MITOCHONDRIAL VARIATION

线粒体变异

• 批准号: 7606615
• 负责人: Douglas C Wallace
• 金额: $ 0.08万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-12-01 至 2007-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7606615
• 关键词: Affinity; Africa; African; Age; Aging; Aging-Related Process; Alanine; American; Anthropology; Base Sequence; Biochemical; Cataloging; Catalogs; Cellular biology; Codon Nucleotides; Computer Retrieval of Information on Scientific Projects Database; DNA; DNA Sequence; DNA Sequence Rearrangement; Data; Defect; Diagnostic; Disease; Dystonia; Elements; European; Evolution; Family; Funding; Genes; Genetic; Genetic Polymorphism; Genetic Research; Genetic Variation; Genome; Geographic Distribution; Grant; Haplogroup; Haplotypes; Hereditary Disease; Hispanics; Human; Human Genetics; Immigrant; Inherited; Institution; Knowledge; Leber' s Hereditary Optic Neuropathy; Link; Logic; Medical; Metabolic; Microsatellite Repeats; Minisatellite Repeats; Mitochondria; Mitochondrial DNA; Molecular; Mutation; NADH dehydrogenase (ubiquinone); Native Americans; Nature; Neurology; Nuclear; Nucleotides; Pathologic; Patients; Phylogenetic Analysis; Population; Process; Rate; Research; Research Personnel; Resources; Restriction fragment length polymorphism; Sampling; Science; Screening procedure; Sequence Analysis; Short Interspersed Nucleotide Elements; Site; Somatic Cell Genetics; Source; Standards of Weights and Measures; Techniques; United States National Institutes of Health; Valine; Variant; Woman; base; clinically relevant; genetic pedigree; genetic variant; insight; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. There is a high degree of genetic variation in human populations. For nuclear DNA (nDNA) about 90% of this variation is distributed among all populations while about 10% is population specific. For the mitochondrial DNA (mtDNA) over 30% of the variation is population specific. Cataloging this variation is essential for understanding the interrelationships between populations and thus human origins (molecular anthropology) and for defining the "normal" genetic variation so that it can be distinguished from the pathogenic variation to be found in patients with disease. Naturally occurring genetic variation of use for studying human origins can be found in both the nDNA and mtDNA by a variety of techniques. Nuclear DNA variation can be identified as restriction site polymorphisms (restriction fragment length polymorphisms, RFLPs), microsatellite repeat variation, variable number of tandem repeat (VNTR) polymorphisms, rearrangements, present or absence of SINE and LINE repeat elements, nucleotide base substitutions, and direct gene sequence analysis. Mitochondrial DNA variation can be analyzed by RFLPs, control region (D-loop) sequencing, nucleotide substitution analysis, and direct sequencing of genes and/or the genome. These types of information can be used to reconstruct population affinities and thus to deduce human origins by a variety of analytic tools. These include genetic distance analyses, population substructure studies, and phylogenetic comparisons. These data, together with estimates of the sequence evolution rate and geographic distribution of the samples provide insights into human origins. This information is also vital for disease and aging studies. All DNA is polymorphic in sequence. Most sequence variants are neutral (innocuous). These have to be identified before the interspersed disease mutations can be identified. This is true for nDNA, but is particularly true for mtDNA. The maternally-inherited mtDNA's sequence is extraordinarily variable, with much of the variation having arisen as women moved out of Africa and occupied all continents of the world. Hence, is the mtDNA sequence from a patient whose ancestors were derived from one continent is compared to the mtDNA of a "control" of a different continental origin, approximately 20 to 80 nucleotide differences will be found, any of which could be the clinically relevant mutation. To overcome this problem, patient mtDNAs sequences must be compared to closely related mtDNAs, those sharing a similar haplotype. In such a comparison, the normal variants are shared between the patient and control. Generally only the recent pathologic mutation is different and hence can be identified (Wallace, 1999 Gene 238: 211-230). Thus, it is essential for all genetic research to have well defined populations representing normal genetic variation for controls in disease studies. As a specific example, we have used this information to identify the disease mutation of a large Hispanic pedigree in which both Leber's Hereditary Optic Neuropathy (LHON) and generalized dystonia occurred along the maternal lineage (Novotny et al., 1986 Neurology 36:1053-60). We sequenced the mtDNA of one of the dystonia patients, and compared it to the "standard" Cambridget sequence. This revealed 40 nucleotide differences, several of which could be argued to be the pathogenic mutation, with no criteria to distinguish between them. Consequently, this project stalled. Concurrently, we were studying the mtDNA variation in Native Americans and discovered that virtually all Native American mtDNAs were derived from four founder haplogroups, A, B, C, and D (Wallace, 1999 Gene 238: 211-230). Subsequent comparison of the dystonia patient's mtDNA with the Native American mtDNAs revealed the unexpected result that this Hispanic family harbored a Native American mtDNA belonging to haplogroup D. We then compared all of the patient's sequence variants to those of other Native American haplogroup D mtNDAs, and we found that all but two of the sequence variants were naturally occurring variants of the haplogroup D lineage and hence non-pathogenic. Of the two remaining nucleotide changes, one was a neutral third codon change and the other was a mssense mutation at nucleotide pair (np) 14459 in the MTND6 gene. This mutation changed a highly conserved alanine to a valine and was heteroplasmic. Hence, this was the probable cause of the disease (Jun et al., 1994 Proceeding Academic of Sciences U S A 91:6206-10). Subsequent screening of other LHON and dystonia patients for this mutation revealed two additional families with the np 14459 mutation, one with LHON and the other with generalized dystonia. The LHON family mutation occured on an African haplogroup L mtDNA while the dystonia patient mutation occurred on a European haplogroup I mtDNA, and all three families were heteroplasmic. Hence, each of these families must be due to independent mutations (Shoffner et al., 1995 Annals of Neurology 38:163-9). Subsequently, biochemical and somatic cell genetic studies linked the np 14459 mutation to a mitochondrial respiratory Complex I defect in all three families (Jun et al., 1996 Molecular Cell Biology 16:771-7). Hence, this study shows how a knowledge of naturally occurring mtDNA variation is essential to identifying and characterizing putative patient disease mutations. This same logic applies to nuclear gene variants as well. We have been collecting and analyzing samples of various human populations for nearly 20 years. Without these resulting reference populations, we would not have been able to identify many of the mtDNA disease mutations which are now routinely used in medical diagnostics (Wallace, 2001 Scriver et al The Metabolic and Molecular Basis of Inherited Disease, 2425-2509). Moreover, the human population, and as a result the immigrant U.S. population in general and Southern Californian population in particular, is highly polymorphic. Hence, we must continue to collect and characterize additional reference populations from various ages and ethnic backgrounds if we are to understand the genetic basis of the common disease processes of the North American population. Objectives: The question being asked by these studies is what is the nature and extent of human genetic variation? Once obtained, this information will be used to explore the origin and prehistory of our species and also provide background information necessary for identifying pathogenic mutations in patients with genetic disease and possible involvement of certain genetic variants in the aging process.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 人群中有很高的遗传变异。 对于核DNA（NDNA），大约90％的这种变异分布在所有人群中，而大约10％的人群是特定于人群的。 对于线粒体DNA（mtDNA），超过30％的变异是人群的特异性。 分类这种变异对于理解人群与人类起源（分子人类学）之间的相互关系至关重要，并定义“正常”的遗传变异，以便可以将其与疾病患者的致病性变异区分开。 可以通过多种技术在NDNA和mtDNA中发现自然存在的用于研究人类起源的遗传变异。 核DNA的变异可以识别为限制位点多态性（限制片段长度多态性，RFLP），微卫星重复变异，串联重复（VNTR）多态性的可变数量，重排，重排，现在或缺乏线和线重复元素的重复元素，核苷酸基础基础基础替代基替代基序列和直接基因序列和直接基因分析。 可以通过RFLP，对照区（D-LOOP）测序，核苷酸取代分析以及基因和/或基因组的直接测序来分析线粒体DNA变异。 这些类型的信息可用于重建人口亲和力，从而通过各种分析工具推断人类起源。 这些包括遗传距离分析，种群子结构研究和系统发育比较。 这些数据以及对样品的序列演化速率和地理分布的估计提供了对人类起源的见解。 该信息对于疾病和衰老研究也至关重要。 所有DNA在序列上都是多态性的。 大多数序列变体都是中性的（无害）。 在可以识别散布的疾病突变之前，必须确定这些。 对于nDNA是正确的，但对于mtDNA尤其如此。 孕妇含有的mtDNA序列是异常可变的，随着妇女搬出非洲并占领了世界上所有大陆，许多变化都出现了。 因此，将祖先从一个大陆派生的患者的mtDNA序列与不同大陆起源的“对照”的mtDNA进行了比较，将发现大约20至80个核苷酸差异，其中任何一个可能是临床相关的突变。 为了克服这个问题，必须将患者MTDNA序列与密切相关的MTDNA进行比较，而MTDNA具有相似的单倍型。 在这种比较中，正常变体在患者和对照之间共享。 通常，只有最近的病理突变是不同的，因此可以鉴定出来（Wallace，1999 Gene 238：211-230）。 因此，所有遗传学研究必须具有明确定义的人群，代表疾病研究中对照的正常遗传变异。 作为一个具体的例子，我们已经使用了这些信息来识别大型西班牙裔谱系的疾病突变，其中Leber的遗传性视神经病（LHON）和广义肌张力障碍都沿着母体血统发生（Novotny等，1986 Neurology 36：1053-60）。 我们对一名肌张力障碍患者的mtDNA进行了测序，并将其与“标准”剑桥序列进行了比较。 这揭示了40个核苷酸差异，其中一些可以说是致病性突变，而没有区分它们的标准。 因此，这个项目停滞了。 同时，我们正在研究美洲原住民的mtDNA变异，并发现几乎所有美国原住民mtdnas均来自四个创始人单倍群A，B，C和D（Wallace，1999 Gene 238：211-230）。 随后将甲状腺抑制性患者的mtDNA与美洲原住民MTDNA进行比较，表明了一个意外的结果，即这个西班牙裔家庭拥有属于HaplogroupD的美洲原住民MtDNA。然后，我们随后将患者的所有序列变体与其他所有序列的序列进行了比较，除了两个序列的序列，我们发现了所有序列的变体，这是序列的变化。因此，非致病性。 在剩余的两个核苷酸变化中，一个是中性的第三密码子变化，另一个是MTND6基因中核苷酸对（NP）14459处的MSSENSE突变。 该突变将高度保守的丙氨酸变为瓣膜，是异质的。 因此，这是该疾病的可能原因（Jun等，1994，科学学术学术学术学术学术学院91：6206-10）。 随后对其他LHON和肌张力障碍患者进行此突变的筛查显示，其他NP 14459突变的家族有两个家庭，一个患有LHON，另一个患有广义肌张力障碍。 LHON家族突变发生在非洲单倍型L mtDNA上，而肌张力障碍患者突变发生在欧洲单倍群I mtDNA上，而这三个家庭都是异质的。 因此，这些家庭中的每个家庭都必须归因于独立的突变（Shoffner等，1995 Annals of Neurology 38：163-9）。 随后，生化和体细胞遗传研究将NP 14459突变与所有三个家族的线粒体呼吸复合物I缺陷联系起来（Jun等，1996 Molecular细胞生物学16：771-7）。 因此，这项研究表明了对自然发生的mtDNA变异的了解对于识别和表征推定的患者疾病突变至关重要。 同样的逻辑也适用于核基因变体。 近20年来，我们一直在收集和分析各种人群的样本。 没有这些由此产生的参考人群，我们将无法识别许多现在在医学诊断中常规使用的mtDNA疾病突变（Wallace，2001 Scriver等人的遗传疾病的代谢和分子基础，2425-2509）。 此外，人口，因此，美国移民人口尤其是南加州人口，是高度多态的。 因此，如果我们要了解北美人口常见疾病过程的遗传基础，我们必须继续收集和表征来自不同年龄和种族背景的其他参考人群。 目标：这些研究提出的问题是人类遗传变异的性质和程度是什么？ 一旦获得，该信息将用于探索我们物种的起源和史前史，还提供了鉴定遗传疾病患者的致病性突变以及某些遗传变异在衰老过程中可能参与的背景信息。