Centro De Genetica Clinica/Cgc Genetics

Summary Statement of Deficiencies D0000 A recertification onsite survey was conducted on 07/25/2024 and standard level deficiencies were cited. D5311 Based on review of written procedures, client services manual, and interview with staff, the laboratory failed to define specimen storage (temperatures), stability, conditions for specimen transportation in their own written procedures for molecular testing. Findings included: 1. Review of the laboratory's molecular procedures (whole exome sequencing, multiplex ligation-dependent probe amplification, triplet repeat primed polymerase chain reaction, and Sanger sequencing) referred to a different procedure for sample handling (UNI-GEN-I-038). 2. Review of "Sample pre- registration procedure" (UNI-GEN-I-038) did not include extracted DNA specimen: a) storage and preservation (collection tube, temperatures), b) conditions for specimen transportation, c) acceptability/rejection criteria for storage, conditions for transport, and stability 3. Review of the client services manual for specimen handling instructions stated, "Shipping should be well conditioned and at room temperature" and for evening or weekend shipments, "Keep sample at room temperature away from sources of cold or heat." Refer to D5317. 4. During an interview on 07/25/2024 at 12: 17 pm, the quality manager and technical supervisor explained extracted DNA was the specimen type accepted for testing (from the U.S.) and it was submitted in an Eppendorf tube or cryotube. After review of the above procedures, the quality manager, technical supervisor, laboratory director and quality director confirmed the preanalytical requirements had not been defined. D5317 Based on review of written procedures, client services manual, and interview with staff, the laboratory failed to ensure all preanalytical requirements were included in their client services manual. Findings included: 1. Review of the laboratory's molecular procedures had not defined specimen storage (temperatures), stability, conditions for specimen transportation for extracted DNA. Refer to D5311. 2. Review of the client services manual for specimen handling instructions stated, "Shipping should be well conditioned and at room temperature" and for evening or weekend Statement of Deficiencies (X1) Provider/Supplier/CLIA Identification Number (X3) Date Survey Completed Name of Provider or Supplier Street Address, City, State -- 1 of 2 -- shipments, "Keep sample at room temperature away from sources of cold or heat." The client services manual did not define "room temperature" and "well conditioned" to avoid compromising specimen integrity. In addition, the client services manual did not include: a) storage and preservation (collection tube, temperatures), b) conditions for specimen transportation, c) acceptability/rejection criteria for storage, conditions for transport, and stability 4. During an interview on 07/25/2024 at 12:17 pm, the quality manager and technical supervisor explained extracted DNA was the specimen type accepted for testing (from the U.S.) and it was submitted in an Eppendorf tube or cryotube. After review of the above procedures, the quality manager, technical supervisor, laboratory director and quality director confirmed the preanalytical requirements had not been defined. -- 2 of 2 --

Summary Statement of Deficiencies D5455 Based on review of the Standard Operative Procedure SOP.804- Next Generation Sequencing and email correspondence with laboratory staff, the laboratory failed to include two quality control materials at least once each day patient samples were assayed. Findings: 1. Review of SOP.804 - Next Generation Sequencing revealed the procedure included criteria for Quality Control. This criteria did not include the testing of two control materials each day patient samples are tested. 2. Email correspondence with the laboratory's quality manager dated July 3, 2018 stated " ...the NGS quality control procedure: every three months we test a male DNA (Human Male Genomic DNA , Promega) as a quality control material in order to evaluate the robustness and reproducibility of our assays." 3. Email correspondence with the laboratory's quality manager dated June 23, 2018 stated " ...the policy of our lab is as follows: In our assays we do not include a positive control. Following the international recommendations (ACMG Practice guidelines, PMID: 23887774), and "similar to Sanger-based sequencing, positive controls do not need to be tested concurrent with routine clinical tests". We have though, strategies to evaluate and control for eventual contaminations. We perform in average three assays per week and samples are tested for different panels, a second technician performs visual double verification of sample ID, and since we perform Sanger sequencing for confirmation of variants reported in result it is common that in each assay at least one sample will be further confirmed independently by a different method (Sanger sequencing)." Statement of Deficiencies (X1) Provider/Supplier/CLIA Identification Number (X3) Date Survey Completed Name of Provider or Supplier Street Address, City, State -- 1 of 1 --