United States Department of Agriculture 

Animal and Plant Health Inspection Service 

Biotechnology Regulatory Services

Document Control:

User’s Guidelines

Version No.:

1.1

General Document Preparation Guidelines 

For Submission to BRS

Effective Date:

09/07/2018

USDA-APHIS Biotechnology Regulatory Services

User’s Guide

General Document Preparation Guidelines 

For Submission to BRS

V1. 2/22/2011, v1.1 09/05/2018
United States Department of Agriculture 

Animal and Plant Health Inspection Service 

Biotechnology Regulatory Services

Document Control:

User’s Guidelines

Version No.:

1.1

General Document Preparation Guidelines 

For Submission to BRS

Effective Date:

09/07/2018

The information contained in this document is intended solely as guidance, and reflects 

APHIS' current interpretation of applicable statues and regulations. Except where noted, 

persons may choose to follow APHIS guidance or follow different procedures, practices, or 

protocols that meet applicable statutes and regulations.

Language implying that guidance is mandatory (e.g. "shall," "must," " required," or 

"requirement") should not be construed as binding unless the terms are used to refer to a 

statutory or regulatory requirement. Throughout the document, sections from applicable 

statutes and regulations are clearly identified in grey-shaded text boxes.

Conversely, following the guidelines contained in this document should not be construed as a 

guarantee of compliance with applicable statutes and regulations.
USDA-APHIS-BRS User’s Guide Document Preparation Guidelines

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General Document Preparation Guidelines 

For Submission to BRS

Table of Contents

Quick Guide to BRS Submissions......................................................................................................2

General Document Preparation Guidelines for Submission to BRS ............................................... 3

Document Preparation Guidelines......................................................................................................3

General Text Formatting .................................................................................................................3

Scientific Names and Terminology ................................................................................................3

References.........................................................................................................................................4

Tables................................................................................................................................................4

Figures...............................................................................................................................................4

Equations........................................................................................................................................... 5

Sequence Data ..................................................................................................................................5

Color Printing .................................................................................................................................... 5

Media Type and Number of Copies................................................................................................5

Data Quality Guidelines.......................................................................................................................6

Data Collection and Experimental Design.....................................................................................6

Statistical Methodology...................................................................................................................6

Statistically Valid Demonstration of Equivalence ........................................................................7

Confidential Business Information (CBI) in Submissions to BRS..................................................8

What is confidential businessinformation (CBI)?........................................................................8

Letter of justification for claimsof CBI.........................................................................................8

Preparation of documents containing CBI.....................................................................................9

How to Find More Information.........................................................................................................10
USDA-APHIS-BRS User’s Guide Document Preparation Guidelines

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Quick Guide to BRS Submissions

Documents submitted to BRS are primarily related to four types of regulatory procedures that are 

discussed in detail in other guidance documents:

• Permits for the introduction of regulated articles

• Notification of the introduction of regulated articles

• Petitions to grant non-regulated status to a regulated article

• Extension of non-regulated status to a regulated article

Although the specific content of individual documents will vary based upon the type of 

submission, all documents submitted to BRS have some features in common.

• General formatting (p. 3-5)

o Documents submitted to BRS should be of professional, publication quality.

o Specific document preparation guidelines are provided in this document.

• Presentation of data and statistical analysis (p. 5-8)

o Data and statistical analysis included in submissions must be of a sufficient 

caliber as for publication in a scientific peer reviewed journal.

o Specific guidelines for presentation of data and statistical analysis are provided in 

this document.

o Particular care must be taken in selecting statistical methods to demonstrate

equivalence.

• Confidential business information (p. 8-10)

o All documents submitted to BRS may be released to the public pursuant to a 

request under the Freedom of Information Act (FOIA).

o Information determined to be "confidential business information" (CBI)is 

protected from public disclosure.

o Applicants must submit a letter justifying any claims of CBI in submitted 

documents.

o Submissions to BRS that include CBI must be formatted to protect this 

information from public disclosure by preparing an additional CBI-deleted 

version.
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General Document Preparation Guidelines for Submission to

BRS

Most documents submitted to BRS are associated with one of the four types of regulatory 

procedures discussed in detail other guidance documents:

• Permits for the introduction of regulated articles

• Notification of the introduction of certain regulated articles

• Petitions to grant non-regulated status to a regulated article

• Extension of non-regulated status to a regulated article

Each guidance document above includes sample documents related to a particular type of 

submission. Although the specific content of individual documents will vary based upon the 

submission type, all documents submitted to BRS have some features in common. This guidance 

document details basic guidelines for document preparation and formatting, presentation of 

statistical information, and handling of confidential business information.

Document Preparation Guidelines

All documents submitted to BRS should be of professional, publication quality, as if for 

submission to a peer reviewed scholarly journal. Language should be clear, well organized, and 

free of typographical and grammatical errors. Documents should generally follow standard 

formatting guidelines similar to those provided by most scientific journals.

Please use the following specific guidelines, where appropriate, for preparation of all documents 

submitted to BRS.

General Text Formatting

Format text in the body of the document for printing on standard U.S. letter-sized paper in 

portrait orientation. Use at least 1" margins on all sides of the text. Line spacing may be single 

or double. Use a 12-point font (for proportionally spaced type) or 10 characters/inch (4 

characters/cm) if the letter spacing is uniform. Number all pages in the document sequentially 

beginning with the first page.

Divide long documents (such as petitions) into sections, and include Table of Contents, and Lists 

of Tables, Figures, etc.

Scientific Names and Terminology

Spell out all symbols, abbreviations and acronyms the first time they are used. Avoid use of 

abbreviations for gene, protein or other specialized names. Define (or avoid) all technical terms 

that may be familiar only to specialists.
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The species name is required for all donor and recipient organisms. Italicize scientific names.

Species name must be fully spelled out the first time it is mentioned in the text (e.g. 

Lycopersicon esculentum), but may be abbreviated with the single-letter generic name thereafter 

(e.g. L. esculentum) as long as no confusion with other species results. Also, cite sub-species, 

cultivar, etc., where relevant. Do not use common and species names interchangeably, but 

common names may be used after scientific names are provided.

The first time an organism is introduced in the text, provide a brief description to clearly identify 

the organism; e.g. "Cornus floridaL. (flowering dogwood), a small deciduous tree."

References

If references are cited in the text of a submission, presenting them in the text as (Author, Year) is 

preferable. The submission should also include a reference list that details reference author(s), 

date, article title, journal title, volume, and page number. Do not abbreviate journal titles. When 

conference proceedings or other books are cited, provide the publisher's name and location. See 

the American Medical Association for an example of an acceptable citation style:

http://www2.liu.edu/cwis/cwp/library/workshop/citama.htm

Copies of literature cited need not be included with the submission. However, APHIS may 

request copies of literature cited if necessary.

Tables

Tables should supplement, not duplicate, the text. Number tables in the order of their citation in 

the text. Provide a short descriptive title at the top of each table; rather than simply repeating the 

labels on columns and rows of the table, the title should reveal the point of grouping certain data 

in the table. Statistical and other details should be provided as footnotes rather than appearing in 

the title. Tables should have footnotes for any abbreviations used in the table. Do not add 

vertical or horizontal lines to tables unless essential to avoid ambiguity. Do not repeat the same 

material in figures and tables; when either is equally clear, a figure is preferable. Do not include 

any class of information in tables that is not discussed in the text of the document.

Small tables may be embedded in the text. Larger tables should be presented on a separate page 

either following the first citation in the text, or at the end of the document or major section. If 

presented on separate page, a table may be in either portrait or landscape orientation.

Figures

Figures should be numbered sequentially, titled, and legends should be brief, self-sufficient 

explanations. The figure title (i.e., Figure 1) should be given as the first two words of the legend. 

Label graph axes with the parameter or variable measured, the units of measure, and the scale.

Definitions of symbols should usually appear in the figure legend. Avoid the use of light lines 

and screen shading, instead use black-and-white, hatched and/or crosshatched designs for

emphasis. Before submitting figures, please photocopy each one to verify that photocopied 

versions of the figures are as clear as the originals.
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Include figures in the document following the guidelines for tables (see above).

Equations

Equations set separately from the text should be broken into two or more lines if they exceed the 

width of one column. Use leading zeroes with all numbers less than one, including probability 

values (e.g., P< 0.001).

Sequence Data

In general, nucleotide and amino acid sequences should be submitted only when the sequences 

are not already available in a public database. Short sequences should be included in the body of 

submissions only when necessary to illustrate a specific point. For example, amino acid 

sequence might be included in a figure to illustrate similarity to other amino acid sequences.

Attach long stretches of sequence (greater than ~100 nucleotides or amino acids) as separate files 

in a standard sequence format. Applicants are encouraged to submit sequence data to public 

databases, such as those maintained by the National Center for Biotechnology Information 

(NCBI), and provide APHIS with accession numbers.

Color Printing

The use of color in submissions is discouraged, unless color is an integral part of the image's 

meaning. Submissions are commonly reproduced in black and white, particularly when 

distributed to the public. In many cases, the use of color may be unavoidable (i.e. photographs). 

If color images are necessary, submit original full-color copies of the image with all required 

copies of the document. Color images should be clear and understandable when printed in black 

and white (e.g. when photocopied or printed in grayscale).

Media Type and Number of Copies

Acceptable media type (printed vs. electronic) and required number of copies varies depending 

upon the type of submission. See other guidance documents for information specific to each 

submission type. When printed documents are accepted, the original document should be printed 

on one side of U.S. letter-sized paper. Any required copies should be of a quality and clarity 

comparable to the original.

Where electronic media are accepted, submit all files on a single CD (if possible) formatted to be 

accessible on a computer with a Microsoft Windows operating system. In some cases, files may 

be submitted via e-mail. Acceptable file formats include Microsoft Word, and Adobe pdf. See 

other guidance documents for information specific to each submission type.
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Data Quality Guidelines

Any experiments performed by the submitter must follow certain guidelines in order to be used 

as supporting data in submissions to BRS. The amount of detailed information given is critical, 

especially for petitions and extensions. Supporting data provided to APHIS is expected to be of 

the same scientific caliber as that published in peer reviewed journals.

In all submissions, fully describe experimental design, use of controls, and appropriate statistical 

methodology, in addition to concurring published data. Acknowledgement of opposing data and 

logical arguments against it should also be included. Note that for most submissions to BRS, 

federal regulations require disclosure of unfavorable evidence.

Data Collection and Experimental Design

Clearly describe sampling designs, experimental designs, and data collection protocols, 

precision of measurements, sampling units, experimental units, and sample sizes. Where 

possible, include some measure of the precision of estimates- standard errors or confidence 

intervals- although this may not be necessary or possible in all instances, especially for unusual 

statistics.

Graphical data presentation is encouraged. Carefully composed graphs often permit the reader to 

decide at a glance if data are in danger of violating statistical assumptions.

Statistical Methodology

Authors are free to interpret statistical analyses as they see fit; however, documents must include 

information sufficient for an independent assessment of the author's analysis. Clearly state the 

assumptions and the model underlying any statistical analysis, and provide sufficient detail in the 

presentation of results.

Assumptions

Assumptions behind any statistical analysis must be articulated and well justified.

Where unusual assumptions are made, unusual procedures are used, or unusual types of data are 

involved, provide sufficient information for an assessor to judge whether any departures from 

assumptions are severe enough to invalidate the conclusions. The amount of detail provided in 

any particular instance will depend on the centrality of the statistical test to the conclusions.

Reporting of analyses

Always state the specific statistical procedure used. If a statistics program or program package was 

used, a complete citation (including version number) should be given. If necessary, the author should 

indicate which procedure within a package was used, and which method within a procedure was 

chosen. Explain unusual statistical procedures in sufficient detail, including references if appropriate, 

for the reader to reconstruct the analysis. To denote levels of significance, actual P values are 

generally more informative than symbols such as * and **.

If conclusions are based on an analysis of variance or regression, information sufficient to permit 

the construction of the full analysis of variance table (at least degrees of freedom, the structure of 
USDA-APHIS-BRS User’s Guide Document Preparation Guidelines

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F-ratios, and P values) must be presented or be clearly implicit. Where ambiguity is possible, the 

authors must indicate which effects were considered fixed or random and why.

Use of controls. In all experimental designs, use appropriate positive and negative control

groups. Include control groups in tables and figures for comparison.

Statistically Valid Demonstration of Equivalence

Much of the data submitted to BRS is used to argue the equivalenceof a transgenic variety and a 

non-transgenic comparator. This is particularly true for petitions to grant non-regulated status, in 

which the petitioner presents evidence that a transgenic organism is no more likely to pose a 

plant pest risk than the unmodified organism from which it was derived.

In support of this, many applicants submit data that, in their view, demonstrates that the 

agronomic and compositional properties of a transgenic line are statistically similar to a nontransgenic line. Applicants often base a conclusion of equivalence upon statistical methods 

designed to detect statistical differences, using an argument as follows:

• The null hypothesis is that there is no difference between two lines.

• The statistical test evaluates the probability of finding the observed difference between 

the lines by chance alone, given that the null hypothesis is true.

• If the difference is statistically significant-that is, the difference is unlikely to have been 

observed by chance- then it seems clear that the two lines are not equivalent.

• If the difference is not statistically significant, it seems to make sense to conclude that 

the two lines are equivalent.

This last conclusion is often used to support the interpretation the variable measured is 

equivalent between the transgenic and non-transgenic lines.

This approach, however, is statistically invalid and leads to invalid conclusions. If this kind of 

test reaches the conclusion of "no statistically significant difference," it means the current 

evidence is not strong enough to demonstrate that the two lines are different; this is not the same 

as demonstrating that the two lines are the same. The procedure establishes evidence against the 

null hypothesis only, not for it. In other words, the absence of evidence is not evidence of 

absence.

A small sample size, for example, can make it difficult to detect statistical significance of a 

difference. If the goal is to establish equivalence, following the flawed methodology above one 

would just run the experiment with few samples or replicates. Furthermore, problems with the 

data itself (e.g. outliers), may hamper the ability to find a result at the specified significance 

level, and so again one could come to a conclusion of equivalence as a result of poor data.

Statistical methods are readily available to determine whether two groups are statistically 

equivalent, and should be used accordingly. Equivalence tests begin with the null hypothesis that 

two samples are different, and seek evidence to reject that hypothesis. For more information on 

statistical methods of equivalence testing, see:
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• M. Clark (2005) Equivalence Tests, available online at

http://www.unt.edu/benchmarks/archives/2005/february05/rss.htm

• Statistical Tests for Equivalence, online at

http://www.graphpad.com/library/BiostatsSpecial/article 182.htm

Confidential Business Information (CBI) in Submissions toBRS

All documents submitted to USDA APHIS BRS are subject to the Freedom of Information Act 

(FOIA), which requires that records submitted to federal agencies be made available to the public. 

BRS provides the public with documents it receives when formally requested through the APHIS 

FOIA office. Additionally, BRS publishes subsets of submitted documents online.

For example, Am I Regulated Letters that seek to confirm regulatory status under CFR part 340 are 

published on this website at the following location: 

https://www.aphis.usda.gov/aphis/ourfocus/biotechnology/am-iregulated/regulated_article_letters_of_inquiry/regulated_article_letters_of_inquiry

Petitions for determination of non-regulated status are also posted online, linked below: 

https://www.aphis.usda.gov/aphis/ourfocus/biotechnology/permits-notificationspetitions/petitions/petition- status

Section (b)(4) of the FOIA, however, exempts from disclosure certain types of information related 

to trade secrets and commercial or financial information, collectively referred to as confidential 

business information (CBI). Documents submitted to BRS that contain CBI require special 

handling.

KNOW: What is CBI?

Information that would be protected from disclosure under section (b)(4) of the FOIA is classified 

as CBI. This includes trade secrets and commercial or financial information found to be 

confidential.

A trade secret is information relating to the production process, including production data, 

formulas, and processes, and quality control tests and data, as well as research methodology and 

data generated in the development of the production process. Such information must be (1) 

commercially valuable, (2) used in one’s business and (3) maintained in secrecy.

Commercial or financial information may be deemed confidential if review establishes that the 

applicant/developer faces active competition in the area to which the information relates and that 

substantial competitive harm would result from disclosure. Information such as safety data, 

efficacy or potency data, and environmental data may be such confidential information.

Information which is published or otherwise publicly available may not be claimed as CBI. USDA 

APHIS BRS reserves the right to accept, challenge, or request further information on each claim of 

CBI.

If an applicant, developer, or other business submitter believes a document to be submitted to BRS 

contains confidential business information, the submitter must include three documents in their 

submission:
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• A CBI Justification - A detailed letter justifying any CBI claims found in the document.

• A CBI Copy – The document containing the CBI.

• A CBI-Deleted Copy – A CBI document with all CBI deleted.

If an applicant, developer, or other business submitter does not intend to claim confidential 

business information in a document to be submitted to BRS the submitter is only required to 

provide one copy of the material. These documents should be clearly marked “No CBI” in the 

upper right corner of the page.

CBI Justification

If an applicant believes that a document to be submitted to BRS contains confidential business 

information, the applicant must include a CBI Justification document justifying all claims of CBI. 

The CBI Justification must be detailed enough to demonstrate that each piece of information 

claimed as CBI meets the definitions of trade secret or commercial or financial information, as 

described above. Claims of CBI must be justified in terms related to competitive harm due to its 

release. Information is not protected from disclosure simply because the applicant does not want 

the information to be made public.

The USDA APHIS BRS Office will consult with the APHIS FOIA Office, if necessary, to make a 

final decision as to whether the information qualifies for protection under the Freedom of 

Information Act.

The following are examples of information often reasonably justified as CBI in submissions to 

BRS:

• Field Test Location Sites -cities, zip codes and descriptions (this does not include County 

and State Names)

• Acreage Location (descriptions, drawings, maps, addresses and GPS coordinates)

• Acreage and Material Quantities

• Literature references that describe gene, genotype, or other area of the submission that are 

claimed as CBI

• Contractual information between the applicant and a cooperator

• Individuals who are connected to a field test site location

• Name, location, and contact information of Regulated Article suppliers or developers 

(except for State and County names)

• Genotypes, phenotypes, donor organisms, gene names, gene descriptions and 

transformation method.

• Points of Origin and Destination: location name and description, address and contacts 

(except for State and County Names)

• Release Site History if it reveals a description of the location

• Detailed descriptions of locations where the donor organism, recipient organism, and vector 

or vector agent were collected, developed and produced;

• Novel methods, processes, procedures or safeguards

• Novel design protocols/production design

• Novel destruction/devitalization methods

• Novel species names of soil microbial biocontrol agents or pests/diseases
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The following kinds of information are not typically considered CBI:

• Field Test Location Site Company Codes, Reference Numbers and BRS assigned numbers

• County and State Names found anywhere in documentation

• Most literature references

• Petitions and Compliance Submissions:

o Applicant/submitter individual names/phone numbers/addresses/email address/fax 

number(s)

• Phenotypic category and identifying line names

• ANY information found on Block 1 of ePermits permit/notification applications

• Responsible person(s)/entity names

• Signatures of responsible person(s) names

• Critical Habitat specific site locations

• Location Site Codes/Coded location identifiers (not distinguishable outside of the 

applicant’s business)

• Common pests and pathogens for which many permits have been issued

• Document or table headings

Please note that while some information is not eligible for withholding as CBI, it may qualify for 

protection as Personally Identifiable Information under Section 6 (b)(6) of the Freedom of 

Information Act.

The language used to prepare your CBI justification should be in non-technical terms when 

possible, and should not reveal any information marked as confidential.

Preparation of documents containing CBI

If a document to be submitted to BRS contains information that the applicant claims as CBI, the 

applicant must submit two versions of the document along with the justification: a complete 

version containing CBI (the “CBI Copy”), and an edited version with the CBI redacted (the ‘CBIdeleted Copy”).

Use the following guidelines to prepare these two versions of the document:

• Each page of a document containing CBI must have “CBI Copy” marked in the upper right 

corner. 

• Each page of a CBI-redacted document must have “CBI-deleted Copy” marked in the upper

right corner.

In a document containing CBI, mark with square brackets (“[ ]”) only the specific words or 

phrases claimed as CBI, and in the right margin for each set of brackets write “CBI.” In the CBIdeleted version, replace with blank spaces the words or phrases marked in the CBI version, mark 

the spaces with square brackets, and in the right margin for each set of brackets write “CBIdeleted.”

The CBI-deleted version should be identical to the CBI version, except 1) blank spaces surrounded 

by square brackets occurring in the text where the CBI text has been redacted and 2) “CBI-deleted 

Copy” should appear in the upper right corner of each page instead of “CBI Copy.”

The CBI-deleted version must be paginated identically to the CBI copy. The CBI-deleted version 

should be made directly from the same document which originally contained CBI.

Do not insert additional text (transitions, paraphrasing, or generic substitutions, etc.) into the spaces 
USDA-APHIS-BRS User’s Guide Document Preparation Guidelines

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of the CBI-deleted version.

All published references that appear in the CBI copy should be included in the reference list of the 

CBI-deleted copy.

Preparation of documents that DO NOT contain CBI

If a document to be submitted to USDA APHIS BRS does not contain CBI, only one copy is 

needed. These documents should be clearly marked “No CBI” in the upper right corner of the page.

How to Find More Information

For information related to submission of specific documents to BRS, please refer to the contact 

information listed within the corresponding guidance document:

• Permits for the introduction of regulated articles

• Notification of the introduction of certain regulated articles

• Petition to grant non-regulated status to a regulated article

• Extension of non-regulated status to a regulated article

If you would like more information about confidential business information in BRS submissions, 

please contact:

Document Control Officer USDAAPHIS-BRS

4700 River Road, Unit 91

Riverdale, Maryland 20737

(301) 851-3892 or (301) 851-3877

To request a copy of BRS documents under the Freedom of Information Act, please contact: 

FOIA Officer

USDA-APHIS

4700 River Road, Unit 50

Riverdale, MD 20737-1232

(301) 851-4102
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Version History

01/16/2007 Original draft.

11/20/2007 Reformatting to remove references to chapter organization ofBRS User’s Guide

02/05/2008 Removal of word "draft" from document.

02/22/2011

09/05/2018

Added table of contents and updated hyperlinks.

Revision to Original draft.