A high observed substitution rate in the human mitochondrial DNA control region.

Abstract:

:The rate and pattern of sequence substitutions in the mitochondrial DNA (mtDNA) control region (CR) is of central importance to studies of human evolution and to forensic identity testing. Here, we report a direct measurement of the intergenerational substitution rate in the human CR. We compared DNA sequences of two CR hypervariable segments from close maternal relatives, from 134 independent mtDNA lineages spanning 327 generational events. Ten substitutions were observed, resulting in an empirical rate of 1/33 generations, or 2.5/site/Myr. This is roughly twenty-fold higher than estimates derived from phylogenetic analyses. This disparity cannot be accounted for simply by substitutions at mutational hot spots, suggesting additional factors that produce the discrepancy between very near-term and long-term apparent rates of sequence divergence. The data also indicate that extremely rapid segregation of CR sequence variants between generations is common in humans, with a very small mtDNA bottleneck. These results have implications for forensic applications and studies of human evolution.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Parsons TJ,Muniec DS,Sullivan K,Woodyatt N,Alliston-Greiner R,Wilson MR,Berry DL,Holland KA,Weedn VW,Gill P,Holland MM

doi

10.1038/ng0497-363

subject

Has Abstract

pub_date

1997-04-01 00:00:00

pages

363-8

issue

4

eissn

1061-4036

issn

1546-1718

journal_volume

15

pub_type

杂志文章,多中心研究
  • Enhancer mutations and phenotype modularity.

    abstract::Only a few mutations in regulatory elements that cause human disease have been identified thus far. A new report identifies cis-regulatory mutations that abolish the activity of a developmental enhancer, thereby causing pancreatic agenesis. ...

    journal_title:Nature genetics

    pub_type: 评论,新闻

    doi:10.1038/ng.2861

    authors: Gordon CT,Lyonnet S

    更新日期:2014-01-01 00:00:00

  • Genome-wide meta-analyses identify multiple loci associated with smoking behavior.

    abstract::Consistent but indirect evidence has implicated genetic factors in smoking behavior. We report meta-analyses of several smoking phenotypes within cohorts of the Tobacco and Genetics Consortium (n = 74,053). We also partnered with the European Network of Genetic and Genomic Epidemiology (ENGAGE) and Oxford-GlaxoSmithKl...

    journal_title:Nature genetics

    pub_type: 杂志文章,meta分析

    doi:10.1038/ng.571

    authors: Tobacco and Genetics Consortium.

    更新日期:2010-05-01 00:00:00

  • Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.

    abstract::We address the challenge of detecting the contribution of noncoding mutations to disease with a deep-learning-based framework that predicts the specific regulatory effects and the deleterious impact of genetic variants. Applying this framework to 1,790 autism spectrum disorder (ASD) simplex families reveals a role in ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-019-0420-0

    authors: Zhou J,Park CY,Theesfeld CL,Wong AK,Yuan Y,Scheckel C,Fak JJ,Funk J,Yao K,Tajima Y,Packer A,Darnell RB,Troyanskaya OG

    更新日期:2019-06-01 00:00:00

  • RAF1 mutations in childhood-onset dilated cardiomyopathy.

    abstract::Dilated cardiomyopathy (DCM) is a highly heterogeneous trait with sarcomeric gene mutations predominating. The cause of a substantial percentage of DCMs remains unknown, and no gene-specific therapy is available. On the basis of resequencing of 513 DCM cases and 1,150 matched controls from various cohorts of distinct ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2963

    authors: Dhandapany PS,Razzaque MA,Muthusami U,Kunnoth S,Edwards JJ,Mulero-Navarro S,Riess I,Pardo S,Sheng J,Rani DS,Rani B,Govindaraj P,Flex E,Yokota T,Furutani M,Nishizawa T,Nakanishi T,Robbins J,Limongelli G,Hajjar RJ,L

    更新日期:2014-06-01 00:00:00

  • Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2.

    abstract::Facioscapulohumeral dystrophy (FSHD) is characterized by chromatin relaxation of the D4Z4 macrosatellite array on chromosome 4 and expression of the D4Z4-encoded DUX4 gene in skeletal muscle. The more common form, autosomal dominant FSHD1, is caused by contraction of the D4Z4 array, whereas the genetic determinants an...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2454

    authors: Lemmers RJ,Tawil R,Petek LM,Balog J,Block GJ,Santen GW,Amell AM,van der Vliet PJ,Almomani R,Straasheijm KR,Krom YD,Klooster R,Sun Y,den Dunnen JT,Helmer Q,Donlin-Smith CM,Padberg GW,van Engelen BG,de Greef JC,Aartsm

    更新日期:2012-12-01 00:00:00

  • Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

    abstract::To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant ex...

    journal_title:Nature genetics

    pub_type: 杂志文章,meta分析

    doi:10.1038/ng.2897

    authors: DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.,Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium.,South Asian Type 2 Diabetes (SAT2D) Consortium.,Mexican American Type 2 Diabetes (MAT2D) Consortium.,

    更新日期:2014-03-01 00:00:00

  • Perlecan, the major proteoglycan of basement membranes, is altered in patients with Schwartz-Jampel syndrome (chondrodystrophic myotonia).

    abstract::Schwartz-Jampel syndrome (SJS1) is a rare autosomal recessive disorder characterized by permanent myotonia (prolonged failure of muscle relaxation) and skeletal dysplasia, resulting in reduced stature, kyphoscoliosis, bowing of the diaphyses and irregular epiphyses. Electromyographic investigations reveal repetitive m...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/82638

    authors: Nicole S,Davoine CS,Topaloglu H,Cattolico L,Barral D,Beighton P,Hamida CB,Hammouda H,Cruaud C,White PS,Samson D,Urtizberea JA,Lehmann-Horn F,Weissenbach J,Hentati F,Fontaine B

    更新日期:2000-12-01 00:00:00

  • Amnionless, essential for mouse gastrulation, is mutated in recessive hereditary megaloblastic anemia.

    abstract::The amnionless gene, Amn, on mouse chromosome 12 encodes a type I transmembrane protein that is expressed in the extraembryonic visceral layer during gastrulation. Mice homozygous with respect to the amn mutation generated by a transgene insertion have no amnion. The embryos are severely compromised, surviving to the ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1098

    authors: Tanner SM,Aminoff M,Wright FA,Liyanarachchi S,Kuronen M,Saarinen A,Massika O,Mandel H,Broch H,de la Chapelle A

    更新日期:2003-03-01 00:00:00

  • Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.

    abstract::Regulatory variants are often context specific, modulating gene expression in a subset of possible cellular states. Although these genetic effects can play important roles in disease, the molecular mechanisms underlying context specificity are poorly understood. Here, we identified shared quantitative trait loci (QTLs...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-018-0046-7

    authors: Alasoo K,Rodrigues J,Mukhopadhyay S,Knights AJ,Mann AL,Kundu K,HIPSCI Consortium.,Hale C,Dougan G,Gaffney DJ

    更新日期:2018-03-01 00:00:00

  • A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization.

    abstract::Extremes of the electrocardiographic QT interval, a measure of cardiac repolarization, are associated with increased cardiovascular mortality. We identified a common genetic variant influencing this quantitative trait through a genome-wide association study on 200 subjects at the extremes of a population-based QT inte...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1790

    authors: Arking DE,Pfeufer A,Post W,Kao WH,Newton-Cheh C,Ikeda M,West K,Kashuk C,Akyol M,Perz S,Jalilzadeh S,Illig T,Gieger C,Guo CY,Larson MG,Wichmann HE,Marbán E,O'Donnell CJ,Hirschhorn JN,Kääb S,Spooner PM,Meitinger T

    更新日期:2006-06-01 00:00:00

  • Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'.

    abstract:: ...

    journal_title:Nature genetics

    pub_type: 评论,信件

    doi:10.1038/s41588-018-0235-4

    authors: Werner B,Williams MJ,Barnes CP,Graham TA,Sottoriva A

    更新日期:2018-12-01 00:00:00

  • Epithelial detachment due to absence of hemidesmosomes in integrin beta 4 null mice.

    abstract::Integrins are heterodimeric transmembrane glycoproteins which are engaged in a variety of cellular functions, such as adhesion, migration and differentiation1. The integrin alpha 6 beta 4 is expressed on squamous epithelia, on subsets of endothelial cells, immature thymocytes and on Schwann cells and fibroblasts in th...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0796-366

    authors: van der Neut R,Krimpenfort P,Calafat J,Niessen CM,Sonnenberg A

    更新日期:1996-07-01 00:00:00

  • An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma.

    abstract::Translocation events are frequent in cancer and may create chimeric fusions or 'regulatory rearrangements' that drive oncogene overexpression. Here we identify super-enhancer translocations that drive overexpression of the oncogenic transcription factor MYB as a recurrent theme in adenoid cystic carcinoma (ACC). Whole...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3502

    authors: Drier Y,Cotton MJ,Williamson KE,Gillespie SM,Ryan RJ,Kluk MJ,Carey CD,Rodig SJ,Sholl LM,Afrogheh AH,Faquin WC,Queimado L,Qi J,Wick MJ,El-Naggar AK,Bradner JE,Moskaluk CA,Aster JC,Knoechel B,Bernstein BE

    更新日期:2016-03-01 00:00:00

  • Plectin deficiency results in muscular dystrophy with epidermolysis bullosa.

    abstract::We report that mutation in the gene for plectin, a cytoskeleton-membrane anchorage protein, is a cause of autosomal recessive muscular dystrophy associated with skin blistering (epidermolysis bullosa simplex). The evidence comes from absence of plectin by antibody staining in affected individuals from four families, s...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0896-450

    authors: Smith FJ,Eady RA,Leigh IM,McMillan JR,Rugg EL,Kelsell DP,Bryant SP,Spurr NK,Geddes JF,Kirtschig G,Milana G,de Bono AG,Owaribe K,Wiche G,Pulkkinen L,Uitto J,McLean WH,Lane EB

    更新日期:1996-08-01 00:00:00

  • Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy.

    abstract::Emery-Dreifuss muscular dystrophy (EDMD) is characterized by early contractures of elbows and Achilles tendons, slowly progressive muscle wasting and weakness, and a cardiomyopathy with conduction blocks which is life-threatening. Two modes of inheritance exist, X-linked (OMIM 310300) and autosomal dominant (EDMD-AD; ...

    journal_title:Nature genetics

    pub_type: 临床试验,杂志文章

    doi:10.1038/6799

    authors: Bonne G,Di Barletta MR,Varnous S,Bécane HM,Hammouda EH,Merlini L,Muntoni F,Greenberg CR,Gary F,Urtizberea JA,Duboc D,Fardeau M,Toniolo D,Schwartz K

    更新日期:1999-03-01 00:00:00

  • Testing for genetic associations in arbitrarily structured populations.

    abstract::We present a new statistical test of association between a trait and genetic markers, which we theoretically and practically prove to be robust to arbitrarily complex population structure. The statistical test involves a set of parameters that can be directly estimated from large-scale genotyping data, such as those m...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3244

    authors: Song M,Hao W,Storey JD

    更新日期:2015-05-01 00:00:00

  • Identification of erythroferrone as an erythroid regulator of iron metabolism.

    abstract::Recovery from blood loss requires a greatly enhanced supply of iron to support expanded erythropoiesis. After hemorrhage, suppression of the iron-regulatory hormone hepcidin allows increased iron absorption and mobilization from stores. We identified a new hormone, erythroferrone (ERFE), that mediates hepcidin suppres...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2996

    authors: Kautz L,Jung G,Valore EV,Rivella S,Nemeth E,Ganz T

    更新日期:2014-07-01 00:00:00

  • Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs.

    abstract::Schizophrenia is a complex disorder caused by both genetic and environmental factors. Using 9,087 affected individuals, 12,171 controls and 915,354 imputed SNPs from the Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium (PGC-SCZ), we estimate that 23% (s.e. = 1%) of variation in liability to sc...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.1108

    authors: Lee SH,DeCandia TR,Ripke S,Yang J,Schizophrenia Psychiatric Genome-Wide Association Study Consortium (PGC-SCZ).,International Schizophrenia Consortium (ISC).,Molecular Genetics of Schizophrenia Collaboration (MGS).,Sullivan PF,Goddard ME

    更新日期:2012-02-19 00:00:00

  • Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.

    abstract::A genome-wide association screen for primary biliary cirrhosis risk alleles was performed in an Italian cohort. The results from the Italian cohort replicated IL12A and IL12RB associations, and a combined meta-analysis using a Canadian dataset identified newly associated loci at SPIB (P = 7.9 x 10(-11), odds ratio (OR...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.627

    authors: Liu X,Invernizzi P,Lu Y,Kosoy R,Lu Y,Bianchi I,Podda M,Xu C,Xie G,Macciardi F,Selmi C,Lupoli S,Shigeta R,Ransom M,Lleo A,Lee AT,Mason AL,Myers RP,Peltekian KM,Ghent CN,Bernuzzi F,Zuin M,Rosina F,Borghesio E

    更新日期:2010-08-01 00:00:00

  • Long-range chromatin regulatory interactions in vivo.

    abstract::Communication between distal chromosomal elements is essential for control of many nuclear processes. For example, genes in higher eukaryotes often require distant enhancer sequences for high-level expression. The mechanisms proposed for long-range enhancer action fall into two basic categories. Non-contact models pro...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1051

    authors: Carter D,Chakalova L,Osborne CS,Dai YF,Fraser P

    更新日期:2002-12-01 00:00:00

  • Mutations in the gene for transglutaminase 1 in autosomal recessive lamellar ichthyosis.

    abstract::We recently mapped the disease locus for severe autosomal recessive lamellar ichthyosis (LI) to chromosome 14q11 and showed complete linkage with TGM1, the gene encoding transglutaminase 1. We have now identified point mutations in TGM1 in two of the multiplex LI families used in the linkage study. Each nucleotide cha...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0395-279

    authors: Russell LJ,DiGiovanna JJ,Rogers GR,Steinert PM,Hashem N,Compton JG,Bale SJ

    更新日期:1995-03-01 00:00:00

  • A missense mutation in the alphaB-crystallin chaperone gene causes a desmin-related myopathy.

    abstract::Desmin-related myopathies (DRM) are inherited neuromuscular disorders characterized by adult onset and delayed accumulation of aggregates of desmin, a protein belonging to the type III intermediate filament family, in the sarcoplasma of skeletal and cardiac muscles. In this paper, we have mapped the locus for DRM in a...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/1765

    authors: Vicart P,Caron A,Guicheney P,Li Z,Prévost MC,Faure A,Chateau D,Chapon F,Tomé F,Dupret JM,Paulin D,Fardeau M

    更新日期:1998-09-01 00:00:00

  • A functional genomics predictive network model identifies regulators of inflammatory bowel disease.

    abstract::A major challenge in inflammatory bowel disease (IBD) is the integration of diverse IBD data sets to construct predictive models of IBD. We present a predictive model of the immune component of IBD that informs causal relationships among loci previously linked to IBD through genome-wide association studies (GWAS) usin...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3947

    authors: Peters LA,Perrigoue J,Mortha A,Iuga A,Song WM,Neiman EM,Llewellyn SR,Di Narzo A,Kidd BA,Telesco SE,Zhao Y,Stojmirovic A,Sendecki J,Shameer K,Miotto R,Losic B,Shah H,Lee E,Wang M,Faith JJ,Kasarskis A,Brodmerkel C

    更新日期:2017-10-01 00:00:00

  • An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHD-type zinc-finger domains.

    abstract::Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is the only described systemic autoimmune disease with established monogenic background, and the first autoimmune disorder localized outside the major histocompatibility complex (MHC) region. The primary biochemical defect in APECED is unknown. We...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1297-399

    authors: Finnish-German APECED Consortium.

    更新日期:1997-12-01 00:00:00

  • The human PAX6 gene is mutated in two patients with aniridia.

    abstract::Aniridia is an inherited ocular disorder of variable expressivity characterized by iris hypoplasia. A candidate aniridia gene, AN, which is the human homologue of the mouse Pax-6 gene, has recently been isolated by positional cloning from the WAGR region of 11p13. Here we describe mutations in this gene in two cases o...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0892-328

    authors: Jordan T,Hanson I,Zaletayev D,Hodgson S,Prosser J,Seawright A,Hastie N,van Heyningen V

    更新日期:1992-08-01 00:00:00

  • LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.

    abstract::Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from a true polygenic signal a...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3211

    authors: Bulik-Sullivan BK,Loh PR,Finucane HK,Ripke S,Yang J,Schizophrenia Working Group of the Psychiatric Genomics Consortium.,Patterson N,Daly MJ,Price AL,Neale BM

    更新日期:2015-03-01 00:00:00

  • iASPP oncoprotein is a key inhibitor of p53 conserved from worm to human.

    abstract::We have previously shown that ASPP1 and ASPP2 are specific activators of p53; one mechanism by which wild-type p53 is tolerated in human breast carcinomas is through loss of ASPP activity. We have further shown that 53BP2, which corresponds to a C-terminal fragment of ASPP2, acts as a dominant negative inhibitor of p5...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1070

    authors: Bergamaschi D,Samuels Y,O'Neil NJ,Trigiante G,Crook T,Hsieh JK,O'Connor DJ,Zhong S,Campargue I,Tomlinson ML,Kuwabara PE,Lu X

    更新日期:2003-02-01 00:00:00

  • A missense mutation in the neuronal nicotinic acetylcholine receptor alpha 4 subunit is associated with autosomal dominant nocturnal frontal lobe epilepsy.

    abstract::Epilepsy affects at least 2% of the population at some time in their lives. The epilepsies are a heterogeneous group of disorders, many with an inherited component. Although specific genes have been identified in a few rare diseases causing seizures as part of a more diffuse brain disorder, the molecular pathology of ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1095-201

    authors: Steinlein OK,Mulley JC,Propping P,Wallace RH,Phillips HA,Sutherland GR,Scheffer IE,Berkovic SF

    更新日期:1995-10-01 00:00:00

  • Exome sequencing of liver fluke-associated cholangiocarcinoma.

    abstract::Opisthorchis viverrini-related cholangiocarcinoma (CCA), a fatal bile duct cancer, is a major public health concern in areas endemic for this parasite. We report here whole-exome sequencing of eight O. viverrini-related tumors and matched normal tissue. We identified and validated 206 somatic mutations in 187 genes us...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2273

    authors: Ong CK,Subimerb C,Pairojkul C,Wongkham S,Cutcutache I,Yu W,McPherson JR,Allen GE,Ng CC,Wong BH,Myint SS,Rajasegaran V,Heng HL,Gan A,Zang ZJ,Wu Y,Wu J,Lee MH,Huang D,Ong P,Chan-on W,Cao Y,Qian CN,Lim KH,Ooi

    更新日期:2012-05-06 00:00:00

  • Mutations in the beta-tubulin gene TUBB2B result in asymmetrical polymicrogyria.

    abstract::Polymicrogyria is a relatively common but poorly understood defect of cortical development characterized by numerous small gyri and a thick disorganized cortical plate lacking normal lamination. Here we report de novo mutations in a beta-tubulin gene, TUBB2B, in four individuals and a 27-gestational-week fetus with bi...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.380

    authors: Jaglin XH,Poirier K,Saillour Y,Buhler E,Tian G,Bahi-Buisson N,Fallet-Bianco C,Phan-Dinh-Tuy F,Kong XP,Bomont P,Castelnau-Ptakhine L,Odent S,Loget P,Kossorotoff M,Snoeck I,Plessis G,Parent P,Beldjord C,Cardoso C,Repr

    更新日期:2009-06-01 00:00:00