Literature DB >> 31332195

X chromosome genetic data in a Spanish children cohort, dataset description and analysis pipeline.

Augusto Anguita-Ruiz1,2,3,4, Julio Plaza-Diaz5,6,7, Francisco Javier Ruiz-Ojeda5,7,8, Azahara I Rupérez5,9,10, Rosaura Leis11,12, Gloria Bueno11,9,10, Mercedes Gil-Campos11,13, Rocío Vázquez-Cobela11,12, Ramón Cañete11,13, Luis A Moreno9, Ángel Gil5,6,7,11, Concepción María Aguilera5,6,7,11.   

Abstract

X chromosome genetic variation has been proposed as a potential source of missing heritability for many complex diseases, including obesity. Currently, there is a lack of public available genetic datasets incorporating X chromosome genotype data. Although several X chromosome-specific statistics have been developed, there is also a lack of readily available implementations for routine analysis. Here, we aimed: (1) to make public and describe a dataset incorporating phenotype and X chromosome genotype data from a cohort of 915 normal-weight, overweight and obese children, and (2) to deeply describe a whole implementation of the special X chromosome analytic process in genetics. Datasets and pipelines like this are crucial to get familiar with the steps in which X chromosome requires special attention and may raise awareness of the importance of this genomic region.

Entities:  

Mesh:

Year:  2019        PMID: 31332195      PMCID: PMC6646348          DOI: 10.1038/s41597-019-0109-3

Source DB:  PubMed          Journal:  Sci Data        ISSN: 2052-4463            Impact factor:   6.444


  35 in total

Review 1.  Five years of GWAS discovery.

Authors:  Peter M Visscher; Matthew A Brown; Mark I McCarthy; Jian Yang
Journal:  Am J Hum Genet       Date:  2012-01-13       Impact factor: 11.025

2.  A note on exact tests of Hardy-Weinberg equilibrium.

Authors:  Janis E Wigginton; David J Cutler; Goncalo R Abecasis
Journal:  Am J Hum Genet       Date:  2005-03-23       Impact factor: 11.025

3.  X chromosome-inactivation patterns of 1,005 phenotypically unaffected females.

Authors:  James M Amos-Landgraf; Amy Cottle; Robert M Plenge; Mike Friez; Charles E Schwartz; John Longshore; Huntington F Willard
Journal:  Am J Hum Genet       Date:  2006-07-27       Impact factor: 11.025

Review 4.  Genetic and environmental factors in relative body weight and human adiposity.

Authors:  H H Maes; M C Neale; L J Eaves
Journal:  Behav Genet       Date:  1997-07       Impact factor: 2.805

5.  The SLC6A14 gene shows evidence of association with obesity.

Authors:  Elina Suviolahti; Laura J Oksanen; Miina Ohman; Rita M Cantor; Martin Ridderstrale; Tiinamaija Tuomi; Jaakko Kaprio; Aila Rissanen; Pertti Mustajoki; Pekka Jousilahti; Erkki Vartiainen; Kaisa Silander; Riika Kilpikari; Veikko Salomaa; Leif Groop; Kimmo Kontula; Leena Peltonen; Päivi Pajukanta
Journal:  J Clin Invest       Date:  2003-12       Impact factor: 14.808

6.  Landscape of X chromosome inactivation across human tissues.

Authors:  Taru Tukiainen; Alexandra-Chloé Villani; Angela Yen; Manuel A Rivas; Jamie L Marshall; Rahul Satija; Matt Aguirre; Laura Gauthier; Mark Fleharty; Andrew Kirby; Beryl B Cummings; Stephane E Castel; Konrad J Karczewski; François Aguet; Andrea Byrnes; Tuuli Lappalainen; Aviv Regev; Kristin G Ardlie; Nir Hacohen; Daniel G MacArthur
Journal:  Nature       Date:  2017-10-11       Impact factor: 49.962

7.  Human body epigenome maps reveal noncanonical DNA methylation variation.

Authors:  Matthew D Schultz; Yupeng He; John W Whitaker; Manoj Hariharan; Eran A Mukamel; Danny Leung; Nisha Rajagopal; Joseph R Nery; Mark A Urich; Huaming Chen; Shin Lin; Yiing Lin; Inkyung Jung; Anthony D Schmitt; Siddarth Selvaraj; Bing Ren; Terrence J Sejnowski; Wei Wang; Joseph R Ecker
Journal:  Nature       Date:  2015-06-01       Impact factor: 49.962

8.  X-inactivation informs variance-based testing for X-linked association of a quantitative trait.

Authors:  Li Ma; Gabriel Hoffman; Alon Keinan
Journal:  BMC Genomics       Date:  2015-03-25       Impact factor: 3.969

9.  Health Effects of Overweight and Obesity in 195 Countries over 25 Years.

Authors:  Ashkan Afshin; Mohammad H Forouzanfar; Marissa B Reitsma; Patrick Sur; Kara Estep; Alex Lee; Laurie Marczak; Ali H Mokdad; Maziar Moradi-Lakeh; Mohsen Naghavi; Joseph S Salama; Theo Vos; Kalkidan H Abate; Cristiana Abbafati; Muktar B Ahmed; Ziyad Al-Aly; Ala’a Alkerwi; Rajaa Al-Raddadi; Azmeraw T Amare; Alemayehu Amberbir; Adeladza K Amegah; Erfan Amini; Stephen M Amrock; Ranjit M Anjana; Johan Ärnlöv; Hamid Asayesh; Amitava Banerjee; Aleksandra Barac; Estifanos Baye; Derrick A Bennett; Addisu S Beyene; Sibhatu Biadgilign; Stan Biryukov; Espen Bjertness; Dube J Boneya; Ismael Campos-Nonato; Juan J Carrero; Pedro Cecilio; Kelly Cercy; Liliana G Ciobanu; Leslie Cornaby; Solomon A Damtew; Lalit Dandona; Rakhi Dandona; Samath D Dharmaratne; Bruce B Duncan; Babak Eshrati; Alireza Esteghamati; Valery L Feigin; João C Fernandes; Thomas Fürst; Tsegaye T Gebrehiwot; Audra Gold; Philimon N Gona; Atsushi Goto; Tesfa D Habtewold; Kokeb T Hadush; Nima Hafezi-Nejad; Simon I Hay; Masako Horino; Farhad Islami; Ritul Kamal; Amir Kasaeian; Srinivasa V Katikireddi; Andre P Kengne; Chandrasekharan N Kesavachandran; Yousef S Khader; Young-Ho Khang; Jagdish Khubchandani; Daniel Kim; Yun J Kim; Yohannes Kinfu; Soewarta Kosen; Tiffany Ku; Barthelemy Kuate Defo; G Anil Kumar; Heidi J Larson; Mall Leinsalu; Xiaofeng Liang; Stephen S Lim; Patrick Liu; Alan D Lopez; Rafael Lozano; Azeem Majeed; Reza Malekzadeh; Deborah C Malta; Mohsen Mazidi; Colm McAlinden; Stephen T McGarvey; Desalegn T Mengistu; George A Mensah; Gert B M Mensink; Haftay B Mezgebe; Erkin M Mirrakhimov; Ulrich O Mueller; Jean J Noubiap; Carla M Obermeyer; Felix A Ogbo; Mayowa O Owolabi; George C Patton; Farshad Pourmalek; Mostafa Qorbani; Anwar Rafay; Rajesh K Rai; Chhabi L Ranabhat; Nikolas Reinig; Saeid Safiri; Joshua A Salomon; Juan R Sanabria; Itamar S Santos; Benn Sartorius; Monika Sawhney; Josef Schmidhuber; Aletta E Schutte; Maria I Schmidt; Sadaf G Sepanlou; Moretza Shamsizadeh; Sara Sheikhbahaei; Min-Jeong Shin; Rahman Shiri; Ivy Shiue; Hirbo S Roba; Diego A S Silva; Jonathan I Silverberg; Jasvinder A Singh; Saverio Stranges; Soumya Swaminathan; Rafael Tabarés-Seisdedos; Fentaw Tadese; Bemnet A Tedla; Balewgizie S Tegegne; Abdullah S Terkawi; J S Thakur; Marcello Tonelli; Roman Topor-Madry; Stefanos Tyrovolas; Kingsley N Ukwaja; Olalekan A Uthman; Masoud Vaezghasemi; Tommi Vasankari; Vasiliy V Vlassov; Stein E Vollset; Elisabete Weiderpass; Andrea Werdecker; Joshua Wesana; Ronny Westerman; Yuichiro Yano; Naohiro Yonemoto; Gerald Yonga; Zoubida Zaidi; Zerihun M Zenebe; Ben Zipkin; Christopher J L Murray
Journal:  N Engl J Med       Date:  2017-06-12       Impact factor: 91.245

Review 10.  Overweight and Obesity in Children under 5 Years: Surveillance Opportunities and Challenges for the WHO European Region.

Authors:  Rebecca E Jones; Jo Jewell; Rhea Saksena; Ximena Ramos Salas; João Breda
Journal:  Front Public Health       Date:  2017-04-13
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