Literature DB >> 26395907

Sparse meta-analysis with high-dimensional data.

Qianchuan He1, Hao Helen Zhang2, Christy L Avery3, D Y Lin4.   

Abstract

Meta-analysis plays an important role in summarizing and synthesizing scientific evidence derived from multiple studies. With high-dimensional data, the incorporation of variable selection into meta-analysis improves model interpretation and prediction. Existing variable selection methods require direct access to raw data, which may not be available in practical situations. We propose a new approach, sparse meta-analysis (SMA), in which variable selection for meta-analysis is based solely on summary statistics and the effect sizes of each covariate are allowed to vary among studies. We show that the SMA enjoys the oracle property if the estimated covariance matrix of the parameter estimators from each study is available. We also show that our approach achieves selection consistency and estimation consistency even when summary statistics include only the variance estimators or no variance/covariance information at all. Simulation studies and applications to high-throughput genomics studies demonstrate the usefulness of our approach.
© The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Keywords:  Fixed-effects models; Genomics studies; Oracle property; Random-effects models; Variable selection; Within-group sparsity

Mesh:

Year:  2015        PMID: 26395907      PMCID: PMC4834947          DOI: 10.1093/biostatistics/kxv038

Source DB:  PubMed          Journal:  Biostatistics        ISSN: 1465-4644            Impact factor:   5.899


  18 in total

1.  Extending DerSimonian and Laird's methodology to perform multivariate random effects meta-analyses.

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3.  Integrative analysis and variable selection with multiple high-dimensional data sets.

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Journal:  Biostatistics       Date:  2011-03-16       Impact factor: 5.899

4.  On the relative efficiency of using summary statistics versus individual-level data in meta-analysis.

Authors:  D Y Lin; D Zeng
Journal:  Biometrika       Date:  2010-04-15       Impact factor: 2.445

5.  Meta-analysis in clinical trials.

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Journal:  Control Clin Trials       Date:  1986-09

6.  A method of moments estimator for random effect multivariate meta-analysis.

Authors:  Han Chen; Alisa K Manning; Josée Dupuis
Journal:  Biometrics       Date:  2012-05-02       Impact factor: 2.571

7.  Hundreds of variants clustered in genomic loci and biological pathways affect human height.

Authors:  Hana Lango Allen; Karol Estrada; Guillaume Lettre; Sonja I Berndt; Michael N Weedon; Fernando Rivadeneira; Cristen J Willer; Anne U Jackson; Sailaja Vedantam; Soumya Raychaudhuri; Teresa Ferreira; Andrew R Wood; Robert J Weyant; Ayellet V Segrè; Elizabeth K Speliotes; Eleanor Wheeler; Nicole Soranzo; Ju-Hyun Park; Jian Yang; Daniel Gudbjartsson; Nancy L Heard-Costa; Joshua C Randall; Lu Qi; Albert Vernon Smith; Reedik Mägi; Tomi Pastinen; Liming Liang; Iris M Heid; Jian'an Luan; Gudmar Thorleifsson; Thomas W Winkler; Michael E Goddard; Ken Sin Lo; Cameron Palmer; Tsegaselassie Workalemahu; Yurii S Aulchenko; Asa Johansson; M Carola Zillikens; Mary F Feitosa; Tõnu Esko; Toby Johnson; Shamika Ketkar; Peter Kraft; Massimo Mangino; Inga Prokopenko; Devin Absher; Eva Albrecht; Florian Ernst; Nicole L Glazer; Caroline Hayward; Jouke-Jan Hottenga; Kevin B Jacobs; Joshua W Knowles; Zoltán Kutalik; Keri L Monda; Ozren Polasek; Michael Preuss; Nigel W Rayner; Neil R Robertson; Valgerdur Steinthorsdottir; Jonathan P Tyrer; Benjamin F Voight; Fredrik Wiklund; Jianfeng Xu; Jing Hua Zhao; Dale R Nyholt; Niina Pellikka; Markus Perola; John R B Perry; Ida Surakka; Mari-Liis Tammesoo; Elizabeth L Altmaier; Najaf Amin; Thor Aspelund; Tushar Bhangale; Gabrielle Boucher; Daniel I Chasman; Constance Chen; Lachlan Coin; Matthew N Cooper; Anna L Dixon; Quince Gibson; Elin Grundberg; Ke Hao; M Juhani Junttila; Lee M Kaplan; Johannes Kettunen; Inke R König; Tony Kwan; Robert W Lawrence; Douglas F Levinson; Mattias Lorentzon; Barbara McKnight; Andrew P Morris; Martina Müller; Julius Suh Ngwa; Shaun Purcell; Suzanne Rafelt; Rany M Salem; Erika Salvi; Serena Sanna; Jianxin Shi; Ulla Sovio; John R Thompson; Michael C Turchin; Liesbeth Vandenput; Dominique J Verlaan; Veronique Vitart; Charles C White; Andreas Ziegler; Peter Almgren; Anthony J Balmforth; Harry Campbell; Lorena Citterio; Alessandro De Grandi; Anna Dominiczak; Jubao Duan; Paul Elliott; Roberto Elosua; Johan G Eriksson; Nelson B Freimer; Eco J C Geus; Nicola Glorioso; Shen Haiqing; Anna-Liisa Hartikainen; Aki S Havulinna; Andrew A Hicks; Jennie Hui; Wilmar Igl; Thomas Illig; Antti Jula; Eero Kajantie; Tuomas O Kilpeläinen; Markku Koiranen; Ivana Kolcic; Seppo Koskinen; Peter Kovacs; Jaana Laitinen; Jianjun Liu; Marja-Liisa Lokki; Ana Marusic; Andrea Maschio; Thomas Meitinger; Antonella Mulas; Guillaume Paré; Alex N Parker; John F Peden; Astrid Petersmann; Irene Pichler; Kirsi H Pietiläinen; Anneli Pouta; Martin Ridderstråle; Jerome I Rotter; Jennifer G Sambrook; Alan R Sanders; Carsten Oliver Schmidt; Juha Sinisalo; Jan H Smit; Heather M Stringham; G Bragi Walters; Elisabeth Widen; Sarah H Wild; Gonneke Willemsen; Laura Zagato; Lina Zgaga; Paavo Zitting; Helene Alavere; Martin Farrall; Wendy L McArdle; Mari Nelis; Marjolein J Peters; Samuli Ripatti; Joyce B J van Meurs; Katja K Aben; Kristin G Ardlie; Jacques S Beckmann; John P Beilby; Richard N Bergman; Sven Bergmann; Francis S Collins; Daniele Cusi; Martin den Heijer; Gudny Eiriksdottir; Pablo V Gejman; Alistair S Hall; Anders Hamsten; Heikki V Huikuri; Carlos Iribarren; Mika Kähönen; Jaakko Kaprio; Sekar Kathiresan; Lambertus Kiemeney; Thomas Kocher; Lenore J Launer; Terho Lehtimäki; Olle Melander; Tom H Mosley; Arthur W Musk; Markku S Nieminen; Christopher J O'Donnell; Claes Ohlsson; Ben Oostra; Lyle J Palmer; Olli Raitakari; Paul M Ridker; John D Rioux; Aila Rissanen; Carlo Rivolta; Heribert Schunkert; Alan R Shuldiner; David S Siscovick; Michael Stumvoll; Anke Tönjes; Jaakko Tuomilehto; Gert-Jan van Ommen; Jorma Viikari; Andrew C Heath; Nicholas G Martin; Grant W Montgomery; Michael A Province; Manfred Kayser; Alice M Arnold; Larry D Atwood; Eric Boerwinkle; Stephen J Chanock; Panos Deloukas; Christian Gieger; Henrik Grönberg; Per Hall; Andrew T Hattersley; Christian Hengstenberg; Wolfgang Hoffman; G Mark Lathrop; Veikko Salomaa; Stefan Schreiber; Manuela Uda; Dawn Waterworth; Alan F Wright; Themistocles L Assimes; Inês Barroso; Albert Hofman; Karen L Mohlke; Dorret I Boomsma; Mark J Caulfield; L Adrienne Cupples; Jeanette Erdmann; Caroline S Fox; Vilmundur Gudnason; Ulf Gyllensten; Tamara B Harris; Richard B Hayes; Marjo-Riitta Jarvelin; Vincent Mooser; Patricia B Munroe; Willem H Ouwehand; Brenda W Penninx; Peter P Pramstaller; Thomas Quertermous; Igor Rudan; Nilesh J Samani; Timothy D Spector; Henry Völzke; Hugh Watkins; James F Wilson; Leif C Groop; Talin Haritunians; Frank B Hu; Robert C Kaplan; Andres Metspalu; Kari E North; David Schlessinger; Nicholas J Wareham; David J Hunter; Jeffrey R O'Connell; David P Strachan; H-Erich Wichmann; Ingrid B Borecki; Cornelia M van Duijn; Eric E Schadt; Unnur Thorsteinsdottir; Leena Peltonen; André G Uitterlinden; Peter M Visscher; Nilanjan Chatterjee; Ruth J F Loos; Michael Boehnke; Mark I McCarthy; Erik Ingelsson; Cecilia M Lindgren; Gonçalo R Abecasis; Kari Stefansson; Timothy M Frayling; Joel N Hirschhorn
Journal:  Nature       Date:  2010-09-29       Impact factor: 49.962

8.  A phenomics-based strategy identifies loci on APOC1, BRAP, and PLCG1 associated with metabolic syndrome phenotype domains.

Authors:  Christy L Avery; Qianchuan He; Kari E North; Jose L Ambite; Eric Boerwinkle; Myriam Fornage; Lucia A Hindorff; Charles Kooperberg; James B Meigs; James S Pankow; Sarah A Pendergrass; Bruce M Psaty; Marylyn D Ritchie; Jerome I Rotter; Kent D Taylor; Lynne R Wilkens; Gerardo Heiss; Dan Yu Lin
Journal:  PLoS Genet       Date:  2011-10-13       Impact factor: 5.917

9.  Meta-analysis of gene-level associations for rare variants based on single-variant statistics.

Authors:  Yi-Juan Hu; Sonja I Berndt; Stefan Gustafsson; Andrea Ganna; Joel Hirschhorn; Kari E North; Erik Ingelsson; Dan-Yu Lin
Journal:  Am J Hum Genet       Date:  2013-07-25       Impact factor: 11.025

10.  Discovery and refinement of loci associated with lipid levels.

Authors:  Cristen J Willer; Ellen M Schmidt; Sebanti Sengupta; Michael Boehnke; Panos Deloukas; Sekar Kathiresan; Karen L Mohlke; Erik Ingelsson; Gonçalo R Abecasis; Gina M Peloso; Stefan Gustafsson; Stavroula Kanoni; Andrea Ganna; Jin Chen; Martin L Buchkovich; Samia Mora; Jacques S Beckmann; Jennifer L Bragg-Gresham; Hsing-Yi Chang; Ayşe Demirkan; Heleen M Den Hertog; Ron Do; Louise A Donnelly; Georg B Ehret; Tõnu Esko; Mary F Feitosa; Teresa Ferreira; Krista Fischer; Pierre Fontanillas; Ross M Fraser; Daniel F Freitag; Deepti Gurdasani; Kauko Heikkilä; Elina Hyppönen; Aaron Isaacs; Anne U Jackson; Åsa Johansson; Toby Johnson; Marika Kaakinen; Johannes Kettunen; Marcus E Kleber; Xiaohui Li; Jian'an Luan; Leo-Pekka Lyytikäinen; Patrik K E Magnusson; Massimo Mangino; Evelin Mihailov; May E Montasser; Martina Müller-Nurasyid; Ilja M Nolte; Jeffrey R O'Connell; Cameron D Palmer; Markus Perola; Ann-Kristin Petersen; Serena Sanna; Richa Saxena; Susan K Service; Sonia Shah; Dmitry Shungin; Carlo Sidore; Ci Song; Rona J Strawbridge; Ida Surakka; Toshiko Tanaka; Tanya M Teslovich; Gudmar Thorleifsson; Evita G Van den Herik; Benjamin F Voight; Kelly A Volcik; Lindsay L Waite; Andrew Wong; Ying Wu; Weihua Zhang; Devin Absher; Gershim Asiki; Inês Barroso; Latonya F Been; Jennifer L Bolton; Lori L Bonnycastle; Paolo Brambilla; Mary S Burnett; Giancarlo Cesana; Maria Dimitriou; Alex S F Doney; Angela Döring; Paul Elliott; Stephen E Epstein; Gudmundur Ingi Eyjolfsson; Bruna Gigante; Mark O Goodarzi; Harald Grallert; Martha L Gravito; Christopher J Groves; Göran Hallmans; Anna-Liisa Hartikainen; Caroline Hayward; Dena Hernandez; Andrew A Hicks; Hilma Holm; Yi-Jen Hung; Thomas Illig; Michelle R Jones; Pontiano Kaleebu; John J P Kastelein; Kay-Tee Khaw; Eric Kim; Norman Klopp; Pirjo Komulainen; Meena Kumari; Claudia Langenberg; Terho Lehtimäki; Shih-Yi Lin; Jaana Lindström; Ruth J F Loos; François Mach; Wendy L McArdle; Christa Meisinger; Braxton D Mitchell; Gabrielle Müller; Ramaiah Nagaraja; Narisu Narisu; Tuomo V M Nieminen; Rebecca N Nsubuga; Isleifur Olafsson; Ken K Ong; Aarno Palotie; Theodore Papamarkou; Cristina Pomilla; Anneli Pouta; Daniel J Rader; Muredach P Reilly; Paul M Ridker; Fernando Rivadeneira; Igor Rudan; Aimo Ruokonen; Nilesh Samani; Hubert Scharnagl; Janet Seeley; Kaisa Silander; Alena Stančáková; Kathleen Stirrups; Amy J Swift; Laurence Tiret; Andre G Uitterlinden; L Joost van Pelt; Sailaja Vedantam; Nicholas Wainwright; Cisca Wijmenga; Sarah H Wild; Gonneke Willemsen; Tom Wilsgaard; James F Wilson; Elizabeth H Young; Jing Hua Zhao; Linda S Adair; Dominique Arveiler; Themistocles L Assimes; Stefania Bandinelli; Franklyn Bennett; Murielle Bochud; Bernhard O Boehm; Dorret I Boomsma; Ingrid B Borecki; Stefan R Bornstein; Pascal Bovet; Michel Burnier; Harry Campbell; Aravinda Chakravarti; John C Chambers; Yii-Der Ida Chen; Francis S Collins; Richard S Cooper; John Danesh; George Dedoussis; Ulf de Faire; Alan B Feranil; Jean Ferrières; Luigi Ferrucci; Nelson B Freimer; Christian Gieger; Leif C Groop; Vilmundur Gudnason; Ulf Gyllensten; Anders Hamsten; Tamara B Harris; Aroon Hingorani; Joel N Hirschhorn; Albert Hofman; G Kees Hovingh; Chao Agnes Hsiung; Steve E Humphries; Steven C Hunt; Kristian Hveem; Carlos Iribarren; Marjo-Riitta Järvelin; Antti Jula; Mika Kähönen; Jaakko Kaprio; Antero Kesäniemi; Mika Kivimaki; Jaspal S Kooner; Peter J Koudstaal; Ronald M Krauss; Diana Kuh; Johanna Kuusisto; Kirsten O Kyvik; Markku Laakso; Timo A Lakka; Lars Lind; Cecilia M Lindgren; Nicholas G Martin; Winfried März; Mark I McCarthy; Colin A McKenzie; Pierre Meneton; Andres Metspalu; Leena Moilanen; Andrew D Morris; Patricia B Munroe; Inger Njølstad; Nancy L Pedersen; Chris Power; Peter P Pramstaller; Jackie F Price; Bruce M Psaty; Thomas Quertermous; Rainer Rauramaa; Danish Saleheen; Veikko Salomaa; Dharambir K Sanghera; Jouko Saramies; Peter E H Schwarz; Wayne H-H Sheu; Alan R Shuldiner; Agneta Siegbahn; Tim D Spector; Kari Stefansson; David P Strachan; Bamidele O Tayo; Elena Tremoli; Jaakko Tuomilehto; Matti Uusitupa; Cornelia M van Duijn; Peter Vollenweider; Lars Wallentin; Nicholas J Wareham; John B Whitfield; Bruce H R Wolffenbuttel; Jose M Ordovas; Eric Boerwinkle; Colin N A Palmer; Unnur Thorsteinsdottir; Daniel I Chasman; Jerome I Rotter; Paul W Franks; Samuli Ripatti; L Adrienne Cupples; Manjinder S Sandhu; Stephen S Rich
Journal:  Nat Genet       Date:  2013-10-06       Impact factor: 38.330

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