Part I: Genetic Tests Currently Available for Clinical Use

Aim

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.

Methods

Database of genetic tests currently available. We considered 3 different categories of information for identifying current genetic tests widely available for cancer use:

1. Scientific literature search.
2. Gray literature search.
3. 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.

Results

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 disease status.

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.

Summary

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 disease recurrence.

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