A framework for ensuring laboratory quality was laid down by Congress in the Clinical Laboratory Improvement Act of 1967. Because of public concerns about the quality of clinical laboratory testing in the United States, Congress passed the Clinical Laboratory Improvement Amendments of 1988 (CLIA'88) setting forth uniform quality standards for all laboratories performing tests for health purposes on human specimens. Laboratories must register with the Department of Health and Human Services (HHS) to obtain and maintain a current CLIA certificate regardless of whether they receive payment from Medicare or Medicaid programs. The Centers for Medicare & Medicaid Services (CMS), formerly the Health Care Financing Administration (HCFA), is a federal agency within HHS and is charged with the implementation of the CLIA'88 regulations. CMS working with the Public Health Services (PHS), specifically the Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA), developed standards for laboratory certification and set forth criteria for categorizing tests based on the level of complexity to perform the test. Tests, therefore, are categorized as waived, moderate complexity including the subcategory of provider-performed microscopy, or high complexity. Waived tests employ methods that are simple and are assumed to pose no risk or harm to the patient if the test is not performed correctly. Laboratories performing waived tests must follow manufacturers' instructions for test performance and are not subject to routine inspections. Tests categorized as moderate and high complexity must meet such CLIA'88 requirements as: (1) maintaining optimal patient specimen integrity and identification throughout the testing process, (2) specifying the responsibilities and qualification for personnel performing the test, (3) establishing and following written Quality Control procedures and (4) having a comprehensive Quality Assurance program in place. The laboratories performing moderate- and high-complexity testing must participate in a proficiency testing program for each specialty, analyte, or test for which they are certified and are subject to inspections by CMS or other private accrediting organizations. The major differences between moderate- and high-complexity testing are in the quality control and personnel standards. On February 29, 1992, these revised CLIA'88 regulations were published in the Federal Register (1) and it is recommended that each laboratory have a copy.

On January 24, 2003, almost 11 yr later, CMS and the CDC published a final rule in the Federal Register (2) revising the quality control and personnel standards for laboratory services and changing the consensus requirements for grading proficiency tests. The rule specifies a common set of quality control (QC) standards for both moderate and high complexity testing (now known as nonwaived testing) and reduces the frequency with which QC is to be done in most specialty and subspecialty areas. Under the new rules, agencies providing proficiency testing programs must grade a laboratory's sample in cases where there is 80%, not the current 90%, agreement among the participants or referee laboratories. This will ensure that more laboratories will be graded and ultimately improve the accuracy of laboratory testing. The CLIA rules now put the onus on the laboratory to review and validate nongraded samples, especially when the results do not agree with the intended response. Another change in the regulations is that directors of high-complexity testing are to be board certified unless they are eligible to be grandfathered under the phase-in requirements.

The CLIA'88 standards were designed to enhance patient safety while making it easier for laboratories to read, understand, and comply with the requirements. Subpart J (Patient Test Management), Subpart K (Quality Control), and Subpart P (Quality Assurance) were consolidated and reorganized into a new Subpart J (Facility Administration for Nonwaived Testing) and a new Subpart K (Quality Systems for Nonwaived Testing). Subpart J clarifies requirements for facility space, utilities, safety, transfusion services, as well as record and specimen retention. Subpart K pertains to the total testing process. The reorganization is written to parallel the flow of a patient specimen through the laboratory from the acquisition of a specimen with the test request, to test performance and reporting of results. Each phase of the testing process now has its own standards. In this way, laboratories have a better chance to identify and prevent errors. This subpart of the rules also incorporates the requirements of quality assurance (QA) (renamed quality assessment to more clearly reflect the activities performed) under each appropriate section, namely: General Laboratory Systems, Pre-analytic Systems, Analytic Systems, and Post-analytic Systems, to ensure that quality services are provided throughout the testing process. The essential component of the QA program is for laboratories to ensure continuous improvement of their performance and services through monitoring and evaluating the effectiveness of their policies and procedures for each phase of the testing system. They are to identify problems and take corrective action, to revise policies to prevent recurrences of problems, and to assess the adequacy and competency of the laboratory staff. Essential to the assessement activities is documentation.

There are quality system standards for 19 different non-waived testing subspecialties that have been set forth in Subpart K of the final CLIA'88 regulations. No standards exist specifically for molecular testing, except for cytogenetics. Because laboratories that test human specimens must comply with CLIA'88 regulations, there are agencies reviewing the current regulations to determine which are applicable or should be amended to cover molecular testing. Until such time, molecular testing laboratories must follow good laboratory practice guidelines and participate in external quality assessment programs because they are considered in the nonwaived testing category. Both federal and state agencies (CLIA and New York State, Department of Health) and professional organizations (College of American Pathologists, American College of Medical Genetics and National Committee for Clinical Laboratory Standards) have available guidelines, recommendation, and checklists pertaining to quality control, quality assurance, proficiency testing, and personnel requirements. Many of the recommendations of the American College of Medical Genetics (ACMG) in the third edition of Standards and Guidelines for Clinical Genetics Laboratories (3) have been endorsed and adopted by the College of American Pathologists (CAP). Jointly, the ACMG and CAP in their proficiency testing program offer surveys that are designed to emphasize the pre-analytic and postanalytic phases of molecular genetic testing and molecular oncology testing (4). The CAP also offers on-site laboratory inspection and a certification program. CAP has been given deemed status by CMS as a laboratory certifying agency under CLIA'88 and is also recognized by the Joint Commission on Accreditation of Healthcare Organization (JCAHO). As such, any laboratory providing molecular testing can seek certification through the CAP Laboratory Accreditation Program as a means to comply with CLIA'88 regulations. CLSI (National Committee for Clinical Laboratory Standards) is a voluntary organization that develops consensus recommendations for the standardization of test methodologies within the healthcare field. Its Molecular Diagnostic Methods for Genetic Diseases; Approved Guidelines (5) covers all phases of operation of a molecular genetics diagnostic laboratory, including: nomenclature, laboratory safety, specimen handling and testing, quality assurance and results reporting.

Even though components of a quality assurance program (preanalytical, analytical, and postanalytical) are well established and consistent among published guidelines, there are concerns that safeguards are not in place to ensure high-quality service in molecular testing laboratories. A report by McGovern (6) concluded that a number of molecular genetic testing laboratories had suboptimal quality assurance practices and suggested that both personnel qualifications and laboratory practice standards need improvement. This was not substantiated by Hofgartner and Tait (7), who inferred that the majority of molecular genetic laboratories were accredited by the CAP, therefore, rigorous quality standards to improve the quality of genetic testing exist.

A framework for a quality assurance program as promulgated by the new CLIA'88 regulations and as guidelines offered by professional organizations as the American College of Medical Genetics (ACMG), College of American Pathologists (CAP), and CLSI (Clinical and Laboratory Standards Institute, formerly NCCLS or National Committee for Clinical Laboratory Standards) is discussed in this chapter. Emphasis will be placed on how to apply quality assurance standards to laboratories to molecular diagnostic testing.

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