Advanced Genomics Llc Dba Geneus Diagnostics

Summary Statement of Deficiencies D0000 Intakes: TX00278069 Complaint TX00278069 was not substantiated. The laboratory was found out of compliance with the CLIA regulations. Immediate jeopardy findings were identified. The conditions not met were: D5300 - 42 C.F.R. 493.1240 Condition: Preanalytic systems; D5400 - 42 C.F.R. 493.1250 Condition: Analytic systems; D6076 - 42 C.F.R. 493.1441 Condition: Laboratories performing high complexity testing; laboratory director; D6108 - 42 C.F.R. 493.1447 Condition: Laboratories performing high complexity testing; technical supervisor; The facility representative was given an opportunity to provide evidence of compliance with the noted deficiencies, and no such evidence was provided prior to survey exit. The laboratory voluntarily ceased the practice of receiving respiratory samples at ambient temperature as documented in a letter signed by the chief executive officer on February 2, 2018. Actual exit date was 2/27/2018 when final documentation was received via email at 3:04 PM (Central Time) D5209 PERSONNEL COMPETENCY ASSESSMENT POLICIES CFR(s): 493.1235 As specified in the personnel requirements in subpart M, the laboratory must establish and follow written policies and procedures to assess employee and, if applicable, consultant competency. This STANDARD is not met as evidenced by: Based on a review of personnel records and interview of facility personnel it was revealed that the laboratory failed to assess clinical consultant competency and failed to have an established procedure to assess technical consultant competency. Findings were: 1. A review of personnel files found that one of one clinical consultant did not have documentation of competency assessment. 2. There was no procedure available for review for assessing the competency of clinical consultant. 3. Interview of the Statement of Deficiencies (X1) Provider/Supplier/CLIA Identification Number (X3) Date Survey Completed Name of Provider or Supplier Street Address, City, State -- 1 of 24 -- general supervisor on 2/1/2018 at 1640 hours in the office confirmed there were no competency assessment records or procedure for assessing the competence of the clinical consultant. D5217 EVALUATION OF PROFICIENCY TESTING PERFORMANCE CFR(s): 493.1236(c)(1) At least twice annually, the laboratory must verify the accuracy of any test or procedure it performs that is not included in subpart I of this part. This STANDARD is not met as evidenced by: Based on review of the laboratory's College of American Pathologists' proficiency testing records from 2017, review of the laboratory's alternate assessment records from 2017, and staff interview, it was revealed the laboratory failed to have documentation of two annual accuracy assessments for the analytes of Influenza A H1, Influenza A H3, Respiratory Syncytial Virus A, Respiratory Syncytial Virus B, Coronavirus 229E, Coronavirus OC43, Coronavirus NL63, Coronavirus HKU1, Parainfluenza virus 4, Human Bocavirus, Chlamydophila pneumoniae and Mycoplasma pneumoniae. The findings were: 1. A review of the laboratory's College of American Pathologists' proficiency testing records from 2017 revealed the laboratory had enrolled in the Infectious Disease Respiratory Panel for Molecular Multiplex Testing IDR. The program did not include the analytes Influenza A H1, Influenza A H3, Respiratory Syncytial Virus A, Respiratory Syncytial Virus B, Coronavirus 229E, Coronavirus OC43, Coronavirus NL63, Coronavirus HKU1, Parainfluenza virus 4, Human Bocavirus, Chlamydophila pneumoniae and Mycoplasma pneumoniae. 2. A review of the laboratory's alternate assessment records from 2017 revealed the laboratory performed one of two accuracy assessments for Influenza A H1, Influenza A H3, Respiratory Syncytial Virus A, Coronavirus 229E, Coronavirus OC43, Coronavirus NL63, Coronavirus HKU1, Parainfluenza virus 4, Human Bocavirus, Chlamydophila pneumoniae and Mycoplasma pneumoniae. 3. A review of the laboratory's alternate assessment records from 2017 revealed no positive sample for Respiratory Syncytial Virus B was included in the accuracy assessment. 3. The laboratory was asked to provide documentation of the missing accuracy assessments. No documentation was provided. 4. An interview with general supervisor on 1/29/2018 at 1430 hours in the office - after her review of the records- confirmed the findings. D5300 PREANALYTIC SYSTEMS CFR(s): 493.1240 Each laboratory that performs nonwaived testing must meet the applicable preanalytic system(s) requirements in 493.1241 and 493.1242, unless HHS approves a procedure, specified in Appendix C of the State Operations Manual (CMS Pub. 7), that provides equivalent quality testing. The laboratory must monitor and evaluate the overall quality of the preanalytic systems and correct identified problems as specified in 493. 1249 for each specialty and subspecialty of testing performed. This CONDITION is not met as evidenced by: Based on a review of laboratory temperature records, quality assurance records, and interview of laboratory personnel, it was revealed that the laboratory did not meet the applicable preanalytic system(s) requirements and failed to monitor and evaluate the -- 2 of 24 -- quality of all preanalytic systems. Findings were: 1. Failure of the laboratory to properly store and preserve all patient specimens (refer to D5311) resulted in the laboratory not being able to ensure the accuracy and reliability of all patient test results. 2. Failure of the laboratory to document the received time for patient samples for Rapid Respiratory Panel testing that were received from outside clinics (D5313) resulted in the laboratory not being able to ensure samples were not tested beyond manufacturer stated stability. 2. Failure of the laboratory to monitor the quality of the preanalytic phase of all testing processes (refer to D5391) caused the laboratory to be unable to identify and correct all preanalytic problems. D5311 SPECIMEN SUBMISSION, HANDLING, AND REFERRAL CFR(s): 493.1242(a) The laboratory must establish and follow written policies and procedures for each of the following, if applicable: (1) Patient preparation. (2) Specimen collection. (3) Specimen labeling, including patient name or unique patient identifier and, when appropriate, specimen source. (4) Specimen storage and preservation. (5) Conditions for specimen transportation. (6) Specimen processing. (7) Specimen acceptability and rejection. (8) Specimen referral. This STANDARD is not met as evidenced by: A. Based on review of the laboratory's policies, review of manufacturer's instructions, review of the laboratory's establishment studies, and staff interview, it was revealed the laboratory failed to have documentation of performing complete preanalytic studies to support the laboratories defined criteria for sample collection and preservation, sample transport, and sample storage for the FDA modified rapid respiratory panel testing using the NxTag Respiratory Pathogen Panel prior to patient testing on 12/19/2016. The findings were: 1. A review of the laboratory Client Services Manual for collection RRP Sample Collection revealed samples would be rejected if "Samples not received within 48 hours." 2. A review of the procedure Intra- Facility Specimen Transport (Procedure 3402 effective 10/02/2017) states: "Specimen Delivery by Transport Specimens received and handled at a location other than the processing laboratory will be transported to the laboratory as follows:" ... "Nasopharyngeal swabs are NOT to be opened or accessioned outside of the laboratory and should be kept in original biohazard bag. Separate specimens based on the following collection/shipping conditions:" "Original Shipment Condition Specimen Collection Time REPACKAGE Specimen Transport Conditions Room Temperature Less than 48hrs Room Temperature Room Temperature Greater than 48hrs 4C Cold Less than 48hrs 4C Cold Greater than 48hrs 4C Frozen Less than 48hrs FROZEN (on ice) Frozen Greater than 48hrs FROZEN (on ice)" 3. A review of the laboratory procedure RRP Specimen Collection (procedure 3501, effective date 12/28 /2016) under the section titled "Policy" revealed the laboratory accepted samples for RRP testing within 48 hours if kept at room temperature or 7 days if refrigerated from the date of collection. "Samples should arrive to Advanced Genomics for testing within 48 hours if kept at room temperature or 7 days if kept in refrigerator storage FROM date of collection." 4. A review of the laboratory procedure NxTag RRP Assay (Procedure 7021, effective date 10/16/17) under the section titled 'SPECIMEN REQUIREMENTS" revealed: "The temperature requirement during transportation is ambient if shipped within 24 hours of collection or on ice if shipped after 24 hours from collection. Specimen is stable at room temperature within 24 hours from collection and refrigerated for up to 7 days after collection in Universal Transport Media." 5. A review of the package insert for the universal transport media utilized by -- 3 of 24 -- the laboratory (Puritan UniTranz-RT Transport System HWP UTZ-RT R1 04/16) revealed the laboratory modified the manufacturer-defined storage/shipping temperatures. "Specimens should be placed in the transport medium immediately following collection and promptly transferred to the laboratory for processing. For optimum recovery, specimens should be refrigerated during transport. For long term storage, specimens should be frozen at -70C or colder." 6. A review of the NxTAG Respiratory Pathogen Panel package insert (MLD-051-KPI-001 Rev B April 2017) revealed the laboratory modified the manufacturer-defined storage/shipping temperatures and allowable times for testing after collection: Under Specimen Collection "Specimen Collection and Nucleic Acid Extraction "Specimens can be stored between 2C and 8C for up to 7 days after collection in Universal Transport Media (UTM (Trademark)) or equivalent. If the specimen is not going to be tested within 7 days of collection, then it may be stored at -70C or below for up to 12 months." 7. Furher review of the NxTAG Respiratory Pathogen Panel package insert (MLD-051-KPI-001 Rev B April 2017) revealed the following organism types and subtypes detected by the test and type of genome (RNA or DNA): Under "Intended Use" "NxTAG Respiratory Pathogen Panel is a qualitative test intended for use on the Luminex MAGPIX instrument for the simultaneous detection and identification of nucleic acids from multiple respiratory viruses and bacteria extracted from nasopharyngeal swabs collected from individuals with clinical signs and symptoms of a respiratory tract infection. The organism types and subtypes detected by the test are Influenza A [RNA], Influenza A H1 [RNA], Influenza A H3 [RNA], Influenza B [RNA], Respiratory Syncytial Virus A [RNA], Respiratory Syncytial Virus B [RNA], Coronavirus 229E [RNA], Coronavirus OC43 [RNA], Coronavirus NL63 [RNA], Coronavirus HKU1 [RNA], Human Metapneumovirus [RNA], Rhinovirus /Enterovirus [RNA], Adenovirus [DNA], Parainfluenza virus 1 [RNA], Parainfluenza virus 2 [RNA], Parainfluenza virus 3 [RNA], Parainfluenza virus 4 [RNA], Human Bocavirus [DNA], Chlamydophila pneumoniae [DNA], and Mycoplasma pneumoniae [DNA]." And Under Specimen Collection "Specimen Collection and Nucleic Acid Extraction "NOTE: Standard precautions should be taken with regard to sample collection, handling, and storage prior to extraction (refer to the latest edition of the CLSI MM13 Guideline; and Farkas et al. (1996)). 6. A review of the document CLSI MM13A available to the surveyor revealed the following for transport and storage: During transport and storage, the specimen must not be exposed to conditions that might result in degradation of target nucleic acids. The storage conditions vary depending on specimen type, analyte (RNA or DNA), and/or microorganism being tested. Proper transport and storage conditions must be determined by the assay manufacturer or in the case of "home-brewed" test, by the laboratory. RNA is highly susceptible to degradation and can be more difficult to recover than DNA." 7. A review of the package insert for the universal transport media utilized by the laboratory (Puritan UniTranz-RT Transport System HWP UTZ-RT R1 04/16) revealed the manufacturer did not evaluate the transport media for survival and recovery for 11 of the 20 pathogens in the NxTAG Respiratory Pathogen Panel. The manufacturer did not evaluate the transport media for Influenza B [RNA], Coronavirus 229E [RNA], Coronavirus OC43 [RNA], Coronavirus NL63 [RNA], Coronavirus HKU1 [RNA], Human Metapneumovirus [RNA], Rhinovirus /Enterovirus [RNA], Parainfluenza virus 1 [RNA], Parainfluenza virus 2 [RNA], Parainfluenza virus 4 [RNA], Human Bocavirus [DNA]. Under "PERFORMANCE CHARACTERISTICS" "Test viruses used for evaluation of the transport medium were adenovirus, cytomegalovirus, echovirus type 30, herpes simplex virus type 1, herpes simplex virus type 2, influenza A, parainfluenza 3, respiratory syncytial virus, and varicella-zoster virus. Among bacteria, Chlamydia pneumoniae, Chlamydia trachomatis, Mycoplasma pneumoniae, Mycoplasma hominis, and Ureaplasma -- 4 of 24 -- urealyticum were used for testing." And "Caution: Viability of microorganisms in the Puritan UniTranz-RT transport system other than the ones tested here is not known and should be validated by the user." 7. Surveyor observation of samples received by the facility on 1/30/2018 at 1010 hours in the pre-amplification room revealed the facility received nasopharyngeal swabs in Puritan UniTranz-RT Transport media shipped overnight by Fed-Ex at ambient temperature. Patients samples RRP18-00803, RRP18-00804, RRP18-00811, RRP18-00812, RRP18-00813, RRP18-00814, RRP18- 00815. 8. A review of the laboratory "RRP Stability Study 04/06/2017" approved by the laboratory director on 4/7/2017 revealed the laboratory's purpose of the study was "extend the time frame from 24-48 hours to possible 72 or 96 hours after collection". The laboratory concluded: "..not all organisms can be detected if the specimen is left at room temperature for longer than 48 hours post collection. Based on this data, Advanced Respiratory cannot extend the expiration of a sample beyond 48 hours post- collection. The criteria for accepting RRP specimens still remains as follows: Specimens are stable at room temperature within 24 hours from collection and at 4C for up to 7 days after collection. Specimens shipped within 24 hours, should be shipped at ambient temperatures. Any specimens shipped after 24 hours of collection, should be shipped refrigerated or on ice." "Stability beyond 48 hours could not be established for Influenza A H1, Respiratory Syncytial Virus A, Parainfluenza virus 1, Parainfluenza virus 2, Parainfluenza virus 4, Coronavirus HKU1, Chlamydophila pneumoniae since none of the patient samples were positive for those organisms during the study." The study did not document: a) Initial (time zero) results. b) Time of collection of specimens and time of receipt of specimens c) The temperature ranges samples were exposed to during shipment - which samples were shipped at "ambient" temperatures - which samples were shipped at "with ice" or refrigerated temperatures d) Definitions of ambient temperature, room temperature, "with ice" temperature and refrigerated temperature acceptable range. e) The acceptability criteria used to evaluate the study results f) Stability studies for 7 of analytes in the panel 9. Further review of the stability study revealed the examples of results which indicated a potential loss in pathogen recovery at laboratory room temperature. a) Influenza A (sample RRP17-00119) showed positive at 24 hours, skipped at 48 hours and negative at 72 hours. b) Coronavirus 229E (sample RRP17-00097) showed positive at 24 hours, invalid at 48 hours. c) Coronavirus OC43 (sample RRP17-00044) showed "NA" at 24 hours, "fail" at 48 hours. d) Human Bocavirus (sample HHRRP17-00021) showed positive at 24 hours, negative at 48 hours. 9. Review of the "Analytical Validation Plan for Rapid Respiratory Panel (RRP) using the NXTAG Respiratory Pathogen Panel Assay (Luminex) and MagPIX Instrumentation" approved by the laboratory director on 2/17/2017 and by the technical supervisor on 5/11/2017 revealed the that in addition to Puritan UniTranz-RT Transport media the laboratory accepted specimens in 5 other types of transport Media: "We accept the following equivalent medias and their associated nasopharyngeal swabs; Becton Dickeinson BD universal Viral Transport System (UVT), Copan UTM Viral Transport Media, Quest VCM, Healthlink Inc UTM, Hary Diagnostics VTM." 9. The laboratory was asked to provide documentation of successful studies which supported the laboratory's specimen storage/preservation, transport, and storage claims to modify the FDA- approved NxTag Respiratory Pathogen Panel for storage of specimens between 2C and 8C for up to 7 days after collection in Puritan UniTranz-RT Transport media as well as studies to evaluate samples sent to the laboratory in different types transport media. No documentation was provided. 10. In an interview of the general supervisor at 1437 hours on 1/31/2018 in the office, she confirmed the above findings. According to the Annual Test Volume & Proficiency Testing Programs Worksheet, the laboratory performs an estimated 54,000 tests annually. Please refer to the RRP Test results statistics 2017 and 2018 alias list for patients tested from 3/1/2017 to 1/29 -- 5 of 24 -- /2018. B. Based on observation, review of the facility Specimen Rejection Policy RRP (rapid respiratory panel) (number 3602 effective 12/27/2016), Client Services Manual, and interview of facility personnel it was revealed that the laboratory failed to establish a specimen rejection policy based on specimen storage and preservation, conditions for specimen transport, and specimen stability for rapid respiratory panel specimens to be tested at the facility. Findings were: 1. Observation of rapid respiratory panel specimen processing on 1/30/2018 at 10:10 hours in the pre- amplification room revealed the testing personnel date stamping specimens received from outside clients. Observation revealed the testing persons were checking specimen type, container and verbally verifying patient identifiers. 2. In an interview of testing person 2 (as listed on the Laboratory Personnel Report) on 1/30/2018 at 1015 hours she stated that samples were good for 24 hours at room temperature. In an interview on 1/30/2018 at 1015 hours testing person 5 stated that samples were good for 48 hours at room temperature. 3. On 1/30/2018 at 1015 hours surveyor requested the facility specimen rejection policy for RRP. Testing person 2 stated the policy was not posted, but was available to all staff electronically. She accessed policy number 3602 "Specimen Rejection Policy RRP" on the computer in the preamplification room. 4. A review of the facility "Specimen Rejection Policy RRP" (number 3602 effective 12/27/2016) revealed no documentation at the time of the survey of a policy for rejecting samples based on specimen storage and preservation, conditions for specimen transport, and specimen stability. The Specimen Rejection Policy for RRP stated: "All specimens received by this Laboratory will be evaluated for acceptability, as follows: a. Adulterated b. Improperly labeled specimen c. Inappropriate specimen container d. Specimen has arrived out of its container e. Wrong specimen submitted f. Broken specimen container (contamination) g. Insufficient patient information or incomplete or incorrect test request form h. Test order without a specimen i. Specimen without a test order" 5. A review of the Client Services Manual for collection RRP Sample Collection revealed samples would be rejected if "Samples not received within 48 hours." 6. An interview of the general supervisor on 1/30/2018 at 1410 hours in the common area confirmed the above findings. B. Based on direct observations, review of establishment studies, and confirmed in interview, it was revealed the laboratory failed to provide documentation of performing complete preanalytic studies for sample storage, transportation and preservation prior to patient testing on May 5, 2015 for pharmacogenetic (PGX) testing and prior to patient testing in January 2017 for Nutrigenomic testing. The findings included: 1. Direct observation of swabs provided to clients for collection of buccal DNA (deoxyribonucleic acid) for PGX testing revealed the laboratory provides Puritan Sterile Polyester Tipped applicators, reference number 25-806-2PD. 2. Direct observation of swabs provided to clients for collection of buccal DNA (deoxyribonucleic acid) for Nutrigenomic testing revealed the laboratory received Copan 4N6FL00QSwabs, reference 4504C. 3. In an interview of the general supervisor on 1/29/2018 at 1515 hours in the common area she stated that they used the Copan swab for Nutrigenomics. For PGX 99% of the samples are received on the Puritan swabs and 1% are Copan swabs. In addition all swabs were shipped to the laboratory by FedEX at ambient temperatures. 4. A review of the facility procedure "DNA Isolation from Buccal Swabs" (Procedure 7001, effective date 6/15/ 2016) revealed the procedure did not identify the type of acceptable Buccal swab: "SPECIMEN REQUIREMENTS All specimens will come from buccal swabs. Swabs will be collected by client and placed inside a clearly marked envelope, and shipped in a clinical package envelope. All specimens are shipped the lab overnight by FedEx. The courier picks the specimen up and delivers them to the lab each day, Monday through Friday. The temperature requirement during transportation is ambient. Specimen is stable at room temperature for 49 days, refrigerated for 49 days or frozen -- 6 of 24 -- for 70 days." 5. A review of the Analytical Validation Plan for DME and SNP OpenArray Genotyping and Copy Number Assays on the QuantStudio 12K Flex Platform for instrument 1 approved by the laboratory director on 12/27/2016, the Analytical Validation Plan for DME and SNP OpenArray Genotyping and Copy Number Assays on the QuantStudio 12K Flex Platform for instrument 2 approved by the laboratory director on 05/04/2015, the March 2015 "Analytical Validation Bridging Study Plan Summary for DME and SNP Open Array Genotyping and Copy Number Variation on the QuantStudio 12K Flex Platform" for instrument 1, approved by the laboratory director on 5/4/2015 and the Analytical Validation Plan for Nutrigenomics 2 (55) Panel SNP Genotyping (OpenArray) on QuantStudion12K Instrument #1" approved by the laboratory director on 5/11/2017 revealed no documentation of swab and/or swab part number used in the validation. 6. A review of the facility validation plans revealed the facility used the MagMax extraction equipment and the protocol MagMax Express-96 DNA Multi-Sample Ultra Kit User Guide. The plans did not identify the extraction kit used. a. A review if the "Analytical Validation Plan for DME and SNP OpenArray Genotyping and Copy Number Assays on the QuantStudio 12K Flex Platform" for instrument 1 approved by the laboratory director on 05/04/2015 listed the MagMax Express-96 DNA Multi- Sample Ultra Kit User Guide under protocols. b. The Analytical Validation Plan for DME and SNP OpenArray Genotyping and Copy Number Assays on the QuantStudio 12K Flex Platform for instrument 2, approved by the laboratory director on 12/27 /2016 listed the MagMax Express-96 DNA Multi-Sample Ultra Kit User Guide under protocols. (A notation on the signature page "The individual supervisor initially responsible for this validation ...departed with this document unsigned. The omission was noted by subsequent personnel after thorough review.") c. The March 2015 "Analytical Validation Bridging Study Plan Summary for DME and SNP Open Array Genotyping and Copy Number Variation on the QuantStudio 12K Flex Platform" for instrument 1 approved by the laboratory director on 5/4/2015 listed the MagMax Express-96 DNA Multi-Sample Ultra Kit User Guide under protocols. 7. In an interview with the general supervisor on 02/01/2018 at 0930 hours she confirmed they had changed the isolation kit from MagMax to Omega Bio-Tek Mag-Bind Blood & Tissue DNA HDQ 96 Kit in March of 2016. She stated the initial validation was done with the MagMax kit. 8. A review of the Thermo Fisher "Pharmacogenomics Experiments APPLICATION GUIDE" (For Research Use Only. Not for use in diagnostic procedures. Publication Number MAN0009612) under "Isolate DNA using the MagMAX (Trademark) DNA Multi-Sample Ultra Kit ", "Required materials not supplied": "One of the following types of buccal swabs, or equivalent buccal swabs with foam tips:" "Puritan (Trademark) PurFlock (Trademark) Ultra Flocked Swabs"; "Fisher Scientific 22-025-192" "Puritan (Trademark) HydraFlock (Trademark) Swabs, standard tip"; "Puritan 25-3306-H" "Sterile Foam Tipped Swabs"; "Puritan 25-1506 1PF" "4N6FLOQSwabs (Trademark), regular tip"; "4473979" 9. A review of the manufacturer's directions "MagMax DNA Multi-Sample Utra Kit (November 28, 2016) revealed Under Sample collection and storage: "Use one of the following polyester swabs with foam tips. Use of cotton or generic polyester swabs may result in lower DNA yields or DNA that contains PCR inhibitors." "Puritan 'Purflock' Ultra Flocked Swabs (Fisher Scientific, Cat. no 22-025-192)" "Puritan 'HydraFlock' Swabs, standard tip (Puritan, Cat. no. 25-3306-H)" "Sterile Foam Tipped Swabs (Puritan, Cat. no. 25-1506 1PF)" "4N6FLOQSwabs, regular tip (Cat. no. 4473979)" A review of the manufacturer's directions "MagMax DNA Multi-Sample Utra Kit (November 28, 2016) revealed Under Sample collection and storage for shipping: "Sample shipping: Shipped dried buccal swabs after sample collection at 25 C or below." 10. A review of the "Pharmacogenomics Copy Number Experiments Best Practices & Troubleshooting Guide" (Revision August 14 2015) revealed: "High DNA yields from -- 7 of 24 -- buccal swabs are not needed specifically for copy number testing, but are needed for the PGx workflow overall. For this reason, it is important to take steps to maximize DNA yield, including use of the recommended buccal swab types and swabbing protocol. The CNV analysis portion of the workflow requires using 5 ng/uL of high quality DNA sample stocks. The presence of PCR inhibitors, from food or other contaminants in the sample preparation, can negatively impact copy number call accuracy." "The following buccal swab types are recommended: 4N6FLOQSwabs (Trademark) (p/n 4473979, Life Technologies) PurFlock Ultra Flocked Swab (p/n 22- 025-192, Fisher Scientific) HydraFlock Flocked Swab (p/n 25-3306-H, Puritan Medical Products) Sterile Foam Tipped Swabs (Puritan, Cat. no. 25-1506 1PF) The following swab types are not supported: Generic Cotton Generic Polyester" Further review of the "Pharmacogenomics Copy Number Experiments Best Practices & Troubleshooting Guide" page 8, revealed a bar graph showing the mean concentration versus swab and the statement: "Cotton and polyester swab yields drop below 50 ng /uL minimum. Note: Each error bar is constructed using 1 standard error from the mean. N=7" 11. A review of the "Analytical Validation Plan for DME and SNP OpenArray Genotyping and Copy Number Assays on the QuantStudio 12K Flex Platform" for instrument 1 and 2, the "Analytical Validation Bridging Study Plan Summary for DME and SNP Open Array Genotyping and Copy Number Variation on the QuantStudio 12K Flex Platform" for instrument 1 and the Analytical Validation Plan for Nutrigenomics 2 (55) Panel SNP Genotyping (OpenArray) on QuantStudion12K Instrument #1" revealed specimen stability was not part of the validation plan: "Specimen stability will be studied by Advanced Genomics, LLC as required outside this validation. It is expected that throughput and turnaround time will minimize any potential impact by specimen stability for sample analysis and results reporting are real - time exercises and not historical analysis." 12. A review of the facility "Sample Stability Study" approved by the laboratory director on April 6, 2016 revealed the study did not specify the type of swab used or mimic specimen collection, storage or transportation of samples received from outside clinics. "Longevity Study to Extend DNA Buccal Swab Expiry from 21d Post-collection to 49d" "Our standard kit polyester buccal swabs were used to swab five lab personnel. Samples were allowed to air-dry for 24 hours at room temperature before storage in one of three locations: " "1. Room temperature in the lab in the kit sample storage envelopes (indicated RT)" "2. Refrigerated on the side near the front, 4C temperature, with regular traffic (4)" "3. Frozen, on the side door that swings out, -20 C temperature, with regular traffic (-20)" "Based on this data as of 4/6/2016 Advanced Genomics can extend their dry buccal swab specimen expiration from 21 to 49 days post-collection (50 day expiration)" 13. A review of "SAMPLE STABILITY STUDY #2" approved by the laboratory director on May 11, 2017 for Copan swabs (4N6FLOQSwabs ref 4504C) revealed the study did not mimic specimen collection, storage or transportation of samples received from outside clinics. "Our COPAN 4N6FLOQSwab Regular flocked swab with Active Drying system were used to swab five lab personnel. Swabs contain an Active Drying System. Samples were allowed to sit for 24 hours at room temperature before storage in one of three locations." "1. Room temperature in the lab in the kit sample storage envelopes (indicated RT)" "2. Refrigerated on the side near the front, 4C temperature, with regular traffic (4)" "3. Frozen, on the side door that swings out, -20 C temperature, with regular traffic (-20)" "Based on this data, Advanced Genomics can extend their dry buccal swab specimen expiration from 49 days to 70 days post-collection." 14. A review of the FAQ's and material data safety sheet section of the Copan website revealed the COPAN 4N6FLOQSwabs were not for diagnostic use. "Can COPAN Genetics 4N6FLOQSwabs (Trademark) be used for diagnostics? No. 4N6FLOQSwabs (Trademark) Genetics are not intended for diagnostic use." "Intended use: Collection -- 8 of 24 -- of samples for forensic investigation." 15. A review of the Copan 4N6FLOQSwabs (RED 4504C) package revealed an acceptable temperature range of 2-30C 16. A review of client instructions for the Copan swab and "Directions for DNA Sample Collection" included in the collection kit revealed no documentation of requiring swabs to dry at room temperature for 24 hours. "Return swab immediately" "Return the swab immediately into the plastic vile and screw lid tight" 17. A review of the document "Sample Stability Evaluation Summary" (no date) revealed a sample stability study was performed at room temperature, 4 to 8C and at outside temperatures for 21 days. The type of swab used was not identified, the outside temperature range was not documented and the study did not support the stability of swabs at outside temperatures for 14 days: "The sample stability assay was conducted to check the integrity of the samples for analysis. 3 different temperature settings for storage were validated: room temperature, refrigerator temperature, and outside temperatures. A total of 3 volunteers were swapped in samples were placed at room temperature (68F to 73F), and outside temperatures (variable) for 21 days. The genotyping, CNV and DNA concentrations results showed consistency with outside temperatures for up to the 7th day, room temperatures up to the 14th day and 4 to 8C temperatures for up to the 21st day." "Sample swabs stored at outside temperatures showed molded or contaminated after the 7th day of collection." "In summary our data show swabs that are kept at room temperature (68F to 73F) and at 4 8C has reproducible results for the validated time-frame." "Therefore, sample stability has been validated as follows: Outside temperatures - samples swabs stable for 14 days Room temperature - sample swab stable for 14 days Refrigerator temperatures (2 - 4C) - sample swab stable for 21 days." 18. A review of the facility Procedure "Specimen Collection" (Procedure 3500, effective date 6/15/2016) for sample collection and transport directions revealed swabs were allowed to air dry for 3-5 minutes, stored in the refrigerator and were to be transported at room temperature. "Place swab back into pouch and into package AFTER the sample is dry. Collect 2-4 swabs and allow for swabs to dry for 3-5 minutes. " Store swabs immediately in the refrigerator until delivery to FedEx." "Special handling o Specimen will be transported at room temperature." 19. A review of the client services manual under PGX sample collection revealed that after collection the directions stated to allow swabs to dry for 5 minutes and ship in FedEx shipping envelope. 20. A review of the "ALL OPEN PGX/ NTG samples" report for all pending samples revealed 43 open PGX panels and 197 NTG (Nutrigenomic) panels pending as of 2/1/2018. (please refer to patient alias list ALL OPEN PGX/ NTG samples) A random sampling of accession and collection dates PGX18-000001 collected 12/07/2017 PGX18-00015 collected 1/11/2018 PGX18-00029 collected 1/17/2018 GFLPGX18-00008 collected 12/22/2017 NUG5518-00116 collected 12/28/2017 NUG5518-00118 collected 12/11 /2017 NUG5518-00111 collected 01/09/2018 NUG5518-00105 collected 01/06/2018 21. In an interview of the testing person 2 (as listed on the Laboratory Personnel Report) on 1/30/2018 at 1030 hours in the laboratory she stated they received PGX samles in FedEx envelopes at ambient temperature and then hold the samples in the refrigerator until they get enough for a batch - need 95 samples for batch. In addition, she stated they try to do at least once a week, so if need to they do 1/2 plate. 22. In an interview of the specimen processor in the receiving area on 2/2/2018 at approximately 0930 hours she stated they received NTG samles in FedEx envelopes at ambient temperatureand and held samples until they receive notification the patient has paid for the test. Once the patient paid, they send the samples to the lab for processing. 23. An interview of the general supervisor on 2/1/2018 at 1500 hours in the common area confirmed the above findings. She stated that the previous manager had performed the studies and after reviewing them, she realized that they would have to be repeated. According to the CMS-116 signed by the laboratory director on 1/29 -- 9 of 24 -- /2018 the facility PGX annual test volume is approximately 347,660 tests. Key: CMS- Centers for Medicare & Medicaid Services PGX- Pharmacogenetic testing D5313 SPECIMEN SUBMISSION, HANDLING, AND REFERRAL CFR(s): 493.1242(b) The laboratory must document the date and time it receives a specimen. This STANDARD is not met as evidenced by: A. Based on direct observation, review of patient requisitions, test reports, client services manual and confirmed in interview, the laboratory failed to document the received time for patient samples for Rapid Respiratory Panel testing that were received from outside clinics. (random sample of 7 specimens received 1/30/2018) Findings Include: 1. Observation of rapid respiratory panel specimen processing on 1 /30/2018 at 1010 hours in the pre-amplification room revealed that incoming specimens were stamped with the date of receipt but not the time of receipt into the laboratory. The stamping instruments in use in the pre-amplification accessioning area were not capable of recording the time. Patients samples RRP18-00803, RRP18- 00804, RRP18-00811, RRP18-00812, RRP18-00813, RRP18-00814, RRP18-00815. 2. Review of tests reports showed time received in the laboratory was not included on the report of test results. Reports RRP18-00803, RRP18-00804, RRP18-00811, RRP18-00812, RRP18-00813, RRP18-00814, RRP18-00815. 3. A review of the Client Services Manual for collection RRP Sample Collection revealed samples would be rejected if "Samples not received within 48 hours." 4. An interview of the general supervisor on 1/30/2018 at 1410 hours in the common area confirmed the above findings. B. Based on interview, review of patient test reports and client service manual instructions, the laboratory failed to document the received date and time for patient samples for Rapid Respiratory Panel testing that were received from outside clinics delivered by Fed-Ex on Saturdays. 1. During an interview of the general supervisor on 1/30/2018 at 1155 hours she stated that specimens collected on Friday were shipped overnight and delivered to a box outside the building on Saturday because the laboratory was closed. An employee would stop by the laboratory on Saturday and remove the specimens from the outside box and place them in the refrigerator. This employee would not date or time stamp the incoming specimens. On Monday, the testing persons would date stamp the specimens as received on Saturday. In addition, the general supervisor admitted that they did not track who or when the employee came in on Saturday to put the respiratory samples in the refrigerator. 2. Review of test reports from the week of 1/29/2018 revealed 43 test reports documented as collected on Friday 1/26/2018 with a received date of Saturday 1/27 /2018 with no received time. PELRRP18-00040 PELRRP18-00041 PELRRP18- 00042 PELRRP18-00043 PELRRP18-00044 PELRRP18-00045 PELRRP18-00046 PELRRP18-00047 PELRRP18-00048 PELRRP18-00049 RRP18-00768 RRP18- 00769 RRP18-00770 RRP18-00771 RRP18-00772 RRP18-00773 RRP18-00774 RRP18-00775 RRP18-00776 RRP18-00777 RRP18-00778 RRP18-00779 RRP18- 00780 RRP18-00782 RRP18-00783 RRP18-00784 RRP18-00785 RRP18-00786 RRP18-00787 RRP18-00788 RRP18-00789 RRP18-00790 RRP18-00791 RRP18- 00792 RRP18-00793 RRP18-00794 RRP18-00795 RRP18-00796 RRP18-00797 RRP18-00798 RRP18-00799 RRP18-00800 RRP18-00801 3. Review of test reports from the week of 1/29/2018 revealed 1 test report documented as colleted on Thursday 1/25/2018 with a received date of Saturday 1/27/2018 with no received time. RRP18-00781 4. A review of the Client Services Manual for collection RRP Sample Collection revealed samples would be rejected if "Samples not received -- 10 of 24 -- within 48 hours." 5. An interview of the general supervisor on 1/30/2018 at 1410 hours in the common area confirmed the above findings. D5391 PREANALYTIC SYSTEMS QUALITY ASSESSMENT CFR(s): 493.1249(a) The laboratory must establish and follow written policies and procedures for an ongoing mechanism to monitor, assess, and when indicated, correct problems identified in the preanalytic systems specified at 493.1241 through 493.1242. This STANDARD is not met as evidenced by: Based on review of the laboratory's quality assessment plan( procedure 5800), and staff interview, it was revealed the laboratory's quality assessment plan failed to identify and correct issues in pre-analytic systems. The findings were: 1. The laboratory's quality assessment ("Quality Assessment", procedure 5800, effective 08 /15/2016) plan failed to identify and correct that the laboratory failed to have documentions of performing pre-analytic studies to support its sample stability claims (refer to D5311). 2. The laboratory's quality assessment ("Quality Assessment", procedure 5800, effective 08/15/2016) plan failed to identify and correct that the laboratory failed to document the time of receipt for Rapid Respiratory Panel testing samples. (refer to D5313) D5400 ANALYTIC SYSTEMS CFR(s): 493.1250 Each laboratory that performs nonwaived testing must meet the applicable analytic systems requirements in 493.1251 through 493.1283, unless HHS approves a procedure, specified in Appendix C of the State Operations Manual (CMS Pub.7), that provides equivalent quality testing. The laboratory must monitor and evaluate the overall quality of the analytic systems and correct identified problems as specified in 493.1289 for each specialty and subspecialty of testing performed. This CONDITION is not met as evidenced by: Based on record review, direct observation and interview with staff, the laboratory failed to ensure the requirements under analytic systems were met as evidenced by: 1. The laboratory failed to document the room temperature of the preamplification room used for Rapid Respiratory Panel testing and room temperature and humidity of the postamplification room used for Rapid Respiratory Panel testing. (refer to D5413) 2. The laboratory failed to have documentation of ensuring expired reagents were not used for patient testing. (refer to D5417) 3. The laboratory the laboratory failed to have documentation of complete establishment studies for 2 of 2 test systems prior to beginning patient testing. (refer to D5423) 4. The laboratory failed to have documentation of performing a negative external control for the NxTAG RRP Assay each day of patient testing for testing days between December 19, 2016 and January 30, 2018. (refer to D5447) 5. The laboratory failed to perform comparison studies for 2 QuantStudio 12 Flex analyzers used for CNV (Copy number variation) for PGX testing twice per year in 2016 or 2017. (refer to D4775) 6. The laboratory failed to have documentation of performing