当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference.

Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference.

Abstract：

:Single nucleotide polymorphisms (SNPs) in commercial arrays have often been discovered in a small number of samples from selected populations. This ascertainment skews patterns of nucleotide diversity and affects population genetic inferences. We propose a demographic inference pipeline that explicitly models the SNP discovery protocol in an Approximate Bayesian Computation (ABC) framework. We simulated genomic regions according to a demographic model incorporating parameters for the divergence of three well-characterized HapMap populations and recreated the SNP distribution of a commercial array by varying the number of haploid samples and the allele frequency cut-off in the given regions. We then calculated summary statistics obtained from both the ascertained and genomic data and inferred ascertainment and demographic parameters. We implemented our pipeline to study the admixture process that gave rise to the present-day Mexican population. Our estimate of the time of admixture is closer to the historical dates than those in previous works which did not consider ascertainment bias. Although the use of whole genome sequences for demographic inference is becoming the norm, there are still underrepresented areas of the world from where only SNP array data are available. Our inference framework is applicable to those cases and will help with the demographic inference.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Quinto-Cortés CD,Woerner AE,Watkins JC,Hammer MF

doi

10.1038/s41598-018-28539-y

subject

Has Abstract

pub_date

2018-07-05 00:00:00

pages

10209

issue

1

issn

2045-2322

pii

10.1038/s41598-018-28539-y

journal_volume

8

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • 5T4-specific chimeric antigen receptor modification promotes the immune efficacy of cytokine-induced killer cells against nasopharyngeal carcinoma stem cell-like cells.

    abstract：:Relapse and metastasis of nasopharyngeal carcinoma (NPC) are presumably attributed to cancer stem cells (CSCs). In recent years, chimeric antigen receptor (CAR)-modified immune effector cells have been shown to have impressive antitumour efficacy. In this study, we aimed to identify appropriate tumour-associated antig...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-04756-9

    authors： Guo X,Zheng H,Luo W,Zhang Q,Liu J,Yao K

    更新日期：2017-07-07 00:00:00

  • Hepatitis B virus X protein is capable of down-regulating protein level of host antiviral protein APOBEC3G.

    abstract：:The apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family proteins bind RNA and single-stranded DNA, and create C-to-U base modifications through cytidine deaminase activity. APOBEC3G restricts human immunodeficiency virus 1 (HIV-1) infection by creating hypermutations in proviral DNA, while HIV-1-e...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep40783

    authors： Chen R,Zhao X,Wang Y,Xie Y,Liu J

    更新日期：2017-01-18 00:00:00

  • Denatured lysozyme-coated carbon nanotubes: a versatile biohybrid material.

    abstract：:Carbon nanotubes (CNTs) are among the most versatile nanomaterials, but their exploitation is hindered by limited dispersibility, especially in aqueous solvents. Here, we show that AP-LYS, a highly cationic soluble derivative of denatured hen egg lysozyme, is a very effective tool for the unbundling and solubilisation...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-52701-9

    authors： Siepi M,Donadio G,Dardano P,De Stefano L,Monti DM,Notomista E

    更新日期：2019-11-12 00:00:00

  • Comparative assessment of transmission-blocking vaccine candidates against Plasmodium falciparum.

    abstract：:Malaria transmission-blocking vaccines (TBVs) target the development of Plasmodium parasites within the mosquito, with the aim of preventing malaria transmission from one infected individual to another. Different vaccine platforms, mainly protein-in-adjuvant formulations delivering the leading candidate antigens, have...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep11193

    authors： Kapulu MC,Da DF,Miura K,Li Y,Blagborough AM,Churcher TS,Nikolaeva D,Williams AR,Goodman AL,Sangare I,Turner AV,Cottingham MG,Nicosia A,Straschil U,Tsuboi T,Gilbert SC,Long CA,Sinden RE,Draper SJ,Hill AV,Cohuet A,

    更新日期：2015-06-11 00:00:00

  • Establishment of induced pluripotent stem cells from normal B cells and inducing AID expression in their differentiation into hematopoietic progenitor cells.

    abstract：:B cell derived induced pluripotent stem cells (BiPSCs) were recently established from peripheral blood B cells by the simultaneous transfection of Yamanaka factors (Oct3/4, Sox2, Klf4, c-Myc) and C/EBPα using a Sendai virus vector. Here, using a different method, we established BiPSCs with immunoglobulin heavy chain (...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-01627-1

    authors： Kawamura F,Inaki M,Katafuchi A,Abe Y,Tsuyama N,Kurosu Y,Yanagi A,Higuchi M,Muto S,Yamaura T,Suzuki H,Noji H,Suzuki S,Yoshida MA,Sasatani M,Kamiya K,Onodera M,Sakai A

    更新日期：2017-05-10 00:00:00

  • How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae).

    abstract：:Microalgae identification is extremely difficult. The efficiency of DNA barcoding in microalgae identification involves ideal gene markers and approaches employed, which however, is still under the way. Although Scenedesmus has obtained much research in producing lipids its identification is difficult. Here we present...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep36822

    authors： Zou S,Fei C,Wang C,Gao Z,Bao Y,He M,Wang C

    更新日期：2016-11-09 00:00:00

  • An atypical phosphodiesterase capable of degrading haloalkyl phosphate diesters from Sphingobium sp. strain TCM1.

    abstract：:Sphingobium sp. strain TCM1 can degrade tris(2-chloroethyl) phosphate (TCEP) to inorganic phosphate and 2-chloroethanol. A phosphotriesterase (PTE), phosphodiesterase (PDE) and phosphomonoesterase (PME) are believed to be involved in the degradation of TCEP. The PTE and PME that respectively catalyze the first and thi...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-03142-9

    authors： Abe K,Mukai N,Morooka Y,Makino T,Oshima K,Takahashi S,Kera Y

    更新日期：2017-06-06 00:00:00

  • Improving femtosecond laser pulse delivery through a hollow core photonic crystal fiber for temporally focused two-photon endomicroscopy.

    abstract：:In this paper, we present a strategy to improve delivery of femtosecond laser pulses from a regenerative amplifier through a hollow core photonic crystal fiber for temporally focused wide-field two-photon endomicroscopy. For endomicroscope application, wide-field two-photon excitation has the advantage of requiring no...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep06626

    authors： Choi H,So PT

    更新日期：2014-10-15 00:00:00

  • Intracerebroventricular injection of ouabain causes mania-like behavior in mice through D2 receptor activation.

    abstract：:Intracerebroventricular (ICV) administration of ouabain, an inhibitor of the Na, K-ATPase, is an approach used to study the physiological functions of the Na, K-ATPase and cardiotonic steroids in the central nervous system, known to cause mania-like hyperactivity in rats. We describe a mouse model of ouabain-induced m...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-52058-z

    authors： Lopachev A,Volnova A,Evdokimenko A,Abaimov D,Timoshina Y,Kazanskaya R,Lopacheva O,Deal A,Budygin E,Fedorova T,Gainetdinov R

    更新日期：2019-10-30 00:00:00

  • Clinical evaluation of silicone gel in the treatment of cleft lip scars.

    abstract：:Upper lip scars are at risk of hypertrophy. Our center therefore uses microporous tape and silicone sheeting for postoperative scar care following cleft lip repair. However, some babies have previously ingested their silicone sheeting, which has the potential for respiratory compromise or gastrointestinal obstruction....

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-25697-x

    authors： Chang CS,Wallace CG,Hsiao YC,Huang JJ,Chen ZC,Chang CJ,Lo LJ,Chen PK,Chen JP,Chen YR

    更新日期：2018-05-09 00:00:00

  • Anthropogenic effects on a tropical forest according to the distance from human settlements.

    abstract：:The protection of tropical forests is one of the most urgent issues in conservation biology because of the rapid deforestation that has occurred over the last 50 years. Even in protected forests, the anthropogenic effects from newly expanding villages such as harvesting of medicinal plants, pasturing cattle and forest...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep14689

    authors： Popradit A,Srisatit T,Kiratiprayoon S,Yoshimura J,Ishida A,Shiyomi M,Murayama T,Chantaranothai P,Outtaranakorn S,Phromma I

    更新日期：2015-10-05 00:00:00

  • Vision Status in Older Adults: The Brazilian Amazon Region Eye Survey.

    abstract：:Older adults living in remote areas with limited access to health services are at higher risk to develop visual impairment and blindness. We conducted a population-based survey to determine the vision status in subjects 45 years of age and older from urban and rural areas of Parintins city, Brazilian Amazon Region. Pa...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-19338-6

    authors： Salomão SR,Berezovsky A,Furtado JM,Fernandes AG,Muñoz S,Cavascan NN,Cypel MC,Cunha CC,Vasconcelos GC,Mitsuhiro MRKH,Sacai PY,Campos M,Morales PHA,Cohen MJ,Cohen JM,Watanabe SES,Belfort R Jr

    更新日期：2018-01-17 00:00:00

  • Hyphal network whole field imaging allows for accurate estimation of anastomosis rates and branching dynamics of the filamentous fungus Podospora anserina.

    abstract：:The success of filamentous fungi in colonizing most natural environments can be largely attributed to their ability to form an expanding interconnected network, the mycelium, or thallus, constituted by a collection of hyphal apexes in motion producing hyphae and subject to branching and fusion. In this work, we charac...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-57808-y

    authors： Dikec J,Olivier A,Bobée C,D'Angelo Y,Catellier R,David P,Filaine F,Herbert S,Lalanne C,Lalucque H,Monasse L,Rieu M,Ruprich-Robert G,Véber A,Chapeland-Leclerc F,Herbert E

    更新日期：2020-02-21 00:00:00

  • Inclusive groups can avoid the tragedy of the commons.

    abstract：:The public goods game is a famous example illustrating the tragedy of the commons (Hardin in Science 162:1243-1248, 1968). In this game cooperating individuals contribute to a pool, which in turn is distributed to all members of the group, including defectors who reap the same rewards as cooperators without having mad...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-79731-y

    authors： Hintze A,Staudacher J,Gelhar K,Pothmann A,Rasch J,Wildegger D

    更新日期：2020-12-28 00:00:00

  • Comparative temporal metabolomics studies to investigate interspecies variation in three Ocimum species.

    abstract：:Ocimum is one of the most revered medicinally useful plants which have various species. Each of the species is distinct in terms of metabolite composition as well as the medicinal property. Some basil types are used more often as an aromatic and flavoring ingredient. It would be informative to know relatedness among t...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-61957-5

    authors： Rastogi S,Shah S,Kumar R,Kumar A,Shasany AK

    更新日期：2020-03-23 00:00:00

  • A novel metabarcoding diagnostic tool to explore protozoan haemoparasite diversity in mammals: a proof-of-concept study using canines from the tropics.

    abstract：:Haemoparasites are responsible for some of the most prevalent and debilitating canine illnesses across the globe, whilst also posing a significant zoonotic risk to humankind. Nowhere are the effects of such parasites more pronounced than in developing countries in the tropics where the abundance and diversity of ectop...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-49118-9

    authors： Huggins LG,Koehler AV,Ng-Nguyen D,Wilcox S,Schunack B,Inpankaew T,Traub RJ

    更新日期：2019-09-02 00:00:00

  • Highly hydrophilic poly(vinylidene fluoride)/meso-titania hybrid mesoporous membrane for photocatalytic membrane reactor in water.

    abstract：:The high hydrophobicity of poly(vinylidene fluoride) (PVDF) membrane remains an obstacle to be applied in some purification processes of water or wastewater. Herein, a highly hydrophilic hybrid mesoporous titania membrane composed of mesoporous anatase titania (meso-TiO2) materials inside the three-dimensional (3D) ma...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep19148

    authors： Wang M,Yang G,Jin P,Tang H,Wang H,Chen Y

    更新日期：2016-01-12 00:00:00

  • In vivo assembly of DNA-fragments in the moss, Physcomitrella patens.

    abstract：:Direct assembly of multiple linear DNA fragments via homologous recombination, a phenomenon known as in vivo assembly or transformation associated recombination, is used in biotechnology to assemble DNA constructs ranging in size from a few kilobases to full synthetic microbial genomes. It has also enabled the complet...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep25030

    authors： King BC,Vavitsas K,Ikram NK,Schrøder J,Scharff LB,Bassard JÉ,Hamberger B,Jensen PE,Simonsen HT

    更新日期：2016-04-29 00:00:00

  • Secrets of virtuoso: neuromuscular attributes of motor virtuosity in expert musicians.

    abstract：:Musical performance requires extremely fast and dexterous limb movements. The underlying biological mechanisms have been an object of interest among scientists and non-scientists for centuries. Numerous studies of musicians and non-musicians have demonstrated that neuroplastic adaptations through early and deliberate ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep15750

    authors： Furuya S,Oku T,Miyazaki F,Kinoshita H

    更新日期：2015-10-27 00:00:00

  • Increasing endogenous activity of NMDARs on GABAergic neurons increases inhibition, alters sensory processing and prevents noise-induced tinnitus.

    abstract：:Selective enhancement of GABAergic inhibition is thought to impact many vital brain functions and interferes with the genesis and/or progression of numerous brain disorders. Here, we show that selectively increasing NMDA receptor activity in inhibitory neurons using an NMDAR positive allosteric modulator (PAM) elevate...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-68652-5

    authors： Deng D,Masri S,Yao L,Ma X,Cao X,Yang S,Bao S,Zhou Q

    更新日期：2020-07-20 00:00:00

  • The NMDA receptor GluN2C subunit controls cortical excitatory-inhibitory balance, neuronal oscillations and cognitive function.

    abstract：:Despite strong evidence for NMDA receptor (NMDAR) hypofunction as an underlying factor for cognitive disorders, the precise roles of various NMDAR subtypes remains unknown. The GluN2C-containing NMDARs exhibit unique biophysical properties and expression pattern, and lower expression of GluN2C subunit has been reporte...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep38321

    authors： Gupta SC,Ravikrishnan A,Liu J,Mao Z,Pavuluri R,Hillman BG,Gandhi PJ,Stairs DJ,Li M,Ugale RR,Monaghan DT,Dravid SM

    更新日期：2016-12-06 00:00:00

  • Irigenin, a novel lead from Western Himalayan chemiome inhibits Fibronectin-Extra Domain A induced metastasis in Lung cancer cells.

    abstract：:Several lines of evidence indicate that Fibronectin Extra Domain A (EDA) promotes metastatic capacity of tumor cells by engaging cell surface α9β1 integrins. This interaction mediated by the C-C loop of EDA activates pro-oncogenic signaling pathways leading to epithelial to mesenchymal transition (EMT) of tumor cells,...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep37151

    authors： Amin A,Chikan NA,Mokhdomi TA,Bukhari S,Koul AM,Shah BA,Gharemirshamlu FR,Wafai AH,Qadri A,Qadri RA

    更新日期：2016-11-16 00:00:00

  • Computational Simulations of Provisional Stenting of a Diseased Coronary Artery Bifurcation Model.

    abstract：:Although stenting of non-branched arterial segments has acceptable clinical outcomes, in-stent restenosis (ISR) and stent thrombosis remain clinically significant issues for vascular bifurcations (15-28% restenosis). Local fluid and solid stresses appear to play an important role in restenosis and thrombosis. The comb...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-66777-1

    authors： Chen HY,Chatzizisis YS,Louvard Y,Kassab GS

    更新日期：2020-06-15 00:00:00

  • Multisensory learning between odor and sound enhances beta oscillations.

    abstract：:Multisensory interactions are essential to make sense of the environment by transforming the mosaic of sensory inputs received by the organism into a unified perception. Brain rhythms allow coherent processing within areas or between distant brain regions and could thus be instrumental in functionally connecting remot...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-47503-y

    authors： Gnaedinger A,Gurden H,Gourévitch B,Martin C

    更新日期：2019-08-02 00:00:00

  • Tandem Mass Tag (TMT)-based quantitative proteomics reveals potential targets associated with onset of Sub-clinical Mastitis in cows.

    abstract：:Bovine milk is vital for infant nutrition and is a major component of the human diet. Bovine mastitis is a common inflammatory disease of mammary gland in cattle. It alters the immune profile of the animal and lowers the quality and yield of milk causing huge economic losses to dairy industry. The incidence of sub-cli...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-66211-6

    authors： Bathla S,Sindhu A,Kumar S,Dubey SK,Pattnaik S,Rawat P,Chopra A,Dang A,Kaushik JK,Mohanty AK

    更新日期：2020-06-09 00:00:00

  • In vivo effect of opticin deficiency in cartilage in a surgically induced mouse model of osteoarthritis.

    abstract：:The SLRP opticin (OPTC) has been demonstrated to be produced and degraded in osteoarthritic (OA) human cartilage. Here, we investigated the in vivo effect of OPTC deficiency in OA cartilage. OA was induced in 10-week-old Optc -/- and Optc +/+ mice. Ten weeks post-surgery, cartilage was processed for histology and immu...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-18047-w

    authors： Farrán A,Valverde-Franco G,Tío L,Lussier B,Fahmi H,Pelletier JP,Bishop PN,Monfort J,Martel-Pelletier J

    更新日期：2018-01-11 00:00:00

  • Paenibacillus polymyxa biofilm polysaccharides antagonise Fusarium graminearum.

    abstract：:Fusarium Head Blight (FHB) caused by Fusarium graminearum pathogens constitutes a major threat to agricultural production because it frequently reduces the yield and quality of the crop. The disease severity is predicted to increase in various regions owing to climate change. Integrated management where biocontrol pla...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-37718-w

    authors： Timmusk S,Copolovici D,Copolovici L,Teder T,Nevo E,Behers L

    更新日期：2019-01-24 00:00:00

  • Sulphur and carbon isotopes as tracers of past sub-seafloor microbial activity.

    abstract：:Microbial life below the seafloor has changed over geological time, but these changes are often not obvious, as they are not recorded in the sediment. Sulphur (S) isotope values in pyrite extracted from a Plio- to Holocene sequence of the Peru Margin (Ocean Drilling Program, ODP, Site 1229) show a down-core pattern th...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-36943-7

    authors： Meister P,Brunner B,Picard A,Böttcher ME,Jørgensen BB

    更新日期：2019-01-24 00:00:00

  • Systematic in vivo evaluation of the time-dependent inflammatory response to steel and Teflon insulin infusion catheters.

    abstract：:Continuous subcutaneous insulin infusion (CSII) catheters are considered the weak link of insulin pump therapy. Wear-time considerably varies between patients and the choice of catheter material is based on personal preferences rather than scientific facts. Therefore, we systematically assessed and quantified the infl...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-18790-0

    authors： Hauzenberger JR,Münzker J,Kotzbeck P,Asslaber M,Bubalo V,Joseph JI,Pieber TR

    更新日期：2018-01-18 00:00:00

  • Reliable variant calling during runtime of Illumina sequencing.

    abstract：:The sequential paradigm of data acquisition and analysis in next-generation sequencing leads to high turnaround times for the generation of interpretable results. We combined a novel real-time read mapping algorithm with fast variant calling to obtain reliable variant calls still during the sequencing process. Thereby...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-52991-z

    authors： Loka TP,Tausch SH,Renard BY

    更新日期：2019-11-11 00:00:00