PhenX RISING: Real world implementation and sharing of PhenX measures

Catherine A. McCarty; Wayne Huggins; Allison E. Aiello; Robert M. Bilder; Ahmad Hariri; Terry L. Jernigan; Erik Newman; Dharambir K. Sanghera; Timothy J. Strauman; Yi Zeng; Erin M. Ramos; Heather A. Junkins

doi:10.1186/1755-8794-7-16

PhenX RISING: Real world implementation and sharing of PhenX measures

Catherine A. McCarty, Wayne Huggins, Allison E. Aiello, Robert M. Bilder, Ahmad Hariri, Terry L. Jernigan, Erik Newman, Dharambir K. Sanghera, Timothy J. Strauman, Yi Zeng, Erin M. Ramos, Heather A. Junkins

Administration (DMED)

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

Abstract

Background: The purpose of this manuscript is to describe the PhenX RISING network and the site experiences in the implementation of PhenX measures into ongoing population-based genomic studies. Methods. Eighty PhenX measures were implemented across the seven PhenX RISING groups, thirty-three of which were used at more than two sites, allowing for cross-site collaboration. Each site used between four and 37 individual measures and five of the sites are validating the PhenX measures through comparison with other study measures. Self-administered and computer-based administration modes are being evaluated at several sites which required changes to the original PhenX Toolkit protocols. A network-wide data use agreement was developed to facilitate data sharing and collaboration. Results: PhenX Toolkit measures have been collected for more than 17,000 participants across the PhenX RISING network. The process of implementation provided information that was used to improve the PhenX Toolkit. The Toolkit was revised to allow researchers to select self- or interviewer administration when creating the data collection worksheets and ranges of specimens necessary to run biological assays has been added to the Toolkit. Conclusions: The PhenX RISING network has demonstrated that the PhenX Toolkit measures can be implemented successfully in ongoing genomic studies. The next step will be to conduct gene/environment studies.

Original language	English (US)
Article number	16
Journal	BMC Medical Genomics
Volume	7
Issue number	1
DOIs	https://doi.org/10.1186/1755-8794-7-16
State	Published - Mar 20 2014

Bibliographical note

Funding Information:
The AIDHS/SDS was established in India in 2002 and was funded by Fogarty International Center of National Institute of Health (NIH) [3]. Of the currently available 4,510 subjects from Phases I & II of the AIDHS/SDS, 1,200 subjects belong to family cohort and remaining 3,310 subjects are unrelated diabetic and healthy individuals recruited from India and the US. The goals of AIDHS/ SDS are to discover unique genetic markers associated with type 2 diabetes (T2D) and related metabolic and lipid traits by performing genome-wide association scans (GWAS) and validation studies. All participants signed a written informed consent for these investigations. The AIHDS/SDS was reviewed and approved by the University of Oklahoma Health Sciences Center’s Institutional Review Board, as well as the Human Subject Protection Committees at the participating hospitals and institutes in India. Institutional certification was obtained for the submission of genotype and phenotype data of AIDHS to dbGaP.

Funding Information:
PhenX is supported by award number U01HG004597 from the National Human Genome Research Institute. PhenX RISING was supported by administrative supplements from the National Human Genome Research Institute, including: R01 DA022720-05S1 (PI: Aiello) 3PL1 MH083271-05S1 (PI: Bilder), 3RC2 DA029475-02S1 and R01 HD61414 (PI: Jernigan), 3U01 HG006389-01S1 (PI: McCarty), R01DK082766-03S1 (PI: Sanghera), 3R01 DA031579-02S1 (PI: Strauman and Hariri), 3R01AG023627-06A2S1 (PI: Yi Zeng).

Funding Information:
Pediatric Imaging, Neurocognition, and Genetics (PING) is a multi-site cross-sectional study of typically developing children, adolescents, and young adults ranging in age from 3 to 20 (see Acknowledgements for a description of participating members from the PING infrastructure) funded by the National Institute on Drug Abuse (NIDA) and the National Institute of Child Health and Human Development (NICHD). The primary goal of PING is to create a pediatric imaging-genomics database of approximately 1400 cases that is freely available to the scientific community. Participants aged 18 and up provided written informed consent to undergo approximately three hours of neurocognitive testing and a one hour neuroimag-ing session, and to provide a saliva sample for [14,15]. The majority of participants also consented to allow these data to be shared in the publicly available database. For participants under the age of 18, parent versions of this consent were signed and the children and adolescents provided their assent where appropriate. This study structure was approved by IRBs at all participating PING sites. Six of the 9 PING sites chose to participate in the PhenX RISING project, and each participating site’s IRB approved this project as well.

Keywords

Epidemiology
Harmonization
PhenX
Phenotype
Risk factors

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10.1186/1755-8794-7-16

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@article{6c46b5b694284e87ab7329f377ce37f9,

title = "PhenX RISING: Real world implementation and sharing of PhenX measures",

abstract = "Background: The purpose of this manuscript is to describe the PhenX RISING network and the site experiences in the implementation of PhenX measures into ongoing population-based genomic studies. Methods. Eighty PhenX measures were implemented across the seven PhenX RISING groups, thirty-three of which were used at more than two sites, allowing for cross-site collaboration. Each site used between four and 37 individual measures and five of the sites are validating the PhenX measures through comparison with other study measures. Self-administered and computer-based administration modes are being evaluated at several sites which required changes to the original PhenX Toolkit protocols. A network-wide data use agreement was developed to facilitate data sharing and collaboration. Results: PhenX Toolkit measures have been collected for more than 17,000 participants across the PhenX RISING network. The process of implementation provided information that was used to improve the PhenX Toolkit. The Toolkit was revised to allow researchers to select self- or interviewer administration when creating the data collection worksheets and ranges of specimens necessary to run biological assays has been added to the Toolkit. Conclusions: The PhenX RISING network has demonstrated that the PhenX Toolkit measures can be implemented successfully in ongoing genomic studies. The next step will be to conduct gene/environment studies.",

keywords = "Epidemiology, Harmonization, PhenX, Phenotype, Risk factors",

author = "McCarty, {Catherine A.} and Wayne Huggins and Aiello, {Allison E.} and Bilder, {Robert M.} and Ahmad Hariri and Jernigan, {Terry L.} and Erik Newman and Sanghera, {Dharambir K.} and Strauman, {Timothy J.} and Yi Zeng and Ramos, {Erin M.} and Junkins, {Heather A.}",

note = "Funding Information: The AIDHS/SDS was established in India in 2002 and was funded by Fogarty International Center of National Institute of Health (NIH) [3]. Of the currently available 4,510 subjects from Phases I & II of the AIDHS/SDS, 1,200 subjects belong to family cohort and remaining 3,310 subjects are unrelated diabetic and healthy individuals recruited from India and the US. The goals of AIDHS/ SDS are to discover unique genetic markers associated with type 2 diabetes (T2D) and related metabolic and lipid traits by performing genome-wide association scans (GWAS) and validation studies. All participants signed a written informed consent for these investigations. The AIHDS/SDS was reviewed and approved by the University of Oklahoma Health Sciences Center{\textquoteright}s Institutional Review Board, as well as the Human Subject Protection Committees at the participating hospitals and institutes in India. Institutional certification was obtained for the submission of genotype and phenotype data of AIDHS to dbGaP. Funding Information: PhenX is supported by award number U01HG004597 from the National Human Genome Research Institute. PhenX RISING was supported by administrative supplements from the National Human Genome Research Institute, including: R01 DA022720-05S1 (PI: Aiello) 3PL1 MH083271-05S1 (PI: Bilder), 3RC2 DA029475-02S1 and R01 HD61414 (PI: Jernigan), 3U01 HG006389-01S1 (PI: McCarty), R01DK082766-03S1 (PI: Sanghera), 3R01 DA031579-02S1 (PI: Strauman and Hariri), 3R01AG023627-06A2S1 (PI: Yi Zeng). Funding Information: Pediatric Imaging, Neurocognition, and Genetics (PING) is a multi-site cross-sectional study of typically developing children, adolescents, and young adults ranging in age from 3 to 20 (see Acknowledgements for a description of participating members from the PING infrastructure) funded by the National Institute on Drug Abuse (NIDA) and the National Institute of Child Health and Human Development (NICHD). The primary goal of PING is to create a pediatric imaging-genomics database of approximately 1400 cases that is freely available to the scientific community. Participants aged 18 and up provided written informed consent to undergo approximately three hours of neurocognitive testing and a one hour neuroimag-ing session, and to provide a saliva sample for [14,15]. The majority of participants also consented to allow these data to be shared in the publicly available database. For participants under the age of 18, parent versions of this consent were signed and the children and adolescents provided their assent where appropriate. This study structure was approved by IRBs at all participating PING sites. Six of the 9 PING sites chose to participate in the PhenX RISING project, and each participating site{\textquoteright}s IRB approved this project as well.",

year = "2014",

month = mar,

day = "20",

doi = "10.1186/1755-8794-7-16",

language = "English (US)",

volume = "7",

journal = "BMC Medical Genomics",

issn = "1755-8794",

publisher = "BioMed Central Ltd.",

number = "1",

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TY - JOUR

T1 - PhenX RISING

T2 - Real world implementation and sharing of PhenX measures

AU - McCarty, Catherine A.

AU - Huggins, Wayne

AU - Aiello, Allison E.

AU - Bilder, Robert M.

AU - Hariri, Ahmad

AU - Jernigan, Terry L.

AU - Newman, Erik

AU - Sanghera, Dharambir K.

AU - Strauman, Timothy J.

AU - Zeng, Yi

AU - Ramos, Erin M.

AU - Junkins, Heather A.

N1 - Funding Information: The AIDHS/SDS was established in India in 2002 and was funded by Fogarty International Center of National Institute of Health (NIH) [3]. Of the currently available 4,510 subjects from Phases I & II of the AIDHS/SDS, 1,200 subjects belong to family cohort and remaining 3,310 subjects are unrelated diabetic and healthy individuals recruited from India and the US. The goals of AIDHS/ SDS are to discover unique genetic markers associated with type 2 diabetes (T2D) and related metabolic and lipid traits by performing genome-wide association scans (GWAS) and validation studies. All participants signed a written informed consent for these investigations. The AIHDS/SDS was reviewed and approved by the University of Oklahoma Health Sciences Center’s Institutional Review Board, as well as the Human Subject Protection Committees at the participating hospitals and institutes in India. Institutional certification was obtained for the submission of genotype and phenotype data of AIDHS to dbGaP. Funding Information: PhenX is supported by award number U01HG004597 from the National Human Genome Research Institute. PhenX RISING was supported by administrative supplements from the National Human Genome Research Institute, including: R01 DA022720-05S1 (PI: Aiello) 3PL1 MH083271-05S1 (PI: Bilder), 3RC2 DA029475-02S1 and R01 HD61414 (PI: Jernigan), 3U01 HG006389-01S1 (PI: McCarty), R01DK082766-03S1 (PI: Sanghera), 3R01 DA031579-02S1 (PI: Strauman and Hariri), 3R01AG023627-06A2S1 (PI: Yi Zeng). Funding Information: Pediatric Imaging, Neurocognition, and Genetics (PING) is a multi-site cross-sectional study of typically developing children, adolescents, and young adults ranging in age from 3 to 20 (see Acknowledgements for a description of participating members from the PING infrastructure) funded by the National Institute on Drug Abuse (NIDA) and the National Institute of Child Health and Human Development (NICHD). The primary goal of PING is to create a pediatric imaging-genomics database of approximately 1400 cases that is freely available to the scientific community. Participants aged 18 and up provided written informed consent to undergo approximately three hours of neurocognitive testing and a one hour neuroimag-ing session, and to provide a saliva sample for [14,15]. The majority of participants also consented to allow these data to be shared in the publicly available database. For participants under the age of 18, parent versions of this consent were signed and the children and adolescents provided their assent where appropriate. This study structure was approved by IRBs at all participating PING sites. Six of the 9 PING sites chose to participate in the PhenX RISING project, and each participating site’s IRB approved this project as well.

PY - 2014/3/20

Y1 - 2014/3/20

N2 - Background: The purpose of this manuscript is to describe the PhenX RISING network and the site experiences in the implementation of PhenX measures into ongoing population-based genomic studies. Methods. Eighty PhenX measures were implemented across the seven PhenX RISING groups, thirty-three of which were used at more than two sites, allowing for cross-site collaboration. Each site used between four and 37 individual measures and five of the sites are validating the PhenX measures through comparison with other study measures. Self-administered and computer-based administration modes are being evaluated at several sites which required changes to the original PhenX Toolkit protocols. A network-wide data use agreement was developed to facilitate data sharing and collaboration. Results: PhenX Toolkit measures have been collected for more than 17,000 participants across the PhenX RISING network. The process of implementation provided information that was used to improve the PhenX Toolkit. The Toolkit was revised to allow researchers to select self- or interviewer administration when creating the data collection worksheets and ranges of specimens necessary to run biological assays has been added to the Toolkit. Conclusions: The PhenX RISING network has demonstrated that the PhenX Toolkit measures can be implemented successfully in ongoing genomic studies. The next step will be to conduct gene/environment studies.

AB - Background: The purpose of this manuscript is to describe the PhenX RISING network and the site experiences in the implementation of PhenX measures into ongoing population-based genomic studies. Methods. Eighty PhenX measures were implemented across the seven PhenX RISING groups, thirty-three of which were used at more than two sites, allowing for cross-site collaboration. Each site used between four and 37 individual measures and five of the sites are validating the PhenX measures through comparison with other study measures. Self-administered and computer-based administration modes are being evaluated at several sites which required changes to the original PhenX Toolkit protocols. A network-wide data use agreement was developed to facilitate data sharing and collaboration. Results: PhenX Toolkit measures have been collected for more than 17,000 participants across the PhenX RISING network. The process of implementation provided information that was used to improve the PhenX Toolkit. The Toolkit was revised to allow researchers to select self- or interviewer administration when creating the data collection worksheets and ranges of specimens necessary to run biological assays has been added to the Toolkit. Conclusions: The PhenX RISING network has demonstrated that the PhenX Toolkit measures can be implemented successfully in ongoing genomic studies. The next step will be to conduct gene/environment studies.

KW - Epidemiology

KW - Harmonization

KW - PhenX

KW - Phenotype

KW - Risk factors

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DO - 10.1186/1755-8794-7-16

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AN - SCOPUS:84899081200

SN - 1755-8794

VL - 7

JO - BMC Medical Genomics

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ER -

PhenX RISING: Real world implementation and sharing of PhenX measures

Abstract

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