Literature DB >> 35308936

Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation.

Spiros Denaxas1,2,3,4,5, Ge Liu6, Qiping Feng6, Ghazaleh Fatemifar6,2, Lisa Bastarache1, Eric V Kerchberger6, Aroon D Hingorani1,2,3, Tom Lumbers1,2, Josh F Peterson6, Wei-Qi Wei6, Harry Hemingway1,2,3,5.   

Abstract

Objective: To establish and validate mappings between primary care clinical terminologies (Read Version 2, Clinical Terms Version 3) and Phecodes.
Methods: We processed 123,662,421 primary care events from 230,096 UK Biobank (UKB) participants. We assessed the validity of the primary care-derived Phecodes by conducting PheWAS analyses for seven pre-selected SNPs in the UKB and compared with estimates from BioVU.
Results: We mapped 92% of Read2 (n=10,834) and 91% of CTV3 (n=21,988) to 1,449 and 1,490 Phecodes. UKB PheWAS using Phecodes from primary care EHR and hospitalizations replicated all (n=22) previously-reported genotype-phenotype associations. When limiting Phecodes to primary care EHR, replication was 81% (n=18).
Conclusion: We introduced a first version of mappings from Read2/CTV3 to Phecodes. The reference list of diseases provided by Phecodes can be extended, enabling researchers to leverage primary care EHR for high-throughput discovery research. ©2021 AMIA - All rights reserved.

Entities:  

Mesh：

Year:  2022        PMID： 35308936      PMCID： PMC8861677     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN： 1559-4076


  14 in total

1.  Development of a large-scale de-identified DNA biobank to enable personalized medicine.

Authors:  D M Roden; J M Pulley; M A Basford; G R Bernard; E W Clayton; J R Balser; D R Masys
Journal:  Clin Pharmacol Ther       Date:  2008-05-21       Impact factor: 6.875

Review 2.  Value for money and the Quality and Outcomes Framework in primary care in the UK NHS.

Authors:  Simon Walker; Anne R Mason; Karl Claxton; Richard Cookson; Elisabeth Fenwick; Robert Fleetcroft; Mark Sculpher
Journal:  Br J Gen Pract       Date:  2010-05       Impact factor: 5.386

3.  Next-generation genotype imputation service and methods.

Authors:  Sayantan Das; Lukas Forer; Sebastian Schönherr; Carlo Sidore; Adam E Locke; Alan Kwong; Scott I Vrieze; Emily Y Chew; Shawn Levy; Matt McGue; David Schlessinger; Dwight Stambolian; Po-Ru Loh; William G Iacono; Anand Swaroop; Laura J Scott; Francesco Cucca; Florian Kronenberg; Michael Boehnke; Gonçalo R Abecasis; Christian Fuchsberger
Journal:  Nat Genet       Date:  2016-08-29       Impact factor: 38.330

4.  PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.

Authors:  Joshua C Denny; Marylyn D Ritchie; Melissa A Basford; Jill M Pulley; Lisa Bastarache; Kristin Brown-Gentry; Deede Wang; Dan R Masys; Dan M Roden; Dana C Crawford
Journal:  Bioinformatics       Date:  2010-03-24       Impact factor: 6.937

5.  Introducing whole-genome sequencing into routine cancer care: the Genomics England 100 000 Genomes Project.

Authors:  C Turnbull
Journal:  Ann Oncol       Date:  2018-04-01       Impact factor: 32.976

6.  Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data.

Authors:  Joshua C Denny; Lisa Bastarache; Marylyn D Ritchie; Robert J Carroll; Raquel Zink; Jonathan D Mosley; Julie R Field; Jill M Pulley; Andrea H Ramirez; Erica Bowton; Melissa A Basford; David S Carrell; Peggy L Peissig; Abel N Kho; Jennifer A Pacheco; Luke V Rasmussen; David R Crosslin; Paul K Crane; Jyotishman Pathak; Suzette J Bielinski; Sarah A Pendergrass; Hua Xu; Lucia A Hindorff; Rongling Li; Teri A Manolio; Christopher G Chute; Rex L Chisholm; Eric B Larson; Gail P Jarvik; Murray H Brilliant; Catherine A McCarty; Iftikhar J Kullo; Jonathan L Haines; Dana C Crawford; Daniel R Masys; Dan M Roden
Journal:  Nat Biotechnol       Date:  2013-12       Impact factor: 54.908

7.  Relationship Between Glycemia and Cognitive Function, Structural Brain Outcomes, and Dementia: A Mendelian Randomization Study in the UK Biobank.

Authors:  Victoria Garfield; Aliki-Eleni Farmaki; Ghazaleh Fatemifar; Sophie V Eastwood; Rohini Mathur; Christopher T Rentsch; Spiros Denaxas; Krishnan Bhaskaran; Liam Smeeth; Nish Chaturvedi
Journal:  Diabetes       Date:  2021-02-25       Impact factor: 9.461

8.  UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER.

Authors:  Spiros Denaxas; Arturo Gonzalez-Izquierdo; Kenan Direk; Natalie K Fitzpatrick; Ghazaleh Fatemifar; Amitava Banerjee; Richard J B Dobson; Laurence J Howe; Valerie Kuan; R Tom Lumbers; Laura Pasea; Riyaz S Patel; Anoop D Shah; Aroon D Hingorani; Cathie Sudlow; Harry Hemingway
Journal:  J Am Med Inform Assoc       Date:  2019-12-01       Impact factor: 4.497

9.  Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation.

Authors:  Patrick Wu; Aliya Gifford; Xiangrui Meng; Xue Li; Harry Campbell; Tim Varley; Juan Zhao; Robert Carroll; Lisa Bastarache; Joshua C Denny; Evropi Theodoratou; Wei-Qi Wei
Journal:  JMIR Med Inform       Date:  2019-11-29

10.  PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records.

Authors:  Neil S Zheng; QiPing Feng; V Eric Kerchberger; Juan Zhao; Todd L Edwards; Nancy J Cox; C Michael Stein; Dan M Roden; Joshua C Denny; Wei-Qi Wei
Journal:  J Am Med Inform Assoc       Date:  2020-11-01       Impact factor: 7.942
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.