河南省首起奥密克戎COVID-19疫情全基因组特征与溯源分析

目的对河南省首起本土奥密克戎COVID-19确诊病例的呼吸道标本进行SARS-CoV-2全基因组测序, 分析基因组突变及分子溯源情况。方法采用全基因组测序技术对2022年1月7日—1月29日疫情相关的COVID-19病例阳性样本进行全基因组测序和序列比对分析, 分析病毒全基因组序列的一致性和变异进化情况。结果通过SARS-CoV-2基因组高通量测序, 共获得120例病例的SARS-CoV-2全基因组序列, 占安阳COVID-19疫情总病例数的25.64%(120/468)。与武汉参考株(NC₀45512.2)相比, 120例病例的全基因组序列存在57～59个核苷酸突变位点, 在共享57个核苷酸位点的基础上增加1～2个核苷酸突变位点, 均属于VOC/Omicron变异株(BA.1.1进化分支), 基因组序列高度同源。其中, 首发病例A全基因组序列含有57个核苷酸突变位点, 首发病例B全基因组序列在含有57个相同的核苷酸突变位点基础上, 增加1个特有变异位点(C1594T), 提示二者为同一传播链。经中国疾病预防控制中心和河南省疾病预防控制中心与国内本土病例和输入病例...     

广西巴马长寿老人的长寿相关线粒体基因组研究

目的 探讨人类线粒体基因与广西巴马长寿的关联性.方法 对广西巴马96岁以上的20个老人外周血液中线粒体全序列进行测定,并与标准剑桥参考序列(Cambridge reference sequence,CRS)比对确定7个候选线粒体基因单核苷酸多态位点.用586名无亲缘关系的健康人群血样作为对照.并进一步用限制性片段长度多态性方法对候选基因进行检验.结果 线粒体DNA(mitochondrial DNA,mtDNA)4824A/G位点突变率在长寿和健康正常对照群体不同年龄段之间,随年龄增加突变频率逐渐提高,且对照人群样本突变率明显高于长寿人群,差异具有统计学意义.结论 mtDNA4824位点不仅是衰老相关位点,也是长寿负相关位点.     

2例线粒体病患者的MT-ND6基因突变分析

目的报道2例携带MT-ND6基因突变的线粒体病患者的临床和分子遗传学特点,探究线粒体DNA突变的致病机制。方法详细收集患者的临床资料,排除常见线粒体病突变位点(如A3243G,A8344G,T8993G/C,G13513A等)后,应用聚合酶链式反应-直接测序法分析16.6kb的线粒体基因组全序列,并应用Mito Tool在线软件进行氨基酸序列保守性分析,PROVEAN、SIFT和Poly Phen-2等软件进行错义突变的功能分析并判定突变性质。结果 2名先证者在ND6基因上各发现1个mt DNA变异,分别为G14453A和T14325C,二者均位于基因保守区,预测显示对蛋白功能有害,父母及100名健康对照中均未发现上述突变。结论 G14453A是MT-ND6基因上罕见的致病突变位点,该突变与MELAS综合征的发生密切相关;T14325C是LHON的可疑致病位点,但其致病性有待进一步研究。线粒体基因全测序不仅有助于常见线粒体病的临床诊断和产前筛查,还能提高一些临床表现不典型的线粒体病的分子诊断水平。     

完全型雄激素不敏感综合征雄激素受体基因突变的鉴定与分析

目的 对l例完全型雄激素不敏感综合征(complete androgen insensitivity syndrome,CAIS)患者的雄激素受体(androgen receptor,AR)基因进行分析,寻找潜在的突变位点,并进一步分析其发病原因.方法 提取患者外周血全基因组DNA,扩增位于X染色体AR基因8个外显子及邻近外显子与内含子剪切位点DNA序列,对扩增产物直接进行DNA序列测定,与GenBank中的基因序列进行比对.结果 该患者AR基因在第6外显子核苷酸序列3507位点缺失一个碱基C而引起移码突变,致使在第808位密码子出现终止密码子(TGA)使得翻译提前终止形成截短的雄激素受体蛋白.该突变可能诱导雄激素受体结合能力发生功能上的变异,导致CAIS的发生.结论 AR基因第6外显子核苷酸序列3507位点缺失碱基C引起的移码突变是一种导致CAIS新的基因突变方式,该研究丰富了AR基因突变谱,为了解CAIS的发病机制提供了新的依据.     

中国Leber遗传性视神经病变G11696A突变两个家系分析

目的对两个中国Leber遗传性视神经病变(Leber’shereditary optic neuropathy,LHON)家系的临床和分子遗传学特征进行分析。方法眼科临床检查发现在这两个家系中只有先证者1人出现视力障碍,发病年龄分别为10岁和17岁。对这两个家系先证者使用24对有部分重叠的引物进行线粒体DNA(mitochondrial DNA,mtDNA)全序列扩增分析。结果没有发现mtDNAG11778A、G3460A和T14484C3个常见的突变位点,而发现了与LHON相关的ND4G11196A同质性突变位点的存在,在167名正常对照只发现1例G11696A突变。结论线粒体DNA全序列分析发现两个家系呈现独特的mtDNA多态性,都属于东亚单体型D4。不完全外显率和正常对照频率(1/167)表明G11696A突变本身不足以导致LHON的发生,说明其它因素在这两个LHON家系的表型表达中也起一定的作用。在这些家系mtDNA中缺乏影响重要功能突变位点的存在,排除了线粒体背景对LHON临床表型的影响。因此,核修饰基因、环境因素可能对两个中国G11696A突变家系的外显率和发病严重程度起促进作用。     

线粒体tRNAThr A15951G可能是与Leber遗传性视神经病变相关的基因突变

目的 进一步分析中国汉族Leber遗传性视神经病变(Leber's hereditary optic neuropathy,LHON)家系的临床和分子遗传学特征,阐明LHON的分子致病机制.方法 对2例具有典型LHON临床特征的先证者和家系其他成员进行眼科学及其临床检查.对这2个家系先证者使用24对有部分重叠的引物进行线粒体DNA(mitochondrial DNA,mtDNA)全序列扩增分析.结果 检查发现这些家系成员中视力损害的外显率分别为5.3％(1/19)、18.2％(4/22).经mtDNA测序分析,并没有发现mtDNA G11778A、G3460A和T14484C 3个常见的突变,在tRNAThr上发现了A15951G同质性突变位点.线粒体DNA全序列分析显示2个家系呈现mtDNA多态性,都属于东亚单倍型D4b1.A15951G突变位于线粒体tRNAThr高度保守区(通用位点为71位),可能导致tRNA空间结构和稳定性发生改变,线粒体蛋白合成功能受损,最终发生视力损害.结论 线粒体tRNAThr A15951G可能是与Leber遗传性视神经病变相关的致病性线粒体基因突变.     

RYR2基因与心脏性猝死的相关性研究

目的探寻RYR2基因的变异位点G1886S,讨论其与心脏性猝死(sudden cardiac death,SCD)的关系。方法提取SCD组及健康对照组血样的基因组DNA,采用PCR法扩增G1886S基因编码区外显子、外显子-内含子交界区以及3′侧翼区序列,直接进行DNA测序以明确遗传变异类型,并进行基因型频率和等位基因频率的统计学分析。结果在SCD组检测到2个变异位点,后者在SCD组合对照组中基因型分布和等位基因频率存在差异,并具有统计学意义(P0.05)。结论 RYR2基因变异位点G1886S与中国人SCD的发生的具有相关性。     

Leber遗传性视神经病变线粒体DNA突变的研究

目的 探讨Leber遗传性视神经病变患者的线粒体DNA突变类型及特点.方法 分别应用等位基因特异性PCR（MSP-PCR）、聚合酶链反应-限制性片段长度多态性（PCR-RFLP）和聚合酶链反应-单链构象多态性（PCR-SSCP）联合DNA测序的方法,对12个家系中21位临床症状疑诊为LHON的患者及其19位无明显眼疾的母系亲属进行线粒体DNA检测.结果 40例受检者中35例发生11778位点突变,2位成员有3460位点突变,有1例发现有4258位点突变（A→G）.结论 11778是LHON患者常见的突变位点,3460突变少见,新发现的突变位点4258可能是新的继发突变或基因多态性.     

新疆汉族、维吾尔族HPV16E6基因变异与子宫颈癌及宫颈病变的关系

目的探讨新疆地区汉族、维吾尔族宫颈癌及宫颈病变中HPV16型E6基因变异分布及频率,比较两个民族之间的差异。方法对140例HPV16阳性标本,设计E6基因特异性引物,通过PCR扩增HPV16E6全长基因,PCR产物直接测序,进行序列分析并与德国标准株对比,筛选突变位点。结果 123例汉族、维吾尔族妇女宫颈癌及宫颈病变标本中均存在HPV16E6变异株,其中突变率分别为:47.37%(27/57)和50%(33/66),E6突变位点主要是L83V、D25E、D64E、I73V、H78Y、D113E,其中L83V变异株在两个民族突变中占的比例均最高,汉族L83V突变频率为29.82%(17/57)显著低于维吾尔族的40.90%(27/66)(P0.05)。而汉族D25E突变频率为19.30%(11/57)显著高于维吾尔族的7.58%(5/66)(P0.05),D64E变异株在维族突变株中占的比例为6.1%,而汉族标本中未检出。结论两个民族HPV16 E6基因变异发生的位置和变异发生的频率存在差异,维吾尔族人群中HPV16E6基因D64E变异株可能与该地区维吾尔族宫颈癌高发存在一定的关系。     

线粒体12S rRNA基因突变与2型糖尿病

目的 观察线粒体12S rRNA 1310、1438及1442位点在中国汉族2型糖尿病患者群体中的突变情况,同时筛查该区域与2型糖尿病发生有关的突变。方法 采用PDR－SSCP及PCR产物直接测序等技术对86例2型糖尿病患者及70名正常对照个体的血细胞线粒体DNA进行突变分析。结果 发现1例患者线粒体DNA 12S rRNA基因1438位点存在G→A的点突变,另1例存在1442位点G→A的点突变,所有对照个体均未发现该两位点的突变。未发现线粒体基因12S rRNA 1310位点C→T点突变。结论 1438位点G→A、1442位点G→A的突变可能与2型糖尿病的发生相关,该两位点突变的具体意义如何尚需进一步研究。1310位点C→T在血细胞中的突变率可能较低,进一步说明2型糖尿病的发生在线粒体遗传上具有一定的异质性。     

Comparative analysis of the complete mitochondrial genome between Tibetan and Han population

OBJECTIVE: To construct the haplogroup and perform an analysis of mitochondrial whole-genome sequence in Tibetan and Han Chinese. Variations of nucleotide of mitochondrial DNA (mtDNA) were identified and compared between the Tibetan and Han population. METHODS: The mtDNA whole sequences of 40 Tibetan and 50 Han individuals were sequenced by an Applied Biosystems 3730 DNA automatic sequencer. The sequences were assembled using software phredPhrap16.0, and all assembled sequences were manually verified according to the criterion of rCRS (revised Cambridge Reference Sequence). The haplogroups of mtDNA were constructed using phylogenetic analysis according to the criteria of MITOMAP by Network method. The data were elucidated by integrated methods. RESULTS: Authors' results showed that all the pooled 90 subjects belonged to the Macrohaplogroup M and N, and were classified into 13 haplogroups. No differences were observed among the haplogroups of the two populations except for M9 haplogroup. A total of 21 variants were detected by comparing the mtDNA whole sequences between Tibetan and Han population; of those, 5 variants have not been reported before. In addition, we constructed the haplotypes of 5 variants harboring the D-loop region, and founded prominent difference in both supertype 1 and supertype 2 between Tibetan and Han population. CONCLUSION: The phylogenetic analysis indicates that the Tibetan and Han ethnic groups shared close maternal relationship in origin. The biological implication of the significant variants is worth elucidating; whether they are the results of adaptive selection or neutral selection or pathological variations need to be further studied.     

Mitochondrial DNA haplogroup R predicts survival advantage in severe sepsis in the Han population

PurposeTo determine whether the main mitochondrial DNA (mtDNA) haplogroups of the Han people have an impact on long-term clinical outcome.MethodsWe prospectively studied 181 individuals who were sequentially admitted to the intensive care unit. Demographic and clinical data were recorded along with clinical outcome over 180 days. Follow-up was completed for all study participants. We then determined the mtDNA haplogroups of the patients and 570 healthy, age-matched Han people from Zhejiang province, Southeast China, by analyzing sequences of hypervariable mtDNA segments and testing diagnostic polymorphisms in the mtDNA coding region with DNA probes.ResultThe frequency of the main subhaplogroups of the Han population in the study cohort did not differ significantly from the control group. mtDNA haplogroup R, one of the three main mtDNA haplogroups of the Han people, was a strong independent predictor for the outcome of severe sepsis, conferring a 4.68-fold (95% CI 1.903–10.844, P = 0.001) increased chance of survival at 180 days compared with those without the haplogroup R.ConclusionIn the Han population, mtDNA haplogroup R was a strong independent predictor for the outcome of severe sepsis, conferring an increased chance of long-term survival compared with individuals without the R haplogroup.     

Review of Croatian genetic heritage as revealed by mitochondrial DNA and Y chromosomal lineages

The aim of this review is to summarize the existing data collected in high-resolution phylogenetic studies of mitochondrial DNA and Y chromosome variation in mainland and insular Croatian populations. Mitochondrial DNA polymorphisms were explored in 721 individuals by sequencing mtDNA HVS-1 region and screening a selection of 24 restriction fragment length polymorphisms (RFLPs), diagnostic for main Eurasian mtDNA haplogroups. Whereas Y chromosome variation was analyzed in 451 men by using 19 single nucleotide polymorphism (SNP)/indel and 8 short tandem repeat (STR) loci. The phylogeography of mtDNA and Y chromosome variants of Croatians can be adequately explained within typical European maternal and paternal genetic landscape, with the exception of mtDNA haplogroup F and Y-chromosomal haplogroup P* which indicate a connection to Asian populations. Similar to other European and Near Eastern populations, the most frequent mtDNA haplogroups in Croatians were H (41.1%), U5 (10.3%), and J (9.7%). The most frequent Y chromosomal haplogroups in Croatians, I-P37 (41.7%) and R1a-SRY1532 (25%), as well as the observed structuring of Y chromosomal variance reveal a clearly evident Slavic component in the paternal gene pool of contemporary Croatian men. Even though each population and groups of populations are well characterized by maternal and paternal haplogroup distribution, it is important to keep in mind that linking phylogeography of various haplogroups with known historic and prehistoric scenarios should be cautiously performed.     

Phylogeographic analysis of mtDNA variation in four ethnic populations from Yunnan Province: new data and a reappraisal

 Two sets of mitochondrial DNA (mtDNA) hypervariable segment I (HVS-I) data from four ethnic populations (Tibetan, Va, Dai, and Lahu) from Yunnan Province, China, were analyzed here by using phylogeographic methods. The results suggest that more attention should be paid to sampling methodology when addressing the genetic relationship and affinity among ethnic populations. Comparison of related data from different labs may serve as a check for the credibility of the data and will help discern the origin of the ethnic populations. Generally, Tibetan populations have more north-prevalent haplogroups (clades of the mtDNA phylogeny), while Dai and Lahu populations have high frequencies of south-prevalent haplogroups. The Vas, although autochthonous according to historical records, show signs of gene admixtures from northern and southern populations, for they harbor high frequencies of the south-prevalent haplogroup F and the north-prevalent haplogroup D as well as other northern mtDNA lineages such as M9 and G2a. The consanguineous marriage customs of the Lahu, together with possible genetic drift during this group's historical migration, left a conspicuous genetic imprint on its current gene pool. Received: February 8, 2002 / Accepted: March 7, 2002     

Analyses of the mitochondrial mutations in the Chinese patients with sporadic Creutzfeldt–Jakob disease

Pathogenic mitochondrial DNA (mtDNA) mutations leading to mitochondrial dysfunction can cause a variety of chronic diseases in central nervous system (CNS). However, the role of mtDNA mutations in sporadic Creutzfeldt–Jakob disease (sCJD) has still been unknown. In this study, we comparatively analyzed complete mtDNA sequences of 31 Chinese sCJD patients and 32 controls. Using MITOMASTER and PhyloTree, we characterized 520 variants in sCJD patients and 507 variants in control by haplogroup and allele frequencies. We classified the mtDNAs into 40 sub-haplogroups of 5 haplogroups, most of them being Asian-specific haplogroups. Haplogroup U, an European-specific haplogroups mtDNA, was found only in sCJD. The analysis to control region (CR) revealed a 31% increase in the frequency of mtDNA CR mutations in sCJD versus controls. In functional elements of the mtDNA CR, six CR mutations were in conserved sequence blocks I (CSBI) in sCJD, while only one in control (P<0.05). More mutants in transfer ribonucleic acid-Leu (tRNA-Leu) were detected in sCJD. The frequencies of two synonymous amino-acid changes, m.11467A>G, p.(=) in NADH dehydrogenase subunit 4 (ND4) and m.12372G>A, p.(=) in NADH dehydrogenase subunit 5 (ND5), in sCJD patients were higher than that of controls. Our study, for the first time, screened the variations of mtDNA of Chinese sCJD patients and identified some potential disease-related mutations for further investigations.     

MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences

We have developed a computer system, MITOMASTER, to make analysis of human mitochondrial DNA (mtDNA) sequences efficient, accurate, and easily available. From imported sequences, the system identifies nucleotide variants, determines the haplogroup, rules out possible pseudogene contamination, identifies novel DNA sequence variants, and evaluates the potential biological significance of each variant. This system should be beneficial for mtDNA analyses of biomedical physicians and investigators, population biologists and forensic scientists. MITOMASTER can be accessed at http://mammag.web.uci.edu/twiki/bin/view/Mitomaster.     

High-Resolution mtDNA Studies of the Indian Population: Implications for Palaeolithic Settlement of the Indian Subcontinent

The population of the Indian subcontinent represents a very complex social and cultural structure. Occupying a geographically central position for the early modern human migrations, indications are that the founder group that migrated out of East Africa also reached India. In the present study we used the twin strategy of mapping the whole mitochondrial DNA (mtDNA) using the standard 14 restriction enzymes, and sequencing the non‐transcribed HVSI region, to derive maximum maternal lineages from a sample of non‐tribal Indians. The essential features of the reduced median network of the two datasets were the same. Both showed two demographic expansions of two major haplogroups, ‘M’ and ‘N’. The reduced median network was drawn with inputs from other studies on the Indian population, and correlated with data from other ethnic populations. The coalescence time of expansions and genetic diversity were estimated. A reduced median network was also drawn combining data from studies on Africans, Southeast Asians and West‐Eurasians, tracing the migration of ‘M’ from East Africa to India. A time estimate of the migration of major mtDNA haplogroups from Africa was attempted. The comparison of a set of Indian maternal lineages belonging to different geographical regions of the country, with other populations revealed the in‐situ differentiation and antiquity of the Indian population. Our analysis places the ‘southern route’ migration as the source of haplogroup ‘M’. Multiple migrations might have brought the other major haplogroups, ‘N’ and ‘R’, found in our sample to India. Archaeological evidence of modern humans in the subcontinent supports this mtDNA study.     

Population genetics and disease susceptibility: characterization of central European haplogroups by mtDNA gene mutations, correlation with D loop variants and association with disease

Mitochondrial (mt)DNA haplogroups in a German control group (n = 67) were characterized by screening mitochondrial coding regions encompassing most of the ND, tRNA and cyt b genes. We used a PCR-SSCP screening approach followed by direct sequencing of polymorphic mtDNA fragments. Five major mtDNA lineages, diverging in at least nine different haplogroups, could be defined by characteristic polymorphic sites in mitochondrial genes. Additional sequencing of two hypervariable segments (HVS-I and II) of the non-coding displacement (D) loop in all control subjects revealed that certain D loop variants were strongly correlated with lineages and haplogroups, while others represented hotspots occurring frequently in different haplogroups. The existence of identified lineages and haplogroups received support from data in the literature, obtained by use of different approaches. Subsequently, we investigated four disease groups for association with these haplogroups: (i) LHON patients (n = 55) carrying at least one of the primary/intermediate LHON mutations at nt 3460, 11778, 14484 and/or 15257; (ii) patients suffering from Wolfram or DIDMOAD syndrome (n = 8); (iii) MELAS patients (n = 9); (iv) a group of children, who died from 'sudden infant death syndrome' (SIDS) (n = 9). The distribution patterns among the haplogroups of the disease groups (LHON, DIDMOAD and SIDS) differed considerably from the control population. LHON and DIDMOAD were significantly under-represented in the most frequent German haplogroup DC, but were concentrated in a mtDNA lineage defined by polymorphisms at nt 4216 + 11251 + 16126. As this lineage diverged into two precisely defined haplogroups, LHON and DIDMOAD could be assigned to the two haplogroups separately. Strikingly, SIDS was often found in association with two rare German haplogroups. MELAS patients were equally distributed among German haplogroups and, moreover, did not reveal any accumulation of specific D loop variants. We conclude that certain European mtDNA haplogroups define a genetic susceptibility basis for various disorders.      

Interference of nuclear mitochondrial DNA segments in mitochondrial DNA testing resembles biparental transmission of mitochondrial DNA in humans

PurposeReports have questioned the dogma of exclusive maternal transmission of human mitochondrial DNA (mtDNA), including the recent report of an admixture of two mtDNA haplogroups in individuals from three multigeneration families. This was interpreted as being consistent with biparental transmission of mtDNA in an autosomal dominant–like mode. The authenticity and frequency of these findings are debated.MethodsWe retrospectively analyzed individuals with two mtDNA haplogroups from 2017 to 2019 and selected four families for further study.ResultsWe identified this phenomenon in 104/27,388 (approximately 1/263) unrelated individuals. Further study revealed (1) a male with two mitochondrial haplogroups transmits only one haplogroup to some of his offspring, consistent with nuclear transmission; (2) the heteroplasmy level of paternally transmitted variants is highest in blood, lower in buccal, and absent in muscle or urine of the same individual, indicating it is inversely correlated with mtDNA content; and (3) paternally transmitted apparent large-scale mtDNA deletions/duplications are not associated with a disease phenotype.ConclusionThese findings strongly suggest that the observed mitochondrial haplogroup of paternal origin resulted from coamplification of rare, concatenated nuclear mtDNA segments with genuine mtDNA during testing. Evaluation of additional specimen types can help clarify the clinical significance of the observed results.     

Relationship between European Mitochondrial Haplogroups and Chronic Renal Allograft Rejection in Patients with Kidney Transplant

Mitochondrial DNA variants may contribute to differences in mitochondrial function, leading to an altered immune system. The aim of this study was to analyze the relationship between mtDNA haplogroups and the development of chronic allograft dysfunction in patients with kidney transplant. A retrospective observational study was carried out on 261 patients who received kidney transplant (114 had stable transplant and 147 patients developed chronic allograft dysfunction). DNA samples were genotyped for 14 mtDNA polymorphisms by using Sequenom''s MassARRAY platform (San Diego, CA, USA). Only European white patients within the N macro-cluster were included. Patients with haplogroups V (odds ratio (OR)=0.32; p=0.037) and J (OR=0.36; p=0.038) showed lower odds for developing CRAD than patients with haplogroup H. After adjusting for the most significant variables, haplogroups V and J tended to statistical significance (p=0.091 and p=0.067 respectively). This is a preliminary study in which mtDNA haplogroups seem to be implicated in susceptibility or protection for developing chronic allograft dysfunction.