Sample Confirmation Testing: A Short Tandem Repeat-Based Quality Assurance and Quality Control Procedure for the eyeGENE Biorepository

Abstract

Quality assurance and quality control (QA/QC) procedures are vital to good biorepository management. The National Eye Institute (NEI) core CLIA-certified laboratory of the eyeGENE(®) Network receives blood from individuals with inherited eye conditions and isolates DNA for clinical genetic diagnostic testing and research. Clinical genetic test results are returned to the affected individuals, making it imperative that sample integrity is preserved throughout laboratory processing. A clinically validated, short tandem repeat (STR)-based approach, termed Sample Confirmation Testing (SCT), was developed to ensure that no significant laboratory errors occurred during processing. SCT uses modified protocols from commercial kits to create and compare STR profiles for each participant's original blood and derived DNA. This QA/QC procedure has been performed on 47% of the more than 6000 participants in the eyeGENE Biorepository and has identified significant laboratory errors in 0.4% of samples tested. SCT improves the quality of the data returned to affected individuals and the data distributed to researchers using eyeGENE samples by ensuring the integrity of the samples and aiding in curation of the biorepository. This approach serves as a model for other repositories to improve sample quality and management procedures.

Trial registration: ClinicalTrials.gov NCT00378742.

Figures

FIG. 1.

K2 EDTA tubes (10.8 mg) containing a total of 24–30 mL of blood are received within 72 hours of the draw (A). Approximately 0.5–1 mL of blood is left in one of the original blood tubes (B) and stored at 4°C. Up to 20 mL of blood (C, D) is processed into two DNA aliquots (E, F) by automated or manual methods using the Gentra Puregene Kit (Qiagen Corp., Hilden, Germany). Any remaining blood is stored. One DNA aliquot (E) is placed at −80°C for long-term storage. The other DNA aliquot (F) is stored at −20°C and accessed regularly for shipping purposes.

FIG. 2.

Flowchart of Sample Confirmation Testing process.

FIG. 3.

Electropherogram of fragments from the blood of Participant A, as amplified by the Phusion Kit. Electropherogram of fragments from the DNA of Participant A as amplified by the PowerPlex® S5 System. *An artifact produced by the Phusion polymerase chain reaction (PCR) that is not considered during interpretation.

FIG. 4.

Electropherogram of fragments from the blood of Participant B, as amplified by the Phusion Kit. Electropherogram of fragments from the DNA labeled as Participant B as amplified by the PowerPlex S5 System. *An artifact produced by the Phusion PCR that is not considered during interpretation.

FIG. 5.

Electropherogram of fragments from the blood of Participant D, as amplified by the Phusion Kit. Electropherogram of fragments from the DNA labeled as Participant D as amplified by the PowerPlex S5 System. Electropherogram of fragments from the blood of Participant E, as amplified by the Phusion Kit. *An artifact produced by the Phusion PCR that is not considered during interpretation.