Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics

被引：7

作者：

Shuey, Megan M. ^{[1
,2
]}

Stead, William W. ^{[3
]}

Aka, Ida ^{[3
]}

Barnado, April L. ^{[3
]}

Bastarache, Julie A. ^{[1
]}

Brokamp, Elly ^{[2
]}

Campbell, Meredith ^{[4
]}

Carroll, Robert J. ^{[3
]}

Goldstein, Jeffrey A. ^{[5
]}

Lewis, Adam ^{[3
]}

Malow, Beth A. ^{[1
]}

Mosley, Jonathan D. ^{[1
,2
]}

Osterman, Travis ^{[3
]}

Padovani-Claudio, Dolly A. ^{[6
]}

Ramirez, Andrea ^{[7
]}

Roden, Dan M. ^{[1
,2
]}

Schuler, Bryce A. ^{[8
]}

Siew, Edward ^{[1
]}

Sucre, Jennifer ^{[8
]}

Thomsen, Isaac ^{[8
]}

Tinker, Rory J. ^{[8
]}

Van Driest, Sara ^{[7
,8
]}

Walsh, Colin ^{[3
]}

Warner, Jeremy L. ^{[8
]}

Wells, Quinn S. ^{[1
]}

Wheless, Lee ^{[1
]}

Bastarache, Lisa ^{[3
]}

机构：

[1] Vanderbilt Univ, Med Ctr, Dept Med, Nashville, TN 37203 USA

[2] Vanderbilt Univ, Vanderbilt Genet Inst, Med Ctr, Nashville, TN 37203 USA

[3] Vanderbilt Univ, Med Ctr, Dept Biomed Informat, Nashville, TN 37203 USA

[4] Virginia Commonwealth Univ, Dept Pediat, Richmond, VA 23219 USA

[5] Northwestern Feinberg Sch Med, Dept Pathol, Chicago, IL 60611 USA

[6] Vanderbilt Univ, Med Ctr, Dept Ophthalmol, Nashville, TN 37232 USA

[7] NIH, All Us Res Program, Bethesda, MD 20892 USA

[8] Vanderbilt Univ, Med Ctr, Dept Pediat, Nashville, TN 37203 USA

来源：

BIOINFORMATICS | 2023年 / 39卷 / 11期

基金：

美国国家卫生研究院;

关键词：

WIDE ASSOCIATION; PHEWAS; DISEASES; RECORD;

D O I：

10.1093/bioinformatics/btad655

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure.Results Here, we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure-including infectious disease, pregnancy, congenital anomalies, and neonatology-and is a more robust representation of the medical phenome for global use in discovery research.Availability and implementation phecodeX is available at https://github.com/PheWAS/phecodeX.

引用

页数：5

共 50 条

[1] LiDAR: An important tool for next-generation phenotyping technology of high potential for plant phenomics?
Lin, Yi
COMPUTERS AND ELECTRONICS IN AGRICULTURE, 2015, 119 : 61 - 73
[2] Next-generation phenomics for the Tree of Life
Burleigh, J. Gordon
Alphonse, Kenzley
Alverson, Andrew J.
Bik, Holly M.
Blank, Carrine
Cirranello, Andrea L.
Cui, Hong
Daly, Marymegan
Dietterich, Thomas G.
Gasparich, Gail
Irvine, Jed
Julius, Matthew
Kaufman, Seth
Law, Edith
Liu, Jing
Moore, Lisa
O'Leary, Maureen A.
Passarotti, Maria
Ranade, Sonali
Simmons, Nancy B.
Stevenson, Dennis W.
Thacker, Robert W.
Theriot, Edward C.
Todorovic, Sinisa
Velazco, Paul M.
Walls, Ramona L.
Wolfe, Joanna M.
Yu, Mengjie
PLOS CURRENTS-TREE OF LIFE, 2013,
[3] Next-Generation Sequencing Demands Next-Generation Phenotyping
Hennekam, Raoul C. M.
Biesecker, Leslie G.
HUMAN MUTATION, 2012, 33 (05) : 884 - 886
[4] Next-generation phenotyping of electronic health records
Hripcsak, George
Albers, David J.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 2013, 20 (01) : 117 - 121
[5] Next-generation antibody discovery platforms
Hardiman, Gary
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (45) : 18245 - 18246
[6] Research and application of next-generation firewall technique in medical network
Zhang, Yonggang
JOURNAL OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING, 2022, 22 (05) : 1461 - 1476
[7] Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding
Esposito, Salvatore
Carputo, Domenico
Cardi, Teodoro
Tripodi, Pasquale
PLANTS-BASEL, 2020, 9 (01):
[8] RDA-Genebank and Digital Phenotyping for Next-Generation Research on Plant Genetic Resources
Kim, Seong-Hoon
Subramanian, Parthiban
Na, Young-Wang
Hahn, Bum-Soo
Kim, Yoonha
PLANTS-BASEL, 2023, 12 (15):
[9] Next-generation epidemiology: the role of high-resolution molecular phenotyping in diabetes research
Paul W. Franks
Hugo Pomares-Millan
Diabetologia, 2020, 63 : 2521 - 2532
[10] Next-generation epidemiology: the role of high-resolution molecular phenotyping in diabetes research
Franks, Paul W.
Pomares-Millan, Hugo
DIABETOLOGIA, 2020, 63 (12) : 2521 - 2532

← 1 2 3 4 5 →