Improving polygenic risk prediction from summary statistics by an empirical Bayes approach.

Abstract:

:Polygenic risk scores (PRS) from genome-wide association studies (GWAS) are increasingly used to predict disease risks. However some included variants could be false positives and the raw estimates of effect sizes from them may be subject to selection bias. In addition, the standard PRS approach requires testing over a range of p-value thresholds, which are often chosen arbitrarily. The prediction error estimated from the optimized threshold may also be subject to an optimistic bias. To improve genomic risk prediction, we proposed new empirical Bayes approaches to recover the underlying effect sizes and used them as weights to construct PRS. We applied the new PRS to twelve cardio-metabolic traits in the Northern Finland Birth Cohort and demonstrated improvements in predictive power (in R2) when compared to standard PRS at the best p-value threshold. Importantly, for eleven out of the twelve traits studied, the predictive performance from the entire set of genome-wide markers outperformed the best R2 from standard PRS at optimal p-value thresholds. Our proposed methodology essentially enables an automatic PRS weighting scheme without the need of choosing tuning parameters. The new method also performed satisfactorily in simulations. It is computationally simple and does not require assumptions on the effect size distributions.

journal_name

Sci Rep

journal_title

Scientific reports

authors

So HC,Sham PC

doi

10.1038/srep41262

subject

Has Abstract

pub_date

2017-02-01 00:00:00

pages

41262

issn

2045-2322

pii

srep41262

journal_volume

7

pub_type

杂志文章
  • Moderate drop in water table increases peatland vulnerability to post-fire regime shift.

    abstract::Northern and tropical peatlands represent a globally significant carbon reserve accumulated over thousands of years of waterlogged conditions. It is unclear whether moderate drying predicted for northern peatlands will stimulate burning and carbon losses as has occurred in their smaller tropical counterparts where the...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08063

    authors: Kettridge N,Turetsky MR,Sherwood JH,Thompson DK,Miller CA,Benscoter BW,Flannigan MD,Wotton BM,Waddington JM

    更新日期:2015-01-27 00:00:00

  • Effects of açai on oxidative stress, ER stress, and inflammation-related parameters in mice with high fat diet-fed induced NAFLD.

    abstract::Non-alcoholic fatty liver disease (NAFLD), the most predominant liver disease worldwide, is a progressive condition that encompasses a spectrum of disorders ranging from steatosis to steatohepatitis, and, ultimately, cirrhosis and hepatocellular carcinoma. Although the underlying mechanism is complex and multifactoria...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-44563-y

    authors: de Freitas Carvalho MM,Lage NN,de Souza Paulino AH,Pereira RR,de Almeida LT,da Silva TF,de Brito Magalhães CL,de Lima WG,Silva ME,Pedrosa ML,da Costa Guerra JF

    更新日期:2019-05-30 00:00:00

  • Construction of a Miniaturized Chromatic Acclimation Sensor from Cyanobacteria with Reversed Response to a Light Signal.

    abstract::Cyanobacteria harbor unique photoreceptors, designated as cyanobacteriochromes (CBCRs). In this study, we attempted to engineer the chromatic acclimation sensor CcaS, a CBCR derived from the cyanobacterium Synechocystis sp. PCC 6803. The wild-type CcaS induces gene expression under green light illumination and repress...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep37595

    authors: Nakajima M,Ferri S,Rögner M,Sode K

    更新日期:2016-11-24 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

  • TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

    abstract::Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-25337-4

    authors: Hou Y,Konen J,Brat DJ,Marcus AI,Cooper LAD

    更新日期:2018-05-08 00:00:00

  • Genome-wide miRNA profiling reinforces the importance of miR-9 in human papillomavirus associated oral and oropharyngeal head and neck cancer.

    abstract::Head and neck cancer is the sixth most common malignancy worldwide, predominantly developing from squamous cell epithelia (HNSCC). The main HNSCC risk factors are tobacco, excessive alcohol use, and the presence of human papillomavirus (HPV). HPV positive (+) cancers are etiologically different from other HNSCC and of...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-38797-z

    authors: Božinović K,Sabol I,Dediol E,Milutin Gašperov N,Manojlović S,Vojtechova Z,Tachezy R,Grce M

    更新日期:2019-02-19 00:00:00

  • Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites.

    abstract::The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08967

    authors: Li ZK,Fu HM,Sha PF,Zhu ZW,Wang AM,Li H,Zhang HW,Zhang HF,Hu ZQ

    更新日期:2015-03-11 00:00:00

  • Metabolic and transcriptional alternations for defense by interfering OsWRKY62 and OsWRKY76 transcriptions in rice.

    abstract::Metabolomic and transcriptomic approaches were used to dissect the enhanced disease resistance in the plants harbouring a RNA interfering construct of OsWRKY62 and OsWRKY76 (dsOW62/76) genes. The primary metabolic pathways were activated in dsOW62/76 compared with wild-type (ZH17) plants, revealed by increased accumul...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-02643-x

    authors: Liang X,Chen X,Li C,Fan J,Guo Z

    更新日期:2017-05-30 00:00:00

  • Attentional Control in Adolescent Mice Assessed with a Modified Five Choice Serial Reaction Time Task.

    abstract::Adolescence is a critical period for the development of higher-order cognitive functions. Unlike in humans, very limited tools are available to assess such cognitive abilities in adolescent rodents. We implemented a modified 5-Choice Serial Reaction Time Task (5CSRTT) to selectively measure attentiveness, impulsivity,...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10112-8

    authors: Ciampoli M,Contarini G,Mereu M,Papaleo F

    更新日期:2017-08-30 00:00:00

  • Hirsutella sinensis mycelium attenuates bleomycin-induced pulmonary inflammation and fibrosis in vivo.

    abstract::Hirsutella sinensis mycelium (HSM), the anamorph of Cordyceps sinensis, is a traditional Chinese medicine that has been shown to possess various pharmacological properties. We previously reported that this fungus suppresses interleukin-1β and IL-18 secretion by inhibiting both canonical and non-canonical inflammasomes...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15282

    authors: Huang TT,Lai HC,Ko YF,Ojcius DM,Lan YW,Martel J,Young JD,Chong KY

    更新日期:2015-10-26 00:00:00

  • Studies of the oligomerisation mechanism of a cystatin-based engineered protein scaffold.

    abstract::Engineered protein scaffolds are an alternative to monoclonal antibodies in research and drug design due to their small size, ease of production, versatility, and specificity for chosen targets. One key consideration when engineering such proteins is retaining the original scaffold structure and stability upon inserti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-45565-6

    authors: Zalar M,Indrakumar S,Levy CW,Tunnicliffe RB,Peters GHJ,Golovanov AP

    更新日期:2019-06-21 00:00:00

  • Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes.

    abstract::Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins whose role as drug targets against pathogens, as well as in valuable chemical production and bioremediation, has been explored. In this study we performed comprehensive comparative analysis of P450s in 13 newly explored oomycete pathogens. Three hundred...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep11572

    authors: Sello MM,Jafta N,Nelson DR,Chen W,Yu JH,Parvez M,Kgosiemang IKR,Monyaki R,Raselemane SC,Qhanya LB,Mthakathi NT,Sitheni Mashele S,Syed K

    更新日期:2015-07-01 00:00:00

  • Neck lymph node status on survival of regionally recurrent or persistent nasopharyngeal carcinoma.

    abstract::The aim of this study was to evaluate the impact of lymph node status from neck dissection pathological specimens on the survival for isolated regional nodal recurrence or persistence after primary treatment of nasopharyngeal carcinoma. Through a retrospective cohort study performed in an academic tertiary referral ho...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-62625-4

    authors: Yeung DCM,Yeung Z,Wong EWY,Vlantis AC,Chan JYK

    更新日期:2020-03-27 00:00:00

  • Low temperature solution process-based defect-induced orange-red light emitting diode.

    abstract::We report low-temperature solution-processed p-CuO nanorods (NRs)/n-ZnO NRs heterojunction light emitting diode (LED), exploiting the native point defects of ZnO NRs. ZnO NRs were synthesized at 90 °C by using hydrothermal method while CuO NRs were synthesized at 100 °C by using microwave reaction system. The electric...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep17961

    authors: Biswas P,Baek SD,Lee SH,Park JH,Lee SJ,Lee TI,Myoung JM

    更新日期:2015-12-09 00:00:00

  • Subacute to chronic Alzheimer-like alterations after controlled cortical impact in human tau transgenic mice.

    abstract::Repetitive traumatic brain injury (TBI) has been linked to late life development of chronic traumatic encephalopathy (CTE), a neurodegenerative disorder histopathologically characterized by perivascular tangles of hyperphosphorylated tau at the depth of sulci to later widespread neurofibrillary pathology. Although tau...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-40678-4

    authors: Zhang Y,Wu F,Iqbal K,Gong CX,Hu W,Liu F

    更新日期:2019-03-07 00:00:00

  • Altered microRNA and target gene expression related to Tetralogy of Fallot.

    abstract::MicroRNAs (miRNAs) play an important role in guiding development and maintaining function of the human heart. Dysregulation of miRNAs has been linked to various congenital heart diseases including Tetralogy of Fallot (TOF), which represents the most common cyanotic heart malformation in humans. Several studies have id...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-55570-4

    authors: Grunert M,Appelt S,Dunkel I,Berger F,Sperling SR

    更新日期:2019-12-13 00:00:00

  • Differential photosynthetic and morphological adaptations to low light affect depth distribution of two submersed macrophytes in lakes.

    abstract::To evaluate the relative importance of photosynthetic versus morphological adaptations of submersed macrophytes to low light intensity in lakes, rapid light curves (RLCs), morphological parameters, relative growth rate (RGR), clonal reproduction and abundance of two submersed macrophytes (Potamogeton maackianus and Va...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep34028

    authors: Chen J,Cao T,Zhang X,Xi Y,Ni L,Jeppesen E

    更新日期:2016-10-03 00:00:00

  • EnSVMB: Metagenomics Fragments Classification using Ensemble SVM and BLAST.

    abstract::Metagenomics brings in new discoveries and insights into the uncultured microbial world. One fundamental task in metagenomics analysis is to determine the taxonomy of raw sequence fragments. Modern sequencing technologies produce relatively short fragments and greatly increase the number of fragments, and thus make th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-09947-y

    authors: Jiang Y,Wang J,Xia D,Yu G

    更新日期:2017-08-25 00:00:00

  • Molecular basis of canalization in an ascidian species complex adapted to different thermal conditions.

    abstract::Canalization is a result of intrinsic developmental buffering that ensures phenotypic robustness under genetic variation and environmental perturbation. As a consequence, animal phenotypes are remarkably consistent within a species under a wide range of conditions, a property that seems contradictory to evolutionary c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep16717

    authors: Sato A,Kawashima T,Fujie M,Hughes S,Satoh N,Shimeld SM

    更新日期:2015-11-18 00:00:00

  • Co-delivery of VEGF and bFGF via a PLGA nanoparticle-modified BAM for effective contracture inhibition of regenerated bladder tissue in rabbits.

    abstract::Graft contracture is a common problem associated with the regeneration processes of tissue-engineered bladders. Currently, most strategies used for incorporating bioactive molecules into biomaterial designs do not work during all phases of tissue regeneration. In this study, we used a growth factor-PLGA nanoparticle t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20784

    authors: Jiang X,Lin H,Jiang D,Xu G,Fang X,He L,Xu M,Tang B,Wang Z,Cui D,Chen F,Geng H

    更新日期:2016-02-08 00:00:00

  • Organelle membrane derived patches: reshaping classical methods for new targets.

    abstract::Intracellular ion channels are involved in multiple signaling processes, including such crucial ones as regulation of cellular motility and fate. With 95% of the cellular membrane belonging to intracellular organelles, it is hard to overestimate the importance of intracellular ion channels. Multiple studies have been ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-13968-y

    authors: Shapovalov G,Ritaine A,Bidaux G,Slomianny C,Borowiec AS,Gordienko D,Bultynck G,Skryma R,Prevarskaya N

    更新日期:2017-10-26 00:00:00

  • ATF4 overexpression induces early onset of hyperlipidaemia and hepatic steatosis and enhances adipogenesis in zebrafish.

    abstract::Activating transcription factor 4 (ATF4) is constitutively expressed in a variety of tissues, and regulates several pathological features associated with metabolic diseases such as non-alcoholic fatty liver diseases (NAFLD) and obesity. However, the role of ATF4 in animal model systems is poorly understood. To investi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-16587-9

    authors: Yeh KY,Lai CY,Lin CY,Hsu CC,Lo CP,Her GM

    更新日期:2017-11-27 00:00:00

  • Droplet Controlled Growth Dynamics in Molecular Beam Epitaxy of Nitride Semiconductors.

    abstract::The growth dynamics of Ga(In)N semiconductors by Plasma-Assisted Molecular Beam Epitaxy (PAMBE) at low temperatures (T = 450 °C) is here investigated. The presence of droplets at the growth surface strongly affects the adatom incorporation dynamics, making the growth rate a decreasing function of the metal flux imping...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-28984-9

    authors: Azadmand M,Barabani L,Bietti S,Chrastina D,Bonera E,Acciarri M,Fedorov A,Tsukamoto S,Nötzel R,Sanguinetti S

    更新日期:2018-07-26 00:00:00

  • DNA-damage and cell cycle arrest initiated anti-cancer potency of super tiny carbon dots on MCF7 cell line.

    abstract::While carbon-based materials have spearheaded numerous breakthroughs in biomedicine, they also have procreated many logical concerns on their overall toxicity. Carbon dots (CDs) as a respectively new member have been extensively explored in nucleus directed delivery and bioimaging due to their intrinsic fluorescence p...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-70796-3

    authors: Şimşek S,Şüküroğlu AA,Yetkin D,Özbek B,Battal D,Genç R

    更新日期:2020-08-17 00:00:00

  • Plk1 phosphorylation of CAP-H2 triggers chromosome condensation by condensin II at the early phase of mitosis.

    abstract::Condensin complexes play crucial roles in chromosome condensation that is a fundamental process to establish the "rod-like" shape of chromosome structure in mitosis. Failure of the chromosome assembly causes chromosome segregation errors and subsequent genomic instability. However, a molecular mechanism that controls ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05986-7

    authors: Kagami Y,Ono M,Yoshida K

    更新日期:2017-07-17 00:00:00

  • A ParDE-family toxin antitoxin system in major resistance plasmids of Enterobacteriaceae confers antibiotic and heat tolerance.

    abstract::Toxin-antitoxin (TA) systems were initially discovered as plasmid addiction systems on low-copy-number plasmids. Thousands of TA loci have since been identified on chromosomes, plasmids and mobile elements in bacteria and archaea with diverse roles in bacterial physiology and in maintenance of genetic elements. Here, ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-46318-1

    authors: Kamruzzaman M,Iredell J

    更新日期:2019-07-08 00:00:00

  • Minority and Majority Charge Carrier Mobility in Cu2ZnSnSe4 revealed by Terahertz Spectroscopy.

    abstract::The mobilities of electrons and holes determine the applicability of any semiconductor, but their individual measurement remains a major challenge. Here, we show that time-resolved terahertz spectroscopy (TRTS) can distinguish the mobilities of minority and majority charge carriers independently of the doping-type and...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-32695-6

    authors: Hempel H,Hages CJ,Eichberger R,Repins I,Unold T

    更新日期:2018-09-27 00:00:00

  • Identification of a peptide for folate receptor alpha by phage display and its tumor targeting activity in ovary cancer xenograft.

    abstract::The expression level of folate receptor alpha (FRα) is located highly rate in ovarian cancer though it is remained absent in normal tissues. This highly tumor restricted expression profile makes FRα a promising target for tumor therapy and diagnosis. In this research we report a FRα binding peptide C7(Met-His-Thr-Ala-...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-26683-z

    authors: Xing L,Xu Y,Sun K,Wang H,Zhang F,Zhou Z,Zhang J,Zhang F,Caliskan B,Qiu Z,Wang M

    更新日期:2018-05-30 00:00:00

  • N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont.

    abstract::Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-70834-0

    authors: Zilius M,Bonaglia S,Broman E,Chiozzini VG,Samuiloviene A,Nascimento FJA,Cardini U,Bartoli M

    更新日期:2020-08-18 00:00:00

  • Upconverting SrF2 nanoparticles doped with Yb3+/Ho3+, Yb3+/Er3+ and Yb3+/Tm3+ ions - optimisation of synthesis method, structural, spectroscopic and cytotoxicity studies.

    abstract::For a number of years nanomaterials have been continuously devised and comprehensively investigated because of the growing demand for them and their multifarious applications, especially in medicine. This paper reports on the properties of SrF2 nanoparticles (NPs) for applications in biomedicine, showing effective way...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-45025-1

    authors: Przybylska D,Ekner-Grzyb A,Grześkowiak BF,Grzyb T

    更新日期:2019-06-17 00:00:00