Literature DB >> 32744321

Fine-mapping genetic associations.

Anna Hutchinson1, Jennifer Asimit1, Chris Wallace1,2,3.   

Abstract

Whilst thousands of genetic variants have been associated with human traits, identifying the subset of those variants that are causal requires a further 'fine-mapping' step. We review the basic fine-mapping approach, which is computationally fast and requires only summary data, but depends on an assumption of a single causal variant per associated region which is recognized as biologically unrealistic. We discuss different ways that the approach has been built upon to accommodate multiple causal variants in a region and to incorporate additional layers of functional annotation data. We further review methods for simultaneous fine-mapping of multiple datasets, either exploiting different linkage disequilibrium (LD) structures across ancestries or borrowing information between distinct but related traits. Finally, we look to the future and the opportunities that will be offered by increasingly accurate maps of causal variants for a multitude of human traits.
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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Year:  2020        PMID: 32744321      PMCID: PMC7733401          DOI: 10.1093/hmg/ddaa148

Source DB:  PubMed          Journal:  Hum Mol Genet        ISSN: 0964-6906            Impact factor:   6.150


  46 in total

1.  Fine Mapping Causal Variants with an Approximate Bayesian Method Using Marginal Test Statistics.

Authors:  Wenan Chen; Beth R Larrabee; Inna G Ovsyannikova; Richard B Kennedy; Iana H Haralambieva; Gregory A Poland; Daniel J Schaid
Journal:  Genetics       Date:  2015-05-06       Impact factor: 4.562

2.  Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits.

Authors:  Jian Yang; Teresa Ferreira; Andrew P Morris; Sarah E Medland; Pamela A F Madden; Andrew C Heath; Nicholas G Martin; Grant W Montgomery; Michael N Weedon; Ruth J Loos; Timothy M Frayling; Mark I McCarthy; Joel N Hirschhorn; Michael E Goddard; Peter M Visscher
Journal:  Nat Genet       Date:  2012-03-18       Impact factor: 38.330

3.  GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals.

Authors:  Valentina Iotchkova; Graham R S Ritchie; Matthias Geihs; Sandro Morganella; Josine L Min; Klaudia Walter; Nicholas John Timpson; Ian Dunham; Ewan Birney; Nicole Soranzo
Journal:  Nat Genet       Date:  2019-01-28       Impact factor: 38.330

4.  GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation.

Authors:  Dongjun Chung; Can Yang; Cong Li; Joel Gelernter; Hongyu Zhao
Journal:  PLoS Genet       Date:  2014-11-13       Impact factor: 5.917

Review 5.  Overview of the BioBank Japan Project: Study design and profile.

Authors:  Akiko Nagai; Makoto Hirata; Yoichiro Kamatani; Kaori Muto; Koichi Matsuda; Yutaka Kiyohara; Toshiharu Ninomiya; Akiko Tamakoshi; Zentaro Yamagata; Taisei Mushiroda; Yoshinori Murakami; Koichiro Yuji; Yoichi Furukawa; Hitoshi Zembutsu; Toshihiro Tanaka; Yozo Ohnishi; Yusuke Nakamura; Michiaki Kubo
Journal:  J Epidemiol       Date:  2017-02-08       Impact factor: 3.211

6.  Stochastic search and joint fine-mapping increases accuracy and identifies previously unreported associations in immune-mediated diseases.

Authors:  Jennifer L Asimit; Daniel B Rainbow; Mary D Fortune; Nastasiya F Grinberg; Linda S Wicker; Chris Wallace
Journal:  Nat Commun       Date:  2019-07-19       Impact factor: 14.919

7.  Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes.

Authors:  Hugues Aschard; Jonathan Beesley; Laura Fachal; Daniel R Barnes; Jamie Allen; Siddhartha Kar; Karen A Pooley; Joe Dennis; Kyriaki Michailidou; Constance Turman; Penny Soucy; Audrey Lemaçon; Michael Lush; Jonathan P Tyrer; Maya Ghoussaini; Mahdi Moradi Marjaneh; Xia Jiang; Simona Agata; Kristiina Aittomäki; M Rosario Alonso; Irene L Andrulis; Hoda Anton-Culver; Natalia N Antonenkova; Adalgeir Arason; Volker Arndt; Kristan J Aronson; Banu K Arun; Bernd Auber; Paul L Auer; Jacopo Azzollini; Judith Balmaña; Rosa B Barkardottir; Daniel Barrowdale; Alicia Beeghly-Fadiel; Javier Benitez; Marina Bermisheva; Katarzyna Białkowska; Amie M Blanco; Carl Blomqvist; William Blot; Natalia V Bogdanova; Stig E Bojesen; Manjeet K Bolla; Bernardo Bonanni; Ake Borg; Kristin Bosse; Hiltrud Brauch; Hermann Brenner; Ignacio Briceno; Ian W Brock; Angela Brooks-Wilson; Thomas Brüning; Barbara Burwinkel; Saundra S Buys; Qiuyin Cai; Trinidad Caldés; Maria A Caligo; Nicola J Camp; Ian Campbell; Federico Canzian; Jason S Carroll; Brian D Carter; Jose E Castelao; Jocelyne Chiquette; Hans Christiansen; Wendy K Chung; Kathleen B M Claes; Christine L Clarke; J Margriet Collée; Sten Cornelissen; Fergus J Couch; Angela Cox; Simon S Cross; Cezary Cybulski; Kamila Czene; Mary B Daly; Miguel de la Hoya; Peter Devilee; Orland Diez; Yuan Chun Ding; Gillian S Dite; Susan M Domchek; Thilo Dörk; Isabel Dos-Santos-Silva; Arnaud Droit; Stéphane Dubois; Martine Dumont; Mercedes Duran; Lorraine Durcan; Miriam Dwek; Diana M Eccles; Christoph Engel; Mikael Eriksson; D Gareth Evans; Peter A Fasching; Olivia Fletcher; Giuseppe Floris; Henrik Flyger; Lenka Foretova; William D Foulkes; Eitan Friedman; Lin Fritschi; Debra Frost; Marike Gabrielson; Manuela Gago-Dominguez; Gaetana Gambino; Patricia A Ganz; Susan M Gapstur; Judy Garber; José A García-Sáenz; Mia M Gaudet; Vassilios Georgoulias; Graham G Giles; Gord Glendon; Andrew K Godwin; Mark S Goldberg; David E Goldgar; Anna González-Neira; Maria Grazia Tibiletti; Mark H Greene; Mervi Grip; Jacek Gronwald; Anne Grundy; Pascal Guénel; Eric Hahnen; Christopher A Haiman; Niclas Håkansson; Per Hall; Ute Hamann; Patricia A Harrington; Jaana M Hartikainen; Mikael Hartman; Wei He; Catherine S Healey; Bernadette A M Heemskerk-Gerritsen; Jane Heyworth; Peter Hillemanns; Frans B L Hogervorst; Antoinette Hollestelle; Maartje J Hooning; John L Hopper; Anthony Howell; Guanmengqian Huang; Peter J Hulick; Evgeny N Imyanitov; Claudine Isaacs; Motoki Iwasaki; Agnes Jager; Milena Jakimovska; Anna Jakubowska; Paul A James; Ramunas Janavicius; Rachel C Jankowitz; Esther M John; Nichola Johnson; Michael E Jones; Arja Jukkola-Vuorinen; Audrey Jung; Rudolf Kaaks; Daehee Kang; Pooja Middha Kapoor; Beth Y Karlan; Renske Keeman; Michael J Kerin; Elza Khusnutdinova; Johanna I Kiiski; Judy Kirk; Cari M Kitahara; Yon-Dschun Ko; Irene Konstantopoulou; Veli-Matti Kosma; Stella Koutros; Katerina Kubelka-Sabit; Ava Kwong; Kyriacos Kyriacou; Yael Laitman; Diether Lambrechts; Eunjung Lee; Goska Leslie; Jenny Lester; Fabienne Lesueur; Annika Lindblom; Wing-Yee Lo; Jirong Long; Artitaya Lophatananon; Jennifer T Loud; Jan Lubiński; Robert J MacInnis; Tom Maishman; Enes Makalic; Arto Mannermaa; Mehdi Manoochehri; Siranoush Manoukian; Sara Margolin; Maria Elena Martinez; Keitaro Matsuo; Tabea Maurer; Dimitrios Mavroudis; Rebecca Mayes; Lesley McGuffog; Catriona McLean; Noura Mebirouk; Alfons Meindl; Austin Miller; Nicola Miller; Marco Montagna; Fernando Moreno; Kenneth Muir; Anna Marie Mulligan; Victor M Muñoz-Garzon; Taru A Muranen; Steven A Narod; Rami Nassir; Katherine L Nathanson; Susan L Neuhausen; Heli Nevanlinna; Patrick Neven; Finn C Nielsen; Liene Nikitina-Zake; Aaron Norman; Kenneth Offit; Edith Olah; Olufunmilayo I Olopade; Håkan Olsson; Nick Orr; Ana Osorio; V Shane Pankratz; Janos Papp; Sue K Park; Tjoung-Won Park-Simon; Michael T Parsons; James Paul; Inge Sokilde Pedersen; Bernard Peissel; Beth Peshkin; Paolo Peterlongo; Julian Peto; Dijana Plaseska-Karanfilska; Karolina Prajzendanc; Ross Prentice; Nadege Presneau; Darya Prokofyeva; Miquel Angel Pujana; Katri Pylkäs; Paolo Radice; Susan J Ramus; Johanna Rantala; Rohini Rau-Murthy; Gad Rennert; Harvey A Risch; Mark Robson; Atocha Romero; Maria Rossing; Emmanouil Saloustros; Estela Sánchez-Herrero; Dale P Sandler; Marta Santamariña; Christobel Saunders; Elinor J Sawyer; Maren T Scheuner; Daniel F Schmidt; Rita K Schmutzler; Andreas Schneeweiss; Minouk J Schoemaker; Ben Schöttker; Peter Schürmann; Christopher Scott; Rodney J Scott; Leigha Senter; Caroline M Seynaeve; Mitul Shah; Priyanka Sharma; Chen-Yang Shen; Xiao-Ou Shu; Christian F Singer; Thomas P Slavin; Snezhana Smichkoska; Melissa C Southey; John J Spinelli; Amanda B Spurdle; Jennifer Stone; Dominique Stoppa-Lyonnet; Christian Sutter; Anthony J Swerdlow; Rulla M Tamimi; Yen Yen Tan; William J Tapper; Jack A Taylor; Manuel R Teixeira; Maria Tengström; Soo Hwang Teo; Mary Beth Terry; Alex Teulé; Mads Thomassen; Darcy L Thull; Marc Tischkowitz; Amanda E Toland; Rob A E M Tollenaar; Ian Tomlinson; Diana Torres; Gabriela Torres-Mejía; Melissa A Troester; Thérèse Truong; Nadine Tung; Maria Tzardi; Hans-Ulrich Ulmer; Celine M Vachon; Christi J van Asperen; Lizet E van der Kolk; Elizabeth J van Rensburg; Ana Vega; Alessandra Viel; Joseph Vijai; Maartje J Vogel; Qin Wang; Barbara Wappenschmidt; Clarice R Weinberg; Jeffrey N Weitzel; Camilla Wendt; Hans Wildiers; Robert Winqvist; Alicja Wolk; Anna H Wu; Drakoulis Yannoukakos; Yan Zhang; Wei Zheng; David Hunter; Paul D P Pharoah; Jenny Chang-Claude; Montserrat García-Closas; Marjanka K Schmidt; Roger L Milne; Vessela N Kristensen; Juliet D French; Stacey L Edwards; Antonis C Antoniou; Georgia Chenevix-Trench; Jacques Simard; Douglas F Easton; Peter Kraft; Alison M Dunning
Journal:  Nat Genet       Date:  2020-01-07       Impact factor: 38.330

8.  Bayesian refinement of association signals for 14 loci in 3 common diseases.

Authors:  Julian B Maller; Gilean McVean; Jake Byrnes; Damjan Vukcevic; Kimmo Palin; Zhan Su; Joanna M M Howson; Adam Auton; Simon Myers; Andrew Morris; Matti Pirinen; Matthew A Brown; Paul R Burton; Mark J Caulfield; Alastair Compston; Martin Farrall; Alistair S Hall; Andrew T Hattersley; Adrian V S Hill; Christopher G Mathew; Marcus Pembrey; Jack Satsangi; Michael R Stratton; Jane Worthington; Nick Craddock; Matthew Hurles; Willem Ouwehand; Miles Parkes; Nazneen Rahman; Audrey Duncanson; John A Todd; Dominic P Kwiatkowski; Nilesh J Samani; Stephen C L Gough; Mark I McCarthy; Panagiotis Deloukas; Peter Donnelly
Journal:  Nat Genet       Date:  2012-10-28       Impact factor: 38.330

Review 9.  Strategies for fine-mapping complex traits.

Authors:  Sarah L Spain; Jeffrey C Barrett
Journal:  Hum Mol Genet       Date:  2015-07-08       Impact factor: 6.150

10.  FINEMAP: efficient variable selection using summary data from genome-wide association studies.

Authors:  Christian Benner; Chris C A Spencer; Aki S Havulinna; Veikko Salomaa; Samuli Ripatti; Matti Pirinen
Journal:  Bioinformatics       Date:  2016-01-14       Impact factor: 6.937

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  9 in total

1.  Performing post-genome-wide association study analysis: overview, challenges and recommendations.

Authors:  Yagoub Adam; Chaimae Samtal; Jean-Tristan Brandenburg; Oluwadamilare Falola; Ezekiel Adebiyi
Journal:  F1000Res       Date:  2021-10-04

2.  Long telomeres in need of a SNP: Germline contributions of telomere maintenance to glioma.

Authors:  Linda Kachuri; Kyle M Walsh
Journal:  Neuro Oncol       Date:  2022-02-01       Impact factor: 13.029

3.  Fine-mapping of Parkinson's disease susceptibility loci identifies putative causal variants.

Authors:  Brian M Schilder; Towfique Raj
Journal:  Hum Mol Genet       Date:  2022-03-21       Impact factor: 5.121

Review 4.  Evolutionary genetics of skin pigmentation in African populations.

Authors:  Yuanqing Feng; Michael A McQuillan; Sarah A Tishkoff
Journal:  Hum Mol Genet       Date:  2021-04-26       Impact factor: 6.150

5.  Phenome-wide and expression quantitative trait locus associations of coronavirus disease 2019 genetic risk loci.

Authors:  Chang Yoon Moon; Brian M Schilder; Towfique Raj; Kuan-Lin Huang
Journal:  iScience       Date:  2021-05-18

6.  Fine Mapping of the MAP2K5 Region Identified rs7175517 as a Causal Variant Related to BMI in China and the United Kingdom Populations.

Authors:  Ce Lu; Hai-Jun Wang; Jie-Yun Song; Shuo Wang; Xue-Ying Li; Tao Huang; Hui Wang
Journal:  Front Genet       Date:  2022-03-16       Impact factor: 4.599

7.  Fine-mapping from summary data with the "Sum of Single Effects" model.

Authors:  Yuxin Zou; Peter Carbonetto; Gao Wang; Matthew Stephens
Journal:  PLoS Genet       Date:  2022-07-19       Impact factor: 6.020

8.  flashfm-ivis: interactive visualisation for fine-mapping of multiple quantitative traits.

Authors:  Feng Zhou; Adam S Butterworth; Jennifer L Asimit
Journal:  Bioinformatics       Date:  2022-07-06       Impact factor: 6.931

Review 9.  Methods for statistical fine-mapping and their applications to auto-immune diseases.

Authors:  Qingbo S Wang; Hailiang Huang
Journal:  Semin Immunopathol       Date:  2022-01-18       Impact factor: 9.623

  9 in total

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