[Federal Register Volume 85, Number 95 (Friday, May 15, 2020)]
[Notices]
[Pages 29456-29457]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2020-10461]
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DEPARTMENT OF HEALTH AND HUMAN SERVICES
Centers for Disease Control and Prevention
[Docket No. CDC-2020-0051]
Request for Information Concerning Personnel and the Retention of
Next Generation Sequencing Data in Clinical and Public Health
Laboratories
AGENCY: Centers for Disease Control and Prevention (CDC), Department of
Health and Human Services (HHS).
ACTION: Notice with request for comment.
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SUMMARY: The Centers for Disease Control and Prevention (CDC) in the
Department of Health and Human Services (HHS) announces the opening of
a docket to obtain public comment on personnel performing
bioinformatics activities in clinical and public health laboratories;
storage and retention of next generation sequencing (NGS) data files;
and maintenance of sequence analysis software. The comments will be
used by the Clinical Laboratory Improvement Advisory Committee (CLIAC)
for deliberation and possible recommendations about future changes to
the Clinical Laboratory Improvement Amendments of 1988 (CLIA)
regulations.
DATES: Written comments must be received on or before July 14, 2020.
ADDRESSES: You may submit comments, identified by Docket No. CDC-2020-
0051 by any of the following methods. CDC does not accept public
comment by email.
Federal eRulemaking Portal: https://www.regulations.gov.
Follow the instructions for submitting comments.
Mail: Heather Stang, MS, MT, Division of Laboratory
Systems, Centers for Disease Control and Prevention, 1600 Clifton Road
NE, Mailstop V24-3, Atlanta, GA 30329, Attn: Docket No. CDC-2020-0051.
Instructions: All submissions received must include the agency name
and Docket Number. All relevant comments received will be posted
without change to https://www.regulations.gov, including any personal
information provided. For access to the docket to read background
documents or comments received, go to https://www.regulations.gov.
FOR FURTHER INFORMATION CONTACT: Heather Stang, MS, MT, Center for
Surveillance, Epidemiology and Laboratory Services, Centers for Disease
Control and Prevention, 1600 Clifton Road NE, Mailstop V24-3, Atlanta,
Georgia 30329-4018, telephone (800) 232-4636; email:
[email protected].
SUPPLEMENTARY INFORMATION:
Public Participation
Interested persons or organizations are invited to participate by
submitting written views, recommendations, and data about topics
related to personnel performing informatics activities, as well as data
storage and retention practices related to the use of next generation
sequencing (NGS) technology. In addition, CDC invites comments
specifically on the following questions:
(1) What are the roles and responsibilities for all personnel
performing bioinformatics or pathology/laboratory informatics
activities? What training is considered essential for each of the
roles? What competencies are considered essential for each of the
roles? What minimum educational requirements (degrees or courses) are
required for each of the roles?
(2) What are the challenges for recruitment and retention of
bioinformatics or pathology/laboratory informatics personnel?
(3) What are examples of how NGS data files are used in addition to
generating a clinical test result?
(4) What NGS data files should be retained for quality assurance,
repeat analyses, or subsequent analyses? How long should these NGS data
files be retained?
(5) What are the challenges and approaches for laboratories to
maintain and utilize previous versions of sequence analysis software?
Please note that comments received, including attachments and other
supporting materials, are part of the public record and are subject to
public disclosure. Comments will be posted on https://www.regulations.gov. Therefore, do not include any information in your
comment or supporting materials that you consider confidential or
inappropriate for public disclosure. If you include your name, contact
information, or other information that identifies you in the body of
your comments, that information will be on public display. Do not
submit public comments by email. CDC will review all submissions and
may choose to redact, or withhold, submissions containing private or
proprietary information such as Social Security numbers, medical
information, inappropriate language, or duplicate/near duplicate
examples of a mass-mail campaign.
Background and Brief Description
Clinical laboratory testing technology has advanced significantly
since the CLIA regulations were first implemented approximately 30
years ago. Next generation sequencing (NGS) technologies provide the
high-throughput capability to rapidly and cost-effectively sequence
large regions and mixed populations of DNA and RNA, when compared to
traditional sequencing methods. This technology results in a
significant increase in data that requires specialized analysis to
derive a clinically meaningful result. NGS has led to improvements in
diagnoses and patient care in many areas of medicine that include
medical genetics, pediatrics, oncology, and microbiology. In some
instances, NGS has led to life-saving diagnoses and treatment pathways,
not achievable using other testing modalities. One element that
differentiates NGS from most laboratory methodologies is its
[[Page 29457]]
significant reliance on informatics to achieve a meaningful and
reportable result. As a consequence, clinical laboratories require
personnel knowledgeable in bioinformatics or pathology/laboratory
informatics to design and manage the bioinformatics analysis.
While CLIA regulations apply to clinical NGS testing, there is a
lack of clarity regarding how the general CLIA quality system and
personnel requirements should be specifically implemented for the NGS
bioinformatics components. In April 2019, CLIAC made eight
recommendations regarding CLIA's application to NGS-based technologies.
This request for information is soliciting comments from the public for
more information on topic areas mentioned in two of the
recommendations, specifically, the qualifications of personnel
performing bioinformatics activities; storage and retention of NGS data
files; and maintenance of sequence analysis software. The April 2019
CLIAC summary is available in the docket under the Supporting Materials
tab and at https://www.cdc.gov/cliac/past-meetings.html.
The qualifications and responsibilities of personnel performing the
informatics component of the testing process are not addressed in the
CLIA regulations. For the purpose of this request for information, the
informatics component of NGS includes the analysis of NGS machine-
generated data and subsequent computational processes. Therefore, CDC
is asking the public to describe different responsibilities of
personnel providing bioinformatics or pathology/laboratory informatics
expertise such as validating and assuring that the informatics pipeline
meets documented performance specifications.
CDC is also interested in learning the skills, training, and
education of personnel who will fill bioinformatics or pathology/
laboratory informatics positions, and how clinical and public health
laboratories can recruit and retain personnel with these identified
skills.
Lastly, the NGS testing process generates large amounts of data and
requires multiple file types. CLIA regulations specify at 42 CFR
493.1105(a)(3) that all analytic systems records must be kept for at
least two years, but the regulations do not specify the types of data
to be captured or the retention time for a given data type. The
regulations do not address the capability to access and reanalyze the
data after the test is performed. This capability may require retention
of the version of software used in the original analysis. CDC requests
comment from the public on this topic.
Dated: May 12, 2020.
Sandra Cashman,
Executive Secretary, Centers for Disease Control and Prevention.
[FR Doc. 2020-10461 Filed 5-14-20; 8:45 am]
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