American Society of Cytopathology Core Curriculum in Molecular Biology

American Society of Cytopathology Core Curriculum in Molecular Biology

American Society of Cytopathology Core Curriculum in Molecular Biology Chapter 4 Stephanie A. Hamilton, EdD, SCT, MB(ASCP) CM MD Anderson Cancer Center Houston, Texas Laboratory Operations Guidelines and Regulations, Personnel and Billing

Quality Control and Quality Improvement Judgment of the acceptability of quality control (QC) data must be made before patient results are reported. Oversight review must occur at least monthly by the Laboratory Director or designee. Laboratory must have a comprehensive quality control (QC) and quality improvement (QI) program in the molecular pathology section of lab System must ensure optimum patient specimen and result integrity throughout the pre analytical, analytical, and post analytical process

Quality Control and Quality Improvement There must be evidence of ongoing evaluation of records of instrument function and maintenance, temperature, etc., on all shifts. The laboratory must have a documented system in operation to detect and correct significant clinical and analytic errors that could affect patient management. There must be documentation of the investigation of failed attempts to isolate nucleic acid and of any required corrective action. The submitting physician (or requestor) must be promptly notified when an inadequate specimen is received or when insufficient nucleic acid is isolated.

Quality Control and Quality Improvement Documentation of the investigation of failed hybridization reactions and any required corrective action taken Documentation that the laboratory monitors sample turnaround times and that they are appropriate for the intended purpose of the test Documentation that preliminary reports are promptly generated, when indicated Documentation that discrepancies between preliminary and final reports are investigated and documented

Quality Control and Quality Improvement Review of laboratory statistics and comparative studies by the Laboratory Director or designee at regular intervals should be documented. This process may detect trends, systematic errors, or local population variations that may affect test results or interpretation A log of unusual, difficult or instructive cases should be maintained.

Quality Control and Quality Improvement Autoradiographs and gel photographs must be of sufficient resolution and quality (high background, poor signal, presence of bubbles, etc.) to permit the reported interpretation. The quality of the in situ hybridization slides and related controls must be improved. These include issues such as high background, poor signal, inadequate morphology and counterstaining, etc.

Quality Control and Quality Improvement Documentation of at least annual review of all policies and procedures in the molecular pathology laboratory section by the current Laboratory Director or designee. The Director or designee must review and approve all new policies and procedures, as well as substantial changes to existing documents before implementation. Current practice must match these documents. All policy and procedure manual changes must be initialed and dated by the Director or designee.

Quality Control and Quality Improvement A paper or electronic copy of a discontinued procedure must be maintained for at least 2 years, recording initial date of use, and retirement date. Does the laboratory have a system documenting that all analysts are knowledgeable about the contents (including changes) of procedure manual relevant to the scope for their testing activities? Documentation that all analysts are knowledgeable about the contents (including changes) of procedure manuals relevant to the scope of their testing activities. Procedures must be written to prevent specimen loss, alteration, or contamination.

Quality Control and Quality Improvement Enzymatic amplification procedures (eg.,pcr) must be designed to minimize carry over (false positive result) using appropriate physical containment and procedural controls. For example, pre and post amplification samples should be manipulated in physically separate areas. Criteria to identify normal and abnormal results for each type of assay performed Protocols for the reporting of results Appropriately referenced internal or external validation studies

Quality Control and Quality Improvement Important data on DNA probes and PCR primers that must be available in the laboratory which may include: Size Complete or partial nucleotide sequence Chromosomal map location of the target sequence Allele frequencies of the mutation in various ethnic groups Recombination frequencies (for linkage probes) Cloning vector Relevant restriction endonuclease sites Method of preparation Relevant literature citations The polymorphic nature of the DNA system used must be detailed and documented in the literature.

In Situ Hybridization Appropriate comparative/validation studies (eg., on known positive and negative samples) must be documented for each probe before its clinical use. The laboratory must adequately document established conditions of tissue pre treatment that varies extensively with changes in fixation and processing. The negative control must give negative results on all test samples. It should be of similar composition to the test probe (i.e., DNA or RNA), single stranded or double stranded, oligonucleotide of same length and GC content) and labeled in the same manner. The results and the specificity of the detection reagents.

In Situ Hybridization Relying on negative areas in the patient sample in hybridizations with the test probe does not adequately address specificity of both detection and hybridization RNA is extremely susceptible to degradation by ribonucleases, which are ubiquitous in the environment. To ensure preservation of target RNA or RNA probes, special precautions are needed.

Health Insurance Portability and Accountability Act (HIPAA) HIPAA prohibits use of genetic information for insurance decisions Informed Consent: May be required by federal, state or local laws for some tests Level of consent depends on whether genetic testing is used for predictive or diagnostic purposes

Regulatory Agencies CLIA FDA JCAHO CAP CLSI

CLIA: Clinical Laboratory Improvement Amendments Brought Congress passed this law in 1988 Established quality standards for all laboratory testing to ensure accuracy, reliability and timeliness of patient test results Centers for Medicare and Medicaid Services (CMS) manages financial operations of CLIA program

CLIA Established 3 categories of laboratory testing based on potential risk to public health Waived tests Tests of moderate complexity Tests of high complexity (all molecular diagnostic testing) Food and Drug Administration (FDA): Assumes primary responsibility for categorizing laboratory testing in these categories, including commercially marketed in vitro diagnostic test systems

Food and Drug Administration (FDA) An agency of the United States Department of Health and Human Services One of the US federal executive departments Responsible for protecting and promoting public health through regulations and supervision of food safety, pharmaceutical drugs, medical devices and other products

FDA: In vitro diagnostic product (IVD) In vitro diagnostic product for the examination of specimens is classified into 3 classes by FDA (Class I, II, and III) Class III devices Come under the most stringent regulatory category since these usually support or sustain human life or are substantial importance to human health Needs a Pre Market Approval (PMA) given by FDA

FDA Designations given by FDA FDA approved FDA Cleared: Allows Class I or II medical devices to be sold in the United States RUO: Research use only IUO: Investigational use only LDT: Laboratory Developed Tests

FDA-Cleared/Approved Products In vitro diagnostic (IVD) products: Intended for use in diagnosis of diseases in patients Premarket notification [510(k)] leads to FDAcleared if successful Premarket approval (PMA) leads to FDA approved Any modifications to FDA cleared/approved tests is called off label use and needs validation of product

Research Use Only (RUO) For laboratory research phase of development Not to be used for diagnostic purposes or as IVD Not registered with FDA thus unregulated Manufacturers may sell these products, unlike Analyte Specific Reagent (ASR) Usually not reimbursable

Investigational Use Only (IUO) May only be used in well controlled clinical trials Used to establish clinical performance characteristics for 510(k) submission or PMA application to FDA Such evaluations must be issued an investigational device exemption (IDE) by FDA and IRB approved before study

Lab Developed Tests (LDT) Home brew tests These non FDA assays are developed, validated and performed by lab Test used before April 24, 2003 are not required to be validated The laboratory that develops an in house test using the ASR shall inform the ordering person of the test result by appending to the test report the statement: This test was developed and its performance characteristics determined by (Laboratory Name). It has not been cleared or approved by the U.S. Food and Drug Administration.

Analyte Specific Reagent (ASR) ASR is the active ingredient of an in house test The laboratory must validate the assay they develop that uses an ASR and determine all performance characteristics (accuracy, precision and appropriate for patient population) The laboratory that develops an in house test using the ASR shall inform the ordering person of the test result by appending to the test report the statement: This test was developed and its performance characteristics determined by (Laboratory Name). It has not been cleared or approved by the U.S. Food and Drug Administration.

JCAHO: Joint Commission on Accreditation of Healthcare Organizations Now referred to as Joint Commission Private sector United States, not for profit organization Accredits health care organizations Majority of state governments have come to recognize accreditation as a condition of licensure and receipt for Medicaid reimbursement

CAP: College of American Pathologists Uses teams of laboratory professionals as inspectors Sets accreditation standards for labs Standards go beyond regulatory compliance Intended to help labs achieve the highest standards of excellence to positively impact patient care

CLSI: Clinical and Laboratory Standards Institute Mission is to develop best practices in clinical and laboratory testing Promote use of these practices throughout the world Uses consensus driven process that balances viewpoints of industry, government and health care professions

Molecular Test Reports Reports must comply with CLIA general test report requirements and should include additional information to ensure accurate understanding and interpretation of test results

Molecular Test Reports CLIA requires that test reports include: Patient name and identification number or a unique patient identifier and identification number Name and address of laboratory where the test was performed Test report date Test performed Specimen source (where appropriate) Test results and if applicable, units of measurement or interpretation Information regarding the condition and disposition of specimens that did not meet laboratory criteria for acceptability

Molecular Test Reports for Heritable Conditions Patient name and any other necessary unique identifies Patient date of birth Indication for testing Date and (if applicable) time of specimen collection and arrival in laboratory Name of referring physician or authorized person who ordered the test Test methods, including the nucleic acid targets of the test and analytic method (eg., targeted mutation detection or DNA sequence analysis) Test performance specifications and limitations (eg., statement on the intended use and the technical limitation of the test methodology)

Molecular Test Reports Nomenclature is evolving Test results should be provided in current recommended standard nomenclature, including clarifications and commonly used terms May need to report all versions of nomenclature to ensure test results are understandable and avoid unnecessary repetition of testing If no mutation is detected, test report should state no mutation detected rather than normal

Interpretation of Test Results Labs are required by CLIA to include interpretation of test results on test reports, if applicable, but always for genetic testing for heritable disease and conditions Interpretation should be provided in a clinically relevant manner that is relative to purpose for test and explain how technical limitations might affect clinical use of results Results can be explained in reference to family members (eg., mutations previously detected in a family member)

Interpretation of Test Results Brought References to literature (if applicable) Recommendation for genetics consultation (when appropriate) Implications of test results for relatives ore family members who might benefit from the information Statement indicating that the test results and interpretation are based on current knowledge and technology

Reports CLIA requires original test report (including final, preliminary, and corrected reports) to be kept for at least 2 years after date of reporting and retain pathology test reports for at least 10 years or longer by state law For genetic tests for heritable diseases and conditions a longer retention time frame required by CLIA is warranted and should be kept at least 25 years

Reports CLIA requires the following to be kept 2 years: Records of patient testing Test requests and authorizations Test procedures Analytic systems records Records of test system performance specifications Proficiency testing records Quality system assessment records Retention policies and procedures must also comply with applicable state laws and other requirements Laboratories should ensure that electronic records are accessible

Personnel Training A new hire training An annual competency testing program An ongoing continuing education program

Competency of Personnel Personnel to be assessed annually Laboratory Director, or designees, selects process to be measures, indicates reason for selection and describes details of task Could be through observations or discussions Documentation of evaluation would indicate methodology used and criteria for satisfactory performance If competency is less than 100%: Document explanation of problem Corrective actions and/or additional training measures Documentation of evaluation signed and dated by evaluator

Proficiency Testing (PT) To assess the skills (competency) of lab personnel performing molecular assays, as well as performance of assay itself The lab must participate in an approved program of interlaboratory comparison testing appropriate to the scope of the laboratory, if available As appropriate, the lab should consider enrollment in suitable College of American Pathologists (CAP) modules or CAP approved alternative PT programs If CAP or other providers have not yet developed a standardized test, PT must be conducted by using blinded samples in the lab or partner with other labs to provide each other with blinded samples

Directors of High Complexity Tests According to CLIA 88, directors must: Hold a doctoral degree in one of the sciences from an accredited institution Be certified Continue to be certified by an approved board The American College of Medical Genetics requires (ACMG): PhD or MD At least 2 years experience or postdoctoral training in a clinical laboratory subspecialty Certified by specialty Boards Director must be on site regularly or accessible

Supervisor Qualifications ACMG requires supervisors to: Hold a Bachelors degree Have at least 3 years of experience in medical field Certification is recommended (ASCP Molecular Biology)

Technologist Qualifications ACMG requires laboratory technologists to: Hold an undergraduate degree in a biological or chemical field, OR, Have at least 5 years of relevant laboratory experience

Billing for Molecular Tests and CPT Coding CPT Codes: CPT stands for Current Procedural Terminology Codes Set forth by the American Medical Association (AMA) Accurately describes medical, surgical and diagnostic services Designed to communicate uniform information about medical procedures among physicians, patients, accreditation organization and payers Used for administrative, financial and analytic purposes

Billing for Molecular Tests and CPT Coding The CPT codes for Molecular Tests: 83890 83909 83912 for interpretation and reporting 88271 and 88272 are for cytogenetics S3818 S3823 deals with susceptibility to breast and ovarian cancer (BRCA1 and BRCA2) Some applicable codes in Chemistry CPT codes (83XXX), and some in Microbiology (87XXX)

Billing for Molecular Tests and CPT Coding An appropriate code is used for each portion of an assay, rather than a single code for the entire assay of one analyte (except infectious agents and cytogenetics) Intended for analysis of nucleic acid Local variations in payment rates depend on Medicare carrier

Tips for Coding Code separately for each procedure in the analysis Correct coding requires an understanding of the method Code precisely and consider the description of the code Know the intent of a code; quality control steps are not billable Ex., 83789 Spectrophotometry, analyte not elsewhere specified should not be billed if step is to verify sufficient DNA for the test Coding compliance is essential for the referring lab and testing lab

Tips for Coding Each organism detected, when laboratory used a kit, is reimbursable, except when kit which tests for multiple organisms gives yes/no answer and requires further testing to identify the specific organism For genetic and infectious agent testing, 83912 Molecular diagnostics; interpretation and report should be billed in addition to specific testing codes

Tips for Coding For ASR based (in house lab tests) Coverage is determined by local Medicare contractor For in house genetic testing The test s standard operating procedure (SOP) must be provided with the coded steps For in house tests for infectious agents Use code specific for infectious agent or not otherwise specified if not available

Tips for Coding Key Coding Questions Is it a quality control (QC) step? Is the assay simplex or multiplex? Does it really fit? Is it codable? Is it diagnostic or confirmatory? Did the reaction occur? Is the code applicable? Is the assay billable to government payers? Reference for billing and coding slides: http://www.g2reports.com/issues/dttr/2006_12/1610561. Accessed 07/01/10