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. 2025 Jun;30(6):2335-2346.
doi: 10.1038/s41380-024-02838-5. Epub 2024 Dec 4.

X-chromosome-wide association study for Alzheimer's disease

Julie Le Borgne #  1 Lissette Gomez #  2 Sami Heikkinen  3 Najaf Amin  4 Shahzad Ahmad  5 Seung Hoan Choi  6 Joshua Bis  7 Benjamin Grenier-Boley  1 Omar Garcia Rodriguez  2 Luca Kleineidam  8   9 Juan Young  2 Kumar Parijat Tripathi  10 Lily Wang  11 Achintya Varma  2 Rafael Campos-Martin  10 Sven van der Lee  12   13 Vincent Damotte  1 Itziar de Rojas  14   15 Sagnik Palmal  1 EADB, GR@ACE, DEGESCO, EADI, GERAD, DemGene, FinnGen, ADGC, CHARGERichard Lipton  16 Eric Reiman  17   18   19   20 Ann McKee  21   22 Philip De Jager  23   24 William Bush  25 Scott Small  26   27 Allan Levey  28 Andrew Saykin  29   30 Tatiana Foroud  30 Marilyn Albert  31 Bradley Hyman  32 Ronald Petersen  33 Steven Younkin  34 Mary Sano  35 Thomas Wisniewski  36   37 Robert Vassar  38   39 Julie Schneider  40   41   42 Victor Henderson  43   44 Erik Roberson  45 Charles DeCarli  46 Frank LaFerla  47 James Brewer  48 Russell Swerdlow  49 Linda Van Eldik  50 Kara Hamilton-Nelson  2 Henry Paulson  51 Adam Naj  52 Oscar Lopez  53 Helena Chui  54 Paul Crane  55 Thomas Grabowski  56   57 Walter Kukull  58 Sanjay Asthana  59   60   61 Suzanne Craft  62 Stephen Strittmatter  63 Carlos Cruchaga  64 James Leverenz  65 Alison Goate  66 M Ilyas Kamboh  53   67 Peter St George-Hyslop  68   69 Otto Valladares  52 Amanda Kuzma  52 Laura Cantwell  52 Matthias Riemenschneider  70 John Morris  71   72 Susan Slifer  2 Carolina Dalmasso  10   73 Atahualpa Castillo  74 Fahri Küçükali  75   76 Oliver Peters  77   78 Anja Schneider  9   79 Martin Dichgans  80   81   82 Dan Rujescu  83 Norbert Scherbaum  84 Jürgen Deckert  85 Steffi Riedel-Heller  86 Lucrezia Hausner  87 Laura Molina-Porcel  88   89 Emrah Düzel  90   91 Timo Grimmer  92 Jens Wiltfang  93   94   95 Stefanie Heilmann-Heimbach  96 Susanne Moebus  97 Thomas Tegos  98 Nikolaos Scarmeas  99   100 Oriol Dols-Icardo  15   101 Fermin Moreno  15   102   103 Jordi Pérez-Tur  15   104   105 María J Bullido  15   106   107   108 Pau Pastor  109   110 Raquel Sánchez-Valle  111 Victoria Álvarez  112   113 Mercè Boada  14   15 Pablo García-González  14 Raquel Puerta  14 Pablo Mir  15   114 Luis M Real  115   116 Gerard Piñol-Ripoll  117   118 Jose María García-Alberca  15   119 Jose Luís Royo  116 Eloy Rodriguez-Rodriguez  15   120 Hilkka Soininen  121 Alexandre de Mendonça  122 Shima Mehrabian  123 Latchezar Traykov  123 Jakub Hort  124 Martin Vyhnalek  124 Jesper Qvist Thomassen  125 Yolande A L Pijnenburg  12 Henne Holstege  12   126 John van Swieten  127 Inez Ramakers  128 Frans Verhey  128 Philip Scheltens  12 Caroline Graff  129 Goran Papenberg  130 Vilmantas Giedraitis  131 Anne Boland  132 Jean-François Deleuze  132 Gael Nicolas  133 Carole Dufouil  134   135 Florence Pasquier  136 Olivier Hanon  137 Stéphanie Debette  138   139 Edna Grünblatt  140   141   142 Julius Popp  143   144   145 Roberta Ghidoni  146 Daniela Galimberti  147   148 Beatrice Arosio  149   150 Patrizia Mecocci  151   152 Vincenzo Solfrizzi  153 Lucilla Parnetti  154 Alessio Squassina  155 Lucio Tremolizzo  156 Barbara Borroni  157   158 Benedetta Nacmias  159   160 Marco Spallazzi  161 Davide Seripa  162 Innocenzo Rainero  163 Antonio Daniele  164   165 Paola Bossù  166 Carlo Masullo  167 Giacomina Rossi  168 Frank Jessen  9   169   170 Victoria Fernandez  14 Patrick Gavin Kehoe  171 Ruth Frikke-Schmidt  125   172 Magda Tsolaki  98   173 Pascual Sánchez-Juan  15   174 Kristel Sleegers  75   76 Martin Ingelsson  131   175   176 Jonathan Haines  177 Lindsay Farrer  21   178   179   180   181 Richard Mayeux  26   182 Li-San Wang  183 Rebecca Sims  74 Anita DeStefano  6 Gerard D Schellenberg  52 Sudha Seshadri  184   185   186 Philippe Amouyel  1 Julie Williams  74   187 Wiesje van der Flier  12 Alfredo Ramirez  8   9   10   188   189 Margaret Pericak-Vance  2   190 Ole A Andreassen  191   192 Cornelia Van Duijn  4   5 Mikko Hiltunen  3 Agustín Ruiz  14   15 Josée Dupuis  6   193 Eden Martin  2   190   194 Jean-Charles Lambert  1 Brian Kunkle  2 Céline Bellenguez  195
Affiliations

X-chromosome-wide association study for Alzheimer's disease

Julie Le Borgne et al. Mol Psychiatry. 2025 Jun.

Abstract

Due to methodological reasons, the X-chromosome has not been featured in the major genome-wide association studies on Alzheimer's Disease (AD). To address this and better characterize the genetic landscape of AD, we performed an in-depth X-Chromosome-Wide Association Study (XWAS) in 115,841 AD cases or AD proxy cases, including 52,214 clinically-diagnosed AD cases, and 613,671 controls. We considered three approaches to account for the different X-chromosome inactivation (XCI) states in females, i.e. random XCI, skewed XCI, and escape XCI. We did not detect any genome-wide significant signals (P ≤ 5 × 10-8) but identified seven X-chromosome-wide significant loci (P ≤ 1.6 × 10-6). The index variants were common for the Xp22.32, FRMPD4, DMD and Xq25 loci, and rare for the WNK3, PJA1, and DACH2 loci. Overall, this well-powered XWAS found no genetic risk factors for AD on the non-pseudoautosomal region of the X-chromosome, but it identified suggestive signals warranting further investigations.

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Conflict of interest statement

Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: Written informed consent was obtained from study participants or, for those with substantial cognitive impairment, a caregiver, legal guardian or other proxy. Study protocols for all cohorts were reviewed and approved by the appropriate institutional review boards.

Figures

Fig. 1
Fig. 1. Study design of the AD-XWAS.
a Main analyses and b sensitivity analyses. Box colors indicate the approach: purple, green, orange and blue represent r-XCI, s-XCI, e-XCI and sex-stratified approaches, respectively. Boxes circled in red are the main r-XCI, s-XCI and e-XCI analyses. *Fixed effect meta-analysis with an inverse-variance weighted approach as implemented in METAL [64]. **Sex-stratified models were adjusted on 1) principal components (PCs) and/or the genotyping center; 2) PCs, center and age; 3) PCs, center, age and APOE.
Fig. 2
Fig. 2. Manhattan plot of the r-XCI approach.
Association results of a the meta-analysis including AD-proxy cases, b the diagnosed AD cases meta-analysis and c the meta-analysis excluding biobanks. The red and blue lines represent the genome-wide significant threshold (5 × 10−8) and the X-chromosome-wide significant threshold (1.6 × 10−6), respectively. The labels show the closest protein-coding gene (according to GENCODE release 45, https://www.gencodegenes.org/human/releases.html) to the index variant of each X-chromosome-wide significant locus.
Fig. 3
Fig. 3. Manhattan plot of the e-XCI approach.
Association results of a the diagnosed AD-cases meta-analysis and b the meta-analysis excluding biobanks. The red and blue lines represent the genome-wide significant threshold (5 × 10−8) and the X-chromosome-wide significant threshold (1.6 × 10−6), respectively.
Fig. 4
Fig. 4. Manhattan plot of the s-XCI approach meta-analysis, which excludes biobanks.
The red and blue lines represent the genome-wide significant threshold (5 × 10−8) and the X-chromosome-wide significant threshold (1.6 × 10−6), respectively.

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