Abstract
Original language | English |
---|---|
Article number | 684 |
Journal | Nature communications |
Volume | 15 |
Issue number | 1 |
DOIs | |
Publication status | Published - 1 Dec 2024 |
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In: Nature communications, Vol. 15, No. 1, 684, 01.12.2024.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Human whole-exome genotype data for Alzheimer’s disease
AU - Leung, Yuk Yee
AU - Naj, Adam C.
AU - Chou, Yi-Fan
AU - Valladares, Otto
AU - Schmidt, Michael
AU - Hamilton-Nelson, Kara
AU - Wheeler, Nicholas
AU - Lin, Honghuang
AU - Gangadharan, Prabhakaran
AU - Qu, Liming
AU - Clark, Kaylyn
AU - Kuzma, Amanda B.
AU - Lee, Wan-Ping
AU - Cantwell, Laura
AU - Nicaretta, Heather
AU - van der Lee, Sven
AU - English, Adam
AU - Kalra, Divya
AU - Muzny, Donna
AU - Skinner, Evette
AU - Doddapeneni, Harsha
AU - Dinh, Huyen
AU - Hu, Jianhong
AU - Santibanez, Jireh
AU - Jayaseelan, Joy
AU - Worley, Kim
AU - Gibbs, Richard A.
AU - Lee, Sandra
AU - Dugan-Perez, Shannon
AU - Korchina, Viktoriya
AU - Nasser, Waleed
AU - Liu, Xiuping
AU - Han, Yi
AU - Zhu, Yiming
AU - Liu, Yue
AU - Khan, Ziad
AU - Zhu, Congcong
AU - Sun, Fangui Jenny
AU - Jun, Gyungah R.
AU - Chung, Jaeyoon
AU - Farrell, John
AU - Zhang, Xiaoling
AU - Banks, Eric
AU - Gupta, Namrata
AU - Gabriel, Stacey
AU - Butkiewicz, Mariusz
AU - Benchek, Penelope
AU - Smieszek, Sandra
AU - Song, Yeunjoo
AU - Vardarajan, Badri
AU - Reitz, Christiane
AU - Reyes-Dumeyer, Dolly
AU - Tosto, Giuseppe
AU - de Jager, Phillip L.
AU - Barral, Sandra
AU - Ma, Yiyi
AU - Beiser, Alexa
AU - Liu, Ching Ti
AU - Dupuis, Josee
AU - Lunetta, Kathy
AU - Cupples, L. Adrienne
AU - Choi, Seung Hoan
AU - Chen, Yuning
AU - Mez, Jesse
AU - Vanderspek, Ashley
AU - Ikram, M. Arfan
AU - Ahmad, Shahzad
AU - Faber, Kelley
AU - Foroud, Tatiana
AU - Mlynarski, Elisabeth
AU - Schmidt, Helena
AU - Schmidt, Reinhold
AU - Kunkle, Brian
AU - Rajabli, Farid
AU - Beecham, Gary
AU - Vance, Jeffrey M.
AU - Adams, Larry D.
AU - Cuccaro, Michael
AU - Mena, Pedro
AU - Booth, Briana M.
AU - Renton, Alan
AU - Goate, Alison
AU - Marcora, Edoardo
AU - Stine, Adam
AU - Feolo, Michael
AU - Launer, Lenore J.
AU - Koboldt, Daniel C.
AU - Wilson, Richard K.
AU - van Duijn, Cornelia
AU - Amin, Najaf
AU - Kapoor, Manav
AU - Salerno, William
AU - Bennett, David A.
AU - Xia, Li Charlie
AU - Malamon, John
AU - Mosley, Thomas H.
AU - Satizabal, Claudia
AU - Jan Bressler, null
AU - Jian, Xueqiu
AU - Nato, Alejandro Q.
AU - Horimoto, Andrea R.
AU - Wang, Bowen
AU - Psaty, Bruce
AU - Witten, Daniela
AU - Tsuang, Debby
AU - Blue, Elizabeth
AU - Wijsman, Ellen
AU - Sohi, Harkirat
AU - Nguyen, Hiep
AU - Bis, Joshua C.
AU - Rice, Kenneth
AU - Brown, Lisa
AU - Dorschner, Michael
AU - Saad, Mohamad
AU - Navas, Pat
AU - Nafikov, Rafael
AU - Thornton, Timothy
AU - Day, Tyler
AU - Haut, Jacob
AU - Sha, Jin
AU - Zhang, Nancy
AU - Iqbal, Taha
AU - Zhao, Yi
AU - Below, Jennifer E.
AU - Larson, David E.
AU - Appelbaum, Elizabeth
AU - Waligorski, Jason
AU - Antonacci-Fulton, Lucinda
AU - Fulton, Robert S.
AU - Haines, Jonathan
AU - Farrer, Lindsay
AU - Seshadri, Sudha
AU - Brkanac, Zoran
AU - Cruchaga, Carlos
AU - Pericak-Vance, Margaret
AU - Mayeux, Richard P.
AU - Bush, William S.
AU - Destefano, Anita
AU - Martin, Eden
AU - Schellenberg, Gerard D.
AU - Wang, Li-San
N1 - Publisher Copyright: © 2024, The Author(s).
PY - 2024/12/1
Y1 - 2024/12/1
N2 - 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 using ten capture kits in fourteen sequencing centers in the Alzheimer’s Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies. We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 1.8% of the variants are with CADD > 30, indicating they are of high predicted pathogenicity. Here we show our new strategy can generate high-quality data from processing these diversely generated WES samples. The improved ability to combine data sequenced in different batches benefits the whole genomics research community.
AB - 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 using ten capture kits in fourteen sequencing centers in the Alzheimer’s Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies. We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 1.8% of the variants are with CADD > 30, indicating they are of high predicted pathogenicity. Here we show our new strategy can generate high-quality data from processing these diversely generated WES samples. The improved ability to combine data sequenced in different batches benefits the whole genomics research community.
UR - http://www.scopus.com/inward/record.url?scp=85182824159&partnerID=8YFLogxK
U2 - 10.1038/s41467-024-44781-7
DO - 10.1038/s41467-024-44781-7
M3 - Article
C2 - 38263370
SN - 2041-1723
VL - 15
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 684
ER -