Human whole-exome genotype data for Alzheimer's disease

被引：0

作者：

Leung, Yuk Yee ^{[1
]}

Naj, Adam C. ^{[1
,2
]}

Chou, Yi-Fan ^{[1
]}

Valladares, Otto ^{[1
]}

Schmidt, Michael ^{[3
,4
]}

Hamilton-Nelson, Kara ^{[3
,4
]}

Wheeler, Nicholas ^{[5
,6
]}

Lin, Honghuang ^{[7
]}

Gangadharan, Prabhakaran ^{[1
]}

Qu, Liming ^{[1
]}

Clark, Kaylyn ^{[1
]}

Kuzma, Amanda B. ^{[1
]}

Lee, Wan-Ping ^{[1
]}

Cantwell, Laura ^{[1
]}

Nicaretta, Heather ^{[1
]}

van der Lee, Sven ^{[18
]}

English, Adam ^{[19
]}

Kalra, Divya ^{[19
]}

Muzny, Donna ^{[19
]}

Skinner, Evette ^{[19
]}

Doddapeneni, Harsha ^{[19
]}

Dinh, Huyen ^{[19
]}

Hu, Jianhong ^{[19
]}

Santibanez, Jireh ^{[19
]}

Jayaseelan, Joy ^{[19
]}

Worley, Kim ^{[19
]}

Gibbs, Richard A. ^{[19
]}

Lee, Sandra ^{[19
]}

Dugan-Perez, Shannon ^{[19
]}

Korchina, Viktoriya ^{[19
]}

Nasser, Waleed ^{[19
]}

Liu, Xiuping ^{[19
]}

Han, Yi ^{[19
]}

Zhu, Yiming ^{[19
]}

Liu, Yue ^{[19
]}

Khan, Ziad ^{[19
]}

Zhu, Congcong ^{[10
]}

Sun, Fangui Jenny ^{[10
]}

Jun, Gyungah R. ^{[10
]}

Chung, Jaeyoon ^{[10
]}

Farrell, John ^{[10
]}

Zhang, Xiaoling ^{[10
]}

Banks, Eric ^{[20
]}

Gupta, Namrata ^{[20
]}

Gabriel, Stacey ^{[20
]}

Butkiewicz, Mariusz ^{[5
,6
]}

Benchek, Penelope ^{[5
,6
]}

Smieszek, Sandra ^{[5
,6
]}

Song, Yeunjoo ^{[5
,6
]}

Vardarajan, Badri ^{[14
,15
,16
]}

机构：

[1] Univ Penn, Penn Neurodegenerat Genom Ctr, Perelman Sch Med, Dept Pathol & Lab Med, Philadelphia, PA 19104 USA

[2] Univ Penn, Perelman Sch Med, Dept Biostat Epidemiol & Informat, Philadelphia, PA USA

[3] Univ Miami, Miller Sch Med, Dr John T Macdonald Fdn Dept Human Genet, Miami, FL 33136 USA

[4] Univ Miami, John P Hussman Inst Human Genom, Miami, FL USA

[5] Case Western Reserve Univ, Dept Populat & Quantitat Hlth Sci, Cleveland Hts, OH USA

[6] Case Western Reserve Univ, Sch Med, Dept Genet & Genome Sci, Cleveland, OH 44106 USA

[7] UMass Chan Med Sch, Dept Med, Worcester, MA USA

[8] Boston Univ, Chobanian & Avedisian Sch Med, Dept Med Biomed Genet, Boston, MA 02215 USA

[9] Boston Univ, Sch Publ Hlth, Dept Biostat, Boston, MA USA

[10] Boston Univ, Sch Med, Boston, MA USA

[11] Univ Texas Hlth Sci Ctr San Antonio, Glenn Biggs Inst Alzheimers & Neurodegenerat Dis, San Antonio, TX 78229 USA

[12] Univ Washington, Dept Psychiat & Behav Sci, Seattle, WA USA

[13] Washington Univ, Sch Med, St Louis, MO USA

[14] Taub Inst Res Alzheimers Dis & Aging Brain, Dept Neurol, 630W 168th St, New York, NY 10032 USA

[15] Columbia Univ, Gertrude H Sergievsky Ctr, New York, NY USA

[16] New York Presbyterian Hosp, New York, NY USA

[17] Boston Univ, Sch Med, Dept Neurol, Boston, MA USA

[18] Amsterdam UMC, Amsterdam, Netherlands

[19] Baylor Coll Med, Houston, TX USA

[20] Broad Inst Harvard, Cambridge, MA USA

[21] Erasmus Univ, Rotterdam, Netherlands

[22] Indiana Univ, Ft Wayne, IN USA

[23] Johnson & Johnson, Titusville, FL USA

[24] Med Univ Graz, Graz, Austria

[25] MITRE, Mclean, VA USA

[26] Mt Sinai Sch Med New York, New York, NY USA

[27] Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA

[28] Natl Inst Aging, Bethesda, MD USA

[29] Nationwide Childrens, Columbus, OH USA

[30] Univ Oxford, Oxford, Oxfordshire, England

[31] Regeneron, Tarrytown, NY USA

[32] Rush Univ, Chicago, IL USA

[33] Stanford Univ, Stanford, CA USA

[34] Univ Colorado, Boulder, CO 80309 USA

[35] Univ Mississippi, Oxford, MS USA

[36] Univ Washington, Seattle, WA USA

[37] Vanderbilt Univ, Nashville, TN USA

来源：

NATURE COMMUNICATIONS | 2024年 / 15卷 / 01期

关键词：

GENOME; FRAMEWORK;

D O I：

10.1038/s41467-024-44781-7

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：15

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