质金属蛋白酶-9（MMP-9）的表达情况。 结果对照组和实验组治疗后肿瘤体积分别为（7 862±1 304）mm³和（6 996±709）mm³,肿瘤的倍增率分别为（291±49）和（232±16）,差异有统计学意义（P < 0.05）。对照组和实验组MMP-9阳性表达率为52.1%和46.3%,差异均有统计学意义（P < 0.05）;实验组中3只实验兔肿瘤倍增率及MMP-9表达率明显高于实验组,属于RF后快速进展亚组,差异有统计学意义（P < 0.05）。 结论部分性消融对大多数肝细胞癌具有一定疗效,但对于少数肿瘤可能加速其生长,而MMP-9的过表达可能是促进残留癌快速进展的原因。     

Understanding the postmortem changes in concentrations of methanol in ocular matrices in rabbits

Death due to abuse and accidental ingestion of methanol is widely known around the globe. The paper presents the postmortem changes in concentrations of methanol in the vitreous humor, aqueous humor, and ocular tissues in a rabbit model in methanol intoxication. Rabbits were intoxicated with methanol at a dose of 6.3 ml/kg through oral gavage. After 3.5 h of methanol administration, the rabbits were sacrificed. Vitreous humor, aqueous humor, and ocular tissues were collected both, perimortem (immediately) and postmortem (17 h post-death). Whole blood and plasma samples were also collected to explore the correlation between levels of methanol in whole blood/plasma and ocular fluids/ocular tissues if any. All the samples were analyzed by Headspace Gas Chromatography. The analysis revealed a decrease in methanol levels at postmortem for all the matrices, except for retina-choroid than its perimortem value. For retina-choroid, no significant change in methanol levels at postmortem was found.     

早期糖尿病肾病预测指标及危险因素研究

目的探讨糖耐量减低（IGT）患者早期糖尿病肾病的预测指标、患病率及影响因素。方法262例受试者中正常糖耐量（NGT）103人、IGT98人、糖尿病（DM）61人，全部进行即刻尿转铁蛋白／肌酐（UTRF／Cr）和尿白蛋白／肌酐（UAlb／Cr）的检测及临床观察指标的测定。结果（1）UTRF／Cr与UAlb／Cr呈显著正相关，r=0．618，P＜0.001。（2）IGT组的UAlb／Cr（中位数，极差）、UTRF／Cr（中位数，极差）高于NGT组（0．015，0．44mg／mg比0.012，0．58mg／mg，t=-1.981，P=0．049；0.064，4.96mg／mg比0.034，7.30mg／mg，t=-2．249，P=0．026）。（3）各组UTRF／Cr比值的阳性率明显高于白蛋白尿的阳性率（41．6％比29．7％，P（0．01）。（4）Logistic回归分析显示白蛋白尿的主要危险因素是DBP，OR=1．064，2hPGOR=1．109，P＜0.01；非糖尿病组的主要危险因素是DBP，OR=1．064，P＜0.01。结论在IGT阶段已存在早期糖尿病肾脏损害，高血压是其重要的危险因素。尿转铁蛋白／肌酐比值的检测较白蛋白尿／肌酐比值更灵敏，但仍需进一步综合比较二者的敏感性和特异性。     

2014－2018年内蒙古自治区杭锦后旗居民死亡趋势及主要慢性病早死概率分析

  目的  分析内蒙古自治区（内蒙古）巴彦淖尔市杭锦后旗居民死亡原因和变化趋势,以及四类主要慢性病的早死概率及变化趋势,为疾病预防和控制措施提供科学依据。  方法  收集2014 — 2018年杭锦后旗居民死因资料,根据国际疾病分类（ICD-10）对根本死因进行分类和编码,通过Excel 2010及SPSS 24.0软件计算粗死亡率、标化死亡率、死因构成比和早死概率等指标;趋势分析采用趋势χ2分析,率的比较采用χ2检验。  结果  2014 — 2018年杭锦后旗居民粗死亡率为558.31/10万,标化死亡率为554.52/10万,男性、女性和全人群粗死亡率及标化死亡率均呈上升趋势;男性粗死亡率和标化死亡率均高于女性。 前5位死因依次为心脏病（203.30/10万）、恶性肿瘤（122.26/10万）、脑血管疾病（96.97/10万）、损伤和中毒（34.02/10万）和呼吸系统疾病（13.22/10万）,共占总死亡的84.14%。 各年龄组死亡率均呈上升趋势,45～64岁年龄组死亡率上升趋势有统计学意义（趋势χ2=9.29,P< 0.05）;死亡主要集中于≥45岁年龄组,占比92.65%。 四类主要慢性病早死概率总体呈上升趋势（趋势χ2=13.30,P<0.001）;男性主要慢性病早死概率均高于女性（P< 0.05）。 砷中毒病区主要死因标化死亡率高于全旗总人群（P< 0.001）,死因顺位前4位与全旗人群相同。  结论  2014 — 2018年杭锦后旗居民死亡呈上升趋势,心脑血管疾病与恶性肿瘤已成为该地区居民死亡的主要原因。 应通过加强慢性病的三级预防等工作,降低慢性病的早死概率,提高居民的健康寿命和生存质量。     

PI3K/AKT/mTOR and TLR4/MyD88/NF-κB Signaling Inhibitors Attenuate Pathological Mechanisms of Allergic Asthma

Inflammation - Asthma is an inflammatory airway disease wherein bronchoconstriction, airway inflammation, and airway obstruction during asthma attacks are the main problems. It is recognized that...