Human whole-exome genotype data for Alzheimer’s disease

Autor: Yuk Yee Leung, Adam C. Naj, Yi-Fan Chou, Otto Valladares, Michael Schmidt, Kara Hamilton-Nelson, Nicholas Wheeler, Honghuang Lin, Prabhakaran Gangadharan, Liming Qu, Kaylyn Clark, Amanda B. Kuzma, Wan-Ping Lee, Laura Cantwell, Heather Nicaretta, Alzheimer’s Disease Sequencing Project, Jonathan Haines, Lindsay Farrer, Sudha Seshadri, Zoran Brkanac, Carlos Cruchaga, Margaret Pericak-Vance, Richard P. Mayeux, William S. Bush, Anita Destefano, Eden Martin, Gerard D. Schellenberg, Li-San Wang

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)

Abstract The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced

Externí odkaz: https://doaj.org/article/378dd02a30dd4635913bd42d5ec182d0

Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities.

Autor: Marzia Antonella Scelsi, Valerio Napolioni, Michael D Greicius, Andre Altmann, Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Alzheimer’s Disease Sequencing Project (ADSP)

Publikováno v: PLoS Computational Biology, Vol 17, Iss 1, p e1008517 (2021)

State-of-the-art rare variant association testing methods aggregate the contribution of rare variants in biologically relevant genomic regions to boost statistical power. However, testing single genes separately does not consider the complex interact

Externí odkaz: https://doaj.org/article/854d9beab71e40a09f04f3efa6b2cb6f

Using linkage analysis to identify novel gene‐gene interactions in Alzheimer’s disease

Autor: Alzheimer’s Disease Sequencing, William S. Bush, Jonathan L. Haines, Nicholas R. Wheeler, Michelle Grunin

Publikováno v: Alzheimer's & Dementia. 16

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ba0e76aef649faa8de6b27820dc61673
https://doi.org/10.1002/alz.043435

Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation

Autor: Joshua C. Bis, Li-San Wang, Waleed Nasser, Giuseppe Tosto, Jean-Charles Lambert, Gary W. Beecham, Lucinda Fulton, Eric Boerwinkle, Reinhold Schmidt, Kara L. Hamilton-Nelson, Josée Dupuis, Cornelia M. van Duijn, Yuning Chen, Stéphanie Debette, Devanshi Patel, Philippe Amouyel, Gaël Nicolas, Farid Rajabli, Mark J. Daly, Richard Redon, Hilkka Soininen, Anita L. DeStefano, Aki S. Havulinna, Weixin Wang, Margaret A. Pericak-Vance, Chloé Sarnowski, Gerard D. Schellenberg, William S. Bush, Eden R. Martin, John J. Farrell, Richard A. Gibbs, Richard Mayeux, Emmanuelle Génin, Yi Zhao, Kwangsik Nho, Céline Bellenguez, Kari Mattila, Jean-François Deleuze, William J Salerno, Alzheimer’s Disease Sequencing, Brian W. Kunkle, Dominique Campion, Mikko Hiltunen, Richard K. Wilson, Sudha Seshadri, Paul K. Crane, Otto Valladares, Jennifer E. Below, Adam C. Naj, Timothy A. Thornton, Stacey Gabriel, Jan Konrad, Markus Perola, Mark Lathrop, Namrata Gupta, Badri N. Vardarajan, Bruce M. Psaty, Seppo Helisalmi, Jonathan L. Haines, Yiyi Ma, Honghuang Lin, Laura B. Cantwell, Carlos Cruchaga, Alan E. Renton, Terho Lehtimäki, Anne M. Remes, Michael A. Schmidt, Benjamin M. Neale, M. Arfan Ikram, Lindsay A. Farrer, Myriam Fornage, Daniel P. Howrigan, Ellen M. Wijsman, Mitja I. Kurki, Helena Schmidt, Aarno Palotie, Daniel Lancour, Camille Charbonnier, Daniela Witten, Liming Qu, Najaf Amin, Eric S. Lander, Alison Goate, Donna M. Muzny, Kathryn L. Lunetta, Jaakko Kaprio, Edoardo Marcora, Amanda B. Kuzma, Sven J. van der Lee, Shahzad Ahmad, Kim C. Worley, Christophe Tzourio, Benjamin Grenier-Boley, Jean-François Dartigues, L. Adrienne Cupples, Veikko Salomaa, Jaeyoon Chung, Christiane Reitz, Xueqiu Jian, Xiaoling Zhang, Olivier Quenez

Publikováno v: Molecular psychiatry
Molecular Psychiatry
Molecular Psychiatry, 2018, 25 (8), pp.1859-1875. ⟨10.1038/s41380-018-0112-7⟩
Molecular Psychiatry, Nature Publishing Group, 2018, 25 (8), pp.1859-1875. ⟨10.1038/s41380-018-0112-7⟩
Molecular Psychiatry, 25(8), 1859-1875. Nature Publishing Group

The Alzheimer’s Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls wer

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ef68fac14439c7451be809c415a34cbd
http://europepmc.org/articles/PMC6375806

Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimer’s Disease Sequencing Project

Autor: Gerard D. Schellenberg, Alejandro Q. Nato, Daniel C. Koboldt, Kara L. Hamilton-Nelson, Honghuang Lin, Badri N. Vardarajan, Seung Hoan Choi, Alzheimer’s Disease Sequencing, Harkirat Sohi, Cornelia M. van Duijn, John Malamon, Michael A. Schmidt, Daniel Lancour, Fangui Sun, Simon White, Anita L. DeStefano, William J Salerno, Eden R. Martin, Sven J. van der Lee, Bowen Wang, Josée Dupuis, Joshua C. Bis, Li-San Wang, William S. Bush, Sudha Seshadri, Ellen M. Wijsman, Brian W. Kunkle, Adam C. Naj, Namrata Gupta, Amanda B. Kuzma, Najaf Amin, L. Adrienne Cupples, Mohamad Saad, Eric Boerwinkle, Yiyi Ma, Mariusz Butkiewicz

Publikováno v: Naj, A C, Lin, H, Vardarajan, B N, White, S, Lancour, D, Ma, Y, Schmidt, M, Sun, F, Butkiewicz, M, Bush, W S, Kunkle, B W, Malamon, J, Amin, N, Choi, S H, Hamilton-Nelson, K L, van der Lee, S J, Gupta, N, Koboldt, D C, Saad, M, Wang, B, Nato, A Q, Sohi, H K, Kuzma, A, Wang, L S, Cupples, L A, van Duijn, C, Seshadri, S, Schellenberg, G D, Boerwinkle, E, Bis, J C, Dupuis, J, Salerno, W J, Wijsman, E M, Martin, E R, DeStefano, A L & Alzheimer's Disease Sequencing Project (ADSP) 2019, ' Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project ', Genomics, vol. 111, no. 4, pp. 808-818 . https://doi.org/10.1016/j.ygeno.2018.05.004
Genomics, 111(4), 808-818. Academic Press Inc.
Genomics, 111(4), 808-818. Academic Press

The Alzheimer’s Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::493a2a982f239b630b656e067f1fbc20