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Part I: Genetic Tests Currently Available for Clinical Use
The aim of Part I of the project was to identify genetic tests already in
clinical practice or tests that are being marketed for use in clinical practice.
As detailed in the Detailed Workplan, the goal of this part of the project
was to generate (1) a database of current genetic tests for cancer, and (2)
a series of one-page summaries for each test in the database, providing additional
detail of the individual tests, including potential literature search strategies.
Database of genetic tests currently available. We considered 3 different categories
of information for identifying current genetic tests widely available for cancer
- Scientific literature search.
- Gray literature search.
- Expert interviews and scientific meetings.
Scientific literature search. We conducted preliminary searches for genetic
tests in sources from the three different categories. A quick MEDLINE search
for "cancer genetic test" revealed thousands of citations of reporting
on various genetic polymorphisms and their possible association with different
cancers. Examples of a few citations include "XPC polymorphisms and lung
cancer risk," "Breast cancer risk associated with genotypic polymorphism
of the mitosis-regulating Aurora-A/STK15/BTAK," and "Genetic alteration
of p53, but not over-expression of intratumoral p53 protein, or serum p53 antibody
is a prognostic factor in sporadic colorectal adenocarcinoma." It was
quickly apparent that further efforts to explore the scientific databases was
likely to reveal thousands of abstracts describing or identifying various gene
or genome associations with cancer biology or tumorigenesis. However, most
of these reported gene associations or potential tumor biomarkers are likely
years removed from becoming a widely available clinically validated test for
commercial cancer use. As a result, we determined that the scientific databases
would not be useful for the purposes of this part of the project.
Gray literature search
The Fourth International Conference on Gray Literature in Washington, DC,
in October 1999 defined gray literature as: "That which is produced on
all levels of government, academics, business and industry in print and electronic
formats, but which is not controlled by commercial publishers."2 Gray
literature can include reports, memoranda, conference proceedings, standards,
technical documentation, and government documents.
According to Alberani et al., gray literature publications are "non-conventional,
fugitive, and sometimes ephemeral publications. They may include, but are not
limited to the following types of materials: reports (pre-prints, preliminary
progress and advanced reports, technical reports, statistical reports, memoranda,
state-of-the-art reports, market research reports, etc.), theses, conference
proceedings, technical specifications and standards, non-commercial translations,
bibliographies, technical and commercial documentation, and official documents
not published commercially (primarily government reports and documents)".3
For the purpose of this report we created a functional definition of gray
literature that included a variety of traditional gray literature databases,
as well as a variety of sources for reports and publications that are not peer-reviewed.
In fact, we found that the most useful and efficient method for identifying
genetic tests currently in use for cancer care was to search for detailed listings
of cancer genetic tests from the corporate Web sites of the major commercial
diagnostic laboratories in the U.S. such as Quest Diagnostics® (Teterboro,
NJ) and LabCorp® (Burlington, NC). Supplemental information and additional
tests were found in other company Web sites such as Myriad Genetics (Salt Lake
City, UT) and Genomic Health (Redwood City, CA), or other pertinent resources
available online such as UpToDate® and www.genetest.org.
In constructing our list of gray literature sources for Part II of this project,
we referred to the National Library of Medicine (NLM)'s Health Technology
Assessment Information Resources. 5 In
their Etext on gray literature for health technology assessments, NLM describes
a general approach to searching gray literature and internet resources. Traditional
types of gray literature identified by NLM include: theses and dissertations,
census, economic and other data sources, databases of ongoing research, electronic
networks, informal communications (telephone conversations, meetings, etc.),
conference proceedings and abstracts, newsletters, research reports (completed
and uncompleted), technical reports, and translations. Tables B and C within
NLM's document lists databases and other sources that include gray literature.
Furthermore, we supplemented this list of gray literature sources with additional
databases through conversations with AHRQ (LexisNexis) and internal investigations
(Google News, Early Research Detection Network, Cambridge HealthTech). The
methods section of Part II of this report includes a more comprehensive list
and description of the gray literature databases used for this project.
Expert interviews and scientific meetings. At the outset of this project,
we anticipated that a scientific literature-based approach would be labor intensive
and likely low yield. As a result, we focused our search on company Web sites,
expert interviews, and attending specialty conferences. In addition to the
gray literature obtained from the Internet, we attended two scientific meetings
during the course of this project to further expand the breadth of our search.
The first conference was a workshop on "Pharmacogenomics in Drug Development," jointly
sponsored by the Drug Information Association, the Food and Drug Administration
(FDA), Pharmacogenetic Working Group, PhRMA, and the Biotechnology Industry
Organization. The theme of this workshop and its focus on diagnostic pharmacogenomic
test and drug co-development was relevant to the aims of Part II of our project.
The second conference attended, the 2005 American Society of Clinical Oncology
(ASCO) Annual Meeting, was applicable to both the first and second parts of
this horizon scan. In particular, the ASCO conference exhibit hall featured
over 400 commercial displays, with representatives from various pharmaceutical,
medical diagnostics, and commercial laboratories involved in cancer care. During
the exhibit hall sessions, we were able to speak with representatives from
companies involved in genetic testing for cancer such as Quest Diagnostics,
LabCorp, Genomic Health, US Labs, Roche Diagnostics, and Veridex.
Finally, we spoke with different experts representing commercial laboratories,
academic hospitals, and the FDA. During these interviews, our goal was to verify
our database of genetic tests available, as well as to obtain knowledge about
cancer genetic tests in development that would apply to Part II of our project.
From our discussions with these experts and our initial explorations with the
scientific and gray literature, it became evident that the most useful and
efficient method for compiling a comprehensive list of genetic tests for cancer
was to focus our search to the comprehensive test catalogs of the largest commercial
diagnostic laboratories in the US, such as Quest Diagnostics® and LabCorp®.
In addition, one of the advantages of using these test catalogs as a resource
is that both catalogs include tests offered or developed by other reference
laboratories (e.g., Myriad Genetics and Exact Sciences) and are used by Quest
and LabCorp for sendouts.
Individual test summaries
Once a the list of current genetic tests was compiled, a series of one-page
summaries of each test in the database was completed using data extracted from
a variety of sources including commercial Web sites and current medical text.
Data included in these summaries are a more detailed description of the test
and its clinical use. In addition, examples of MEDLINE searches using exploratory
search terms and the number of citations generated is provided to give an estimate
of the scientific literature available on each test. However, this number is
preliminary and subject to change from the use of a more fully developed search
strategy and the application of specific screening criteria.
The main results for this part of the project can be found in two attachments:
Database of genetic tests currently available (Database I). Database I contains
an overview of 62 cancer-related genetic tests currently available for clinical
use in oncology. These tests are used in a variety of solid tumors and hematologic
malignancies. Fifteen tests have applications for breast cancer, 5 in prostate,
9 in lung, 15 in colorectal, 12 in pancreas, 7 in ovarian, 5 in liver, 11 in
lymphoma, and 11 in leukemia.
These tests have applications in primary prevention, secondary prevention,
and in the diagnosis and management of disease. The majority of tests (87 percent,
54 of 62) are utilized for the diagnosis and management of cancer, while 18
percent (11 of 62) of tests can be used for secondary prevention and 8 percent
(5 of 62) for primary prevention. Among the tests used in the diagnosis and
management of cancer, 54 percent (29 of 54) have diagnostic roles, 57 percent
(31 of 54) have prognostic roles, 41 percent (22 of 54) may be used to detect
disease recurrence, and 52 percent (28 of 54) are used to monitor patient and
Individual test summaries (Database II). Database II is a compilation of summaries
for each of the 62 tests listed in Database I. The one-page summaries provide
additional detail on the individual genetic tests, including further discussion
on their clinical use and potential literature search strategies for future
investigation of that particular genetic test.
After considering the three types of data sources (scientific literature,
gray literature, and expert interviews) and the limited time allocated for
this project, we chose a very focused approach to compiling a database of cancer
genetic tests currently available for clinical use. We found 62 genetic tests
for 9 different cancers. One-third of the tests are used in hematologic malignancies
(leukemia, lymphoma) while the remaining tests have applications in the solid
tumors (breast, lung, colorectal, pancreas, etc.). Approximately one-fourth
of the tests may be used for primary or secondary prevention of cancer. However,
the majority of genetic tests that we found can be used to provide diagnostic
and prognostic information, as well as to monitor patient status and detect
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