80_FR_20309 80 FR 20237 - List of Environmentally Responsive Human Genes Selected for Use In Screening Large Numbers of Substances Using Toxicogenomic Approaches

80 FR 20237 - List of Environmentally Responsive Human Genes Selected for Use In Screening Large Numbers of Substances Using Toxicogenomic Approaches

DEPARTMENT OF HEALTH AND HUMAN SERVICES
National Institutes of Health

Federal Register Volume 80, Issue 72 (April 15, 2015)

Page Range20237-20238
FR Document2015-08529

The National Institute of Environmental Health Sciences (NIEHS)/National Toxicology Program (NTP) requests comments on a set of human genes that have been identified and prioritized as environmentally responsive genes. These genes will be used in toxicogenomics approaches to screen cells or tissues obtained from humans against large numbers of chemicals. The goal was to generate a set of approximately 1500 human genes to evaluate transcriptional changes in response to chemical exposures. Similar gene sets will be developed for screening cells or tissues from other species such as rats, mice, zebrafish, and Caenorhabditis elegans. The human gene set should provide maximal toxicogenomic information on effects from chemical exposures that reflect general cellular responses, independent of cell type or species, and gene expression changes that are specific by organ and/or cell type. Such a list of environmentally responsive genes may also be useful in biomarker development and basic research efforts. This list of genes, referred to as the ``S1500'' gene list, or gene set, is available for public comment.

Federal Register, Volume 80 Issue 72 (Wednesday, April 15, 2015)
[Federal Register Volume 80, Number 72 (Wednesday, April 15, 2015)]
[Notices]
[Pages 20237-20238]
From the Federal Register Online  [www.thefederalregister.org]
[FR Doc No: 2015-08529]


-----------------------------------------------------------------------

DEPARTMENT OF HEALTH AND HUMAN SERVICES

National Institutes of Health


List of Environmentally Responsive Human Genes Selected for Use 
In Screening Large Numbers of Substances Using Toxicogenomic Approaches

    Request for Comments: The National Institute of Environmental 
Health Sciences/National Toxicology Program requests comments on a list 
of environmentally responsive human genes selected for use in screening 
large numbers of substances using toxicogenomic approaches.

SUMMARY: The National Institute of Environmental Health Sciences 
(NIEHS)/National Toxicology Program (NTP) requests comments on a set of 
human genes that have been identified and prioritized as 
environmentally responsive genes. These genes will be used in 
toxicogenomics approaches to screen cells or tissues obtained from 
humans against large numbers of chemicals. The goal was to generate a 
set of approximately 1500 human genes to evaluate transcriptional 
changes in response to chemical exposures. Similar gene sets will be 
developed for screening cells or tissues from other species such as 
rats, mice, zebrafish, and Caenorhabditis elegans. The human gene set 
should provide maximal toxicogenomic information on effects from 
chemical exposures that reflect general cellular responses, independent 
of cell type or species, and gene expression changes that are specific 
by organ and/or cell type. Such a list of environmentally responsive 
genes may also be useful in biomarker development and basic research 
efforts. This list of genes, referred to as the ``S1500'' gene list, or 
gene set, is available for public comment.

DATES: The deadline for receipt of comments is May 15, 2015.

ADDRESSES: Comments on the human S1500 gene set should be submitted 
electronically in Microsoft Excel or Word formats to 
[email protected]. Nominations for genes to be added to the S1500 
must be accompanied with a strong scientific justification for 
inclusion.

FOR FURTHER INFORMATION CONTACT: Dr. Elizabeth Maull, NIEHS, P.O. Box 
12233 (MD K2-17), Research Triangle Park, NC 27709; email: 
[email protected].

SUPPLEMENTARY INFORMATION:
    Background: In 2008, NIEHS/NTP, the U.S. Environmental Protection 
Agency's (EPA) National Center for Computational Toxicology (NCCT), and 
the National Human Genome Research Institute (NHGRI)/NIH Chemical 
Genomics Center (NCGC) (now located within the National Center for 
Advancing Translational Sciences (NCATS)) entered into a formal 
agreement to develop a vision and devise an implementation strategy to 
shift the assessment of chemical hazards from traditional, experimental 
animal, toxicology studies to target-specific, mechanism-based, 
biological observations largely obtained using in vitro assays. In mid-
2010, the U.S. Food and Drug Administration (FDA) joined the 
collaboration that is known informally as Tox21.
    Tox21 partner agencies collaborate to research, develop, validate, 
and translate innovative testing methods for characterization of 
toxicity pathways; identify compounds, assays, informatic analyses, and 
targeted testing needed to support the development of new methods; 
identify patterns of compound-induced biological response(s) in order 
to characterize toxicity pathways; facilitate cross-species and low-
dose extrapolation; prioritize compounds for more extensive 
toxicological evaluation; and develop predictive models for biological 
response in humans. The primary activity of Tox21 Phase I was the 
development of a quantitative high throughput screening (qHTS) approach 
for toxicology. The goal of Phase II was the implementation of the qHTS 
approach in screening a 10,000 compound library through a variety of 
nuclear receptor agonist/antagonist and stress response pathway assays, 
utilizing primarily reporter gene platforms. In Phase III, the focus is 
on assaying chemicals in high-content screens and mid to high 
throughput transcriptomic screens. High throughput gene expression 
changes will be the primary metric that is employed in Phase III to 
measure biological effects from chemical exposures.
    To conduct Tox21 Phase III, Tox21 partners initiated the ``S1500 
Genes High Throughput Transcriptomics'' project to capture information 
from the whole transcriptome (i.e., the entirety of all expressed RNA 
molecules in a cell or biological sample). This project will use a 
targeted subset of genes in a HTS or semi-HTS platform to gain insight 
into how biological systems respond to chemical exposures. Neither the 
actual number of genes to be utilized, nor the specific transcriptomics 
platform(s) needed to carry out the project, have been finalized.
    In an effort to select an appropriate subset of key representative 
or ``sentinel'' genes, the NTP previously requested input from the 
scientific community (78 FR 45542, July 29, 2013) on the ``Nomination 
and Prioritization of Environmentally Responsive Genes for Use in 
Screening Large Numbers of Substances Using Toxicogenomic 
Technologies.'' An interagency working group composed of members of the 
Tox21 partnership considered the input provided in response to the 
Federal Register notice as they developed a consensus strategy to 
select appropriate genes.
    The working group's goal was to select the most relevant and 
biologically diverse set of sentinel genes to represent transcriptomic 
responses to injury. Criteria for the selection and evaluation of an 
appropriate gene set are: (1) Representative of highly diverse gene 
expression changes reported to date, (2) capable of predicting the gene 
expression changes observed across the transcriptome, and (3) coverage 
of all major biological pathways.
    The current version of the human S1500 gene set can be found at 
http://ntp.niehs.nih.gov/go/S1500. This site will be updated as changes 
to the list are made. The consensus strategy for selection of an 
appropriate sentinel gene set can be accessed at the same site.
    Comments on the human S1500 gene set should be submitted 
electronically in Microsoft Excel or Word format to 
[email protected].
    Respondents to this request are asked to provide their name, 
affiliation, address, and contact information (including telephone and 
fax numbers, and email address). The deadline for receipt of comments 
is May 15, 2015.

[[Page 20238]]

    Responses to this request are voluntary. This notice does not 
obligate the U.S. Government to award a contract or otherwise pay for 
the information provided in response to this request. The U.S. 
Government reserves the right to use information provided by 
respondents for any purpose deemed necessary and legally appropriate. 
Any organization responding to this request should ensure that its 
response is complete and sufficiently detailed. Respondents are advised 
that the U.S. Government is under no obligation to acknowledge receipt 
of the information received or provide feedback to respondents with 
respect to any information submitted. No proprietary, classified, 
confidential, or sensitive information should be included in your 
response.
    Background Information on the NTP: The NTP is an interagency 
program established in 1978 (43 FR 53060) to strengthen the 
Department's activities in toxicology research and testing and to 
develop and validate new and better testing methods. Other activities 
of the program focus on strengthening the science base in toxicology 
and providing information about potentially toxic chemicals to health-
regulatory and research agencies, scientific and medical communities, 
and the public. The NTP is located administratively at the NIEHS. 
Information about NTP and NIEHS is available at http://ntp.niehs.nih.gov and http://www.niehs.nih.gov, respectively.

    Dated: April 8, 2015.
John R. Bucher,
Associate Director, National Toxicology Program.
[FR Doc. 2015-08529 Filed 4-14-15; 8:45 am]
 BILLING CODE 4140-01-P



                                                                           Federal Register / Vol. 80, No. 72 / Wednesday, April 15, 2015 / Notices                                           20237

                                                Place: Doubletree Hotel Washington, 1515              environmentally responsive genes may                  platforms. In Phase III, the focus is on
                                              Rhode Island Ave. NW., Washington, DC                   also be useful in biomarker                           assaying chemicals in high-content
                                              20005.                                                  development and basic research efforts.               screens and mid to high throughput
                                                Contact Person: CARLA T. WALLS, Ph.D.,                This list of genes, referred to as the                transcriptomic screens. High throughput
                                              Scientific Review Officer, Scientific Review
                                              Branch, EUNICE KENNEDY SHRIVER
                                                                                                      ‘‘S1500’’ gene list, or gene set, is                  gene expression changes will be the
                                              NATIONAL INSTITUTE OF CHILD HEALTH                      available for public comment.                         primary metric that is employed in
                                              AND HUMAN DEVELOPMENT, NIH, 6100                        DATES: The deadline for receipt of                    Phase III to measure biological effects
                                              EXECUTIVE BOULEVARD, ROOM 5B01,                         comments is May 15, 2015.                             from chemical exposures.
                                              BETHESDA, MD 20892–9304, (301) 435–                     ADDRESSES: Comments on the human                         To conduct Tox21 Phase III, Tox21
                                              6898, wallsc@mail.nih.gov.                              S1500 gene set should be submitted                    partners initiated the ‘‘S1500 Genes
                                              (Catalogue of Federal Domestic Assistance               electronically in Microsoft Excel or                  High Throughput Transcriptomics’’
                                              Program Nos. 93.864, Population Research;               Word formats to Genelist@niehs.nih.gov.               project to capture information from the
                                              93.865, Research for Mothers and Children;              Nominations for genes to be added to                  whole transcriptome (i.e., the entirety of
                                              93.929, Center for Medical Rehabilitation                                                                     all expressed RNA molecules in a cell
                                                                                                      the S1500 must be accompanied with a
                                              Research; 93.209, Contraception and
                                                                                                      strong scientific justification for                   or biological sample). This project will
                                              Infertility Loan Repayment Program, National
                                              Institutes of Health, HHS)                              inclusion.                                            use a targeted subset of genes in a HTS
                                                                                                      FOR FURTHER INFORMATION CONTACT: Dr.
                                                                                                                                                            or semi-HTS platform to gain insight
                                                Dated: April 9, 2015.                                                                                       into how biological systems respond to
                                              Carolyn Baum,                                           Elizabeth Maull, NIEHS, P.O. Box 12233
                                                                                                      (MD K2–17), Research Triangle Park, NC                chemical exposures. Neither the actual
                                              Program Analyst, Office of Federal Advisory                                                                   number of genes to be utilized, nor the
                                              Committee Policy.
                                                                                                      27709; email: maull@niehs.nih.gov.
                                                                                                                                                            specific transcriptomics platform(s)
                                                                                                      SUPPLEMENTARY INFORMATION:
                                              [FR Doc. 2015–08572 Filed 4–14–15; 8:45 am]
                                                                                                         Background: In 2008, NIEHS/NTP, the                needed to carry out the project, have
                                              BILLING CODE 4140–01–P
                                                                                                      U.S. Environmental Protection Agency’s                been finalized.
                                                                                                      (EPA) National Center for                                In an effort to select an appropriate
                                                                                                      Computational Toxicology (NCCT), and                  subset of key representative or
                                              DEPARTMENT OF HEALTH AND                                                                                      ‘‘sentinel’’ genes, the NTP previously
                                              HUMAN SERVICES                                          the National Human Genome Research
                                                                                                      Institute (NHGRI)/NIH Chemical                        requested input from the scientific
                                                                                                      Genomics Center (NCGC) (now located                   community (78 FR 45542, July 29, 2013)
                                              National Institutes of Health                                                                                 on the ‘‘Nomination and Prioritization
                                                                                                      within the National Center for
                                              List of Environmentally Responsive                      Advancing Translational Sciences                      of Environmentally Responsive Genes
                                              Human Genes Selected for Use In                         (NCATS)) entered into a formal                        for Use in Screening Large Numbers of
                                              Screening Large Numbers of                              agreement to develop a vision and                     Substances Using Toxicogenomic
                                              Substances Using Toxicogenomic                          devise an implementation strategy to                  Technologies.’’ An interagency working
                                              Approaches                                              shift the assessment of chemical hazards              group composed of members of the
                                                                                                      from traditional, experimental animal,                Tox21 partnership considered the input
                                                Request for Comments: The National                    toxicology studies to target-specific,                provided in response to the Federal
                                              Institute of Environmental Health                       mechanism-based, biological                           Register notice as they developed a
                                              Sciences/National Toxicology Program                    observations largely obtained using in                consensus strategy to select appropriate
                                              requests comments on a list of                          vitro assays. In mid-2010, the U.S. Food              genes.
                                              environmentally responsive human                        and Drug Administration (FDA) joined                     The working group’s goal was to
                                              genes selected for use in screening large               the collaboration that is known                       select the most relevant and biologically
                                              numbers of substances using                             informally as Tox21.                                  diverse set of sentinel genes to represent
                                              toxicogenomic approaches.                                  Tox21 partner agencies collaborate to              transcriptomic responses to injury.
                                              SUMMARY: The National Institute of                      research, develop, validate, and                      Criteria for the selection and evaluation
                                              Environmental Health Sciences                           translate innovative testing methods for              of an appropriate gene set are: (1)
                                              (NIEHS)/National Toxicology Program                     characterization of toxicity pathways;                Representative of highly diverse gene
                                              (NTP) requests comments on a set of                     identify compounds, assays, informatic                expression changes reported to date, (2)
                                              human genes that have been identified                   analyses, and targeted testing needed to              capable of predicting the gene
                                              and prioritized as environmentally                      support the development of new                        expression changes observed across the
                                              responsive genes. These genes will be                   methods; identify patterns of                         transcriptome, and (3) coverage of all
                                              used in toxicogenomics approaches to                    compound-induced biological                           major biological pathways.
                                              screen cells or tissues obtained from                   response(s) in order to characterize                     The current version of the human
                                              humans against large numbers of                         toxicity pathways; facilitate cross-                  S1500 gene set can be found at http://
                                              chemicals. The goal was to generate a                   species and low-dose extrapolation;                   ntp.niehs.nih.gov/go/S1500. This site
                                              set of approximately 1500 human genes                   prioritize compounds for more                         will be updated as changes to the list are
                                              to evaluate transcriptional changes in                  extensive toxicological evaluation; and               made. The consensus strategy for
                                              response to chemical exposures. Similar                 develop predictive models for biological              selection of an appropriate sentinel gene
                                              gene sets will be developed for                         response in humans. The primary                       set can be accessed at the same site.
                                              screening cells or tissues from other                   activity of Tox21 Phase I was the                        Comments on the human S1500 gene
                                              species such as rats, mice, zebrafish,                  development of a quantitative high                    set should be submitted electronically
                                              and Caenorhabditis elegans. The human                   throughput screening (qHTS) approach                  in Microsoft Excel or Word format to
tkelley on DSK3SPTVN1PROD with NOTICES




                                              gene set should provide maximal                         for toxicology. The goal of Phase II was              Genelist@niehs.nih.gov.
                                              toxicogenomic information on effects                    the implementation of the qHTS                           Respondents to this request are asked
                                              from chemical exposures that reflect                    approach in screening a 10,000                        to provide their name, affiliation,
                                              general cellular responses, independent                 compound library through a variety of                 address, and contact information
                                              of cell type or species, and gene                       nuclear receptor agonist/antagonist and               (including telephone and fax numbers,
                                              expression changes that are specific by                 stress response pathway assays,                       and email address). The deadline for
                                              organ and/or cell type. Such a list of                  utilizing primarily reporter gene                     receipt of comments is May 15, 2015.


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                                              20238                        Federal Register / Vol. 80, No. 72 / Wednesday, April 15, 2015 / Notices

                                                 Responses to this request are                          The meeting will be closed to the                   DEPARTMENT OF HEALTH AND
                                              voluntary. This notice does not obligate                public in accordance with the                         HUMAN SERVICES
                                              the U.S. Government to award a contract                 provisions set forth in sections
                                              or otherwise pay for the information                    552b(c)(4) and 552b(c)(6), Title 5 U.S.C.,            National Institutes of Health
                                              provided in response to this request.                   as amended. The grant applications and
                                              The U.S. Government reserves the right                  the discussions could disclose                        National Institute on Deafness and
                                              to use information provided by                          confidential trade secrets or commercial              Other Communication Disorders;
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                                              necessary and legally appropriate. Any                  and personal information concerning                     Pursuant to section 10(d) of the
                                              organization responding to this request                 individuals associated with the grant                 Federal Advisory Committee Act, as
                                              should ensure that its response is                      applications, the disclosure of which                 amended (5 U.S.C. App.), notice is
                                              complete and sufficiently detailed.                     would constitute a clearly unwarranted                hereby given of the following meetings.
                                              Respondents are advised that the U.S.                   invasion of personal privacy.                           The meetings will be closed to the
                                              Government is under no obligation to                      Name of Committee: National Advisory                public in accordance with the
                                              acknowledge receipt of the information                  Council on Aging.                                     provisions set forth in sections
                                              received or provide feedback to                           Date: May 12–13, 2015.                              552b(c)(4) and 552b(c)(6), Title 5 U.S.C.,
                                              respondents with respect to any                           Closed: May 12, 2015, 3:00 p.m. to 5:00             as amended. The grant applications and
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                                              classified, confidential, or sensitive                    Agenda: To review and evaluate grant
                                                                                                      applications.
                                                                                                                                                            confidential trade secrets or commercial
                                              information should be included in your                                                                        property such as patentable material,
                                                                                                        Place: National Institutes of Health,
                                              response.                                               Natcher Building—Building 45, P2 Level,               and personal information concerning
                                                 Background Information on the NTP:                   Conference Room E1/E2, 45 Center Drive,               individuals associated with the grant
                                              The NTP is an interagency program                       Bethesda, MD 20892.                                   applications, the disclosure of which
                                              established in 1978 (43 FR 53060) to                      Open: May 13, 2015, 8:00 a.m. to 1:00 p.m.          would constitute a clearly unwarranted
                                              strengthen the Department’s activities in                 Agenda: Call to order and report from the           invasion of personal privacy.
                                              toxicology research and testing and to                  Director; discussion of future meeting dates;
                                                                                                      consideration of minutes of last meeting;               Name of Committee: National Institute on
                                              develop and validate new and better                                                                           Deafness and Other Communication
                                              testing methods. Other activities of the                reports from Task Force on Minority Aging
                                                                                                      Research, Council of Councils, NACA                   Disorders Special Emphasis Panel; AHHC
                                              program focus on strengthening the                      Physician Scientist Working Group, Working            Review.
                                              science base in toxicology and                          Group on Program; Council Speaker; Program              Date: May 14, 2015.
                                              providing information about potentially                 Highlights.                                             Time: 11:00 a.m. to 3:00 p.m.
                                              toxic chemicals to health-regulatory and                  Place: National Institutes of Health,                 Agenda: To review and evaluate grant
                                              research agencies, scientific and                       Natcher Building—Building 45, P2 Level,               applications.
                                              medical communities, and the public.                    Conference Room E1/E2, 45 Center Drive,                 Place: National Institutes of Health,
                                              The NTP is located administratively at                  Bethesda, MD 20892.                                   Neuroscience Center, 6001 Executive
                                                                                                         Contact Person: Robin Barr, Ph.D.,                 Boulevard, Rockville, MD 20852 (Telephone
                                              the NIEHS. Information about NTP and                                                                          Conference Call).
                                                                                                      Director, National Institute on Aging, Office
                                              NIEHS is available at http://                           of Extramural Activities, Gateway Building,             Contact Person: Shiguang Yang, DVM,
                                              ntp.niehs.nih.gov and http://                           7201 Wisconsin Avenue, Bethesda, MD                   Ph.D., Scientific Review Officer, Division of
                                              www.niehs.nih.gov, respectively.                        20814, (301) 496–9322, barrr@nia.nih.gov.             Extramural Activities, NIDCD, NIH, 6001
                                                Dated: April 8, 2015.                                    Any interested person may file written             Executive Blvd., Room 8349, Bethesda, MD
                                                                                                      comments with the committee by forwarding             20892, 301–496–8683, yangshi@
                                              John R. Bucher,
                                                                                                      the statement to the Contact Person listed on         nidcd.nih.gov.
                                              Associate Director, National Toxicology                 this notice. The statement should include the           Name of Committee: National Institute on
                                              Program.                                                name, address, telephone number and when              Deafness and Other Communication
                                              [FR Doc. 2015–08529 Filed 4–14–15; 8:45 am]             applicable, the business or professional              Disorders Special Emphasis Panel;
                                              BILLING CODE 4140–01–P                                  affiliation of the interested person.                 Translational—VSL.
                                                                                                         In the interest of security, NIH has                 Date: June 1, 2015.
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                                              DEPARTMENT OF HEALTH AND                                onto the NIH campus. All visitor vehicles,              Agenda: To review and evaluate grant
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                                              National Institute on Aging; Notice of
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                                                 Pursuant to section 10(d) of the                        Information is also available on the               on Deafness and Other Communication
                                              Federal Advisory Committee Act, as                      Institute’s/Center’s home page: www.nih.gov/
                                                                                                                                                            Disorders, National Institutes of Health,
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                                              amended (5 U.S.C. App.), notice is                                                                            Rockville, MD 20850, 301–402–3587, rayk@
                                                                                                      additional information for the meeting will
                                              hereby given of a meeting of the                                                                              nidcd.nih.gov.
                                                                                                      be posted when available.
                                              National Advisory Council on Aging.                                                                             Name of Committee: Communication
                                                                                                      (Catalogue of Federal Domestic Assistance
                                                 The meeting will be open to the                                                                            Disorders Review Committee.
                                                                                                      Program Nos. 93.866, Aging Research,
                                              public as indicated below, with                                                                                 Date: June 18–19, 2015.
                                                                                                      National Institutes of Health, HHS)
                                                                                                                                                              Time: 8:00 a.m. to 5:00 p.m.
tkelley on DSK3SPTVN1PROD with NOTICES




                                              attendance limited to space available.
                                              Individuals who plan to attend and                        Dated: April 9, 2015.                                 Agenda: To review and evaluate grant
                                                                                                      Melanie J. Gray,                                      applications.
                                              need special assistance, such as sign                                                                           Place: Ritz-Carlton Hotel at Pentagon City,
                                              language interpretation or other                        Program Analyst, Office of Federal Advisory
                                                                                                                                                            1250 South Hayes Street, Arlington, VA
                                              reasonable accommodations, should                       Committee Policy.
                                                                                                                                                            22202.
                                              notify the Contact Person listed below                  [FR Doc. 2015–08569 Filed 4–14–15; 8:45 am]             Contact Person: Eliane Lazar-Wesley,
                                              in advance of the meeting.                              BILLING CODE 4140–01–P                                Scientific Review Officer, Division of



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Document Created: 2015-12-18 11:13:50
Document Modified: 2015-12-18 11:13:50
CategoryRegulatory Information
CollectionFederal Register
sudoc ClassAE 2.7:
GS 4.107:
AE 2.106:
PublisherOffice of the Federal Register, National Archives and Records Administration
SectionNotices
DatesThe deadline for receipt of comments is May 15, 2015.
ContactDr. Elizabeth Maull, NIEHS, P.O. Box 12233 (MD K2-17), Research Triangle Park, NC 27709; email: [email protected]
FR Citation80 FR 20237 

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