Sample Traceability in PGT-A

Sample traceability is crucial to ensure reliable embryo classification. This process involves tracking from the initial collection of the biopsy through to the final analysis.

For sample collection we recommend Cap^2™ tubes, with 2D datamatrix code, free of DNAse, Rnase, human genomic DNA and compatible with automation.

To track samples individually we take advantage of the mitochondrial genome.

The mitochondrial genome is maternally derived and contains single nucleotide variants that can be used to distinguish between individuals. Revvity has shown that correct grouping of sibling embryos can be achieved in >98% of cases using mitochondrial DNA SNV profiling. The new mtDetect™ web app extracts mitochondrial DNA information from data obtained during the standard PG-Seq™ Rapid v2 workflow enabling the monitoring of external DNA contamination and the ability to detect sample swapping and mislabeled samples.

Figure 1 shows 90% coverage of the mtDNA genome using the PG-Seq Rapid v2 kit without any protocol modification. Embryo biopsies processed with the PG-Seq™ Rapid v2 kit analyzed with mtDetect™ web app can successfully be identified and grouped based on their mitochondrial DNA SNV profiles. Identity determination allows sample tracking and can assist in the identification and monitoring of possible external sample contamination along with mislabeled samples.

Figure 1: IGV coverage track of the full mitochondrial genome (chrM: 1-16364bp) from a PG-Seq Rapid v2 amplified 5-cell sample with 1,000,000 sequencing reads shows 90% coverage of the mtDNA genome.

Easy-to-Use, Highly Customizable Analysis Software

Two analysis options, self-reference and reference based, to accommodate every laboratory’s individual needs. Multiple visualization features including selecting which chromosomes to view and report, a single check box to view the raw vs smoothed data, unlimited color options, multiple result images. User adjustable event calling thresholds that can be used to designate mosaic, 1 copy or 2 copy gains and losses. An easy to interpret result overview screen allows the results of every sample to be easily analyzed and for general data trends to be observed.

A modifiable binning distance allowing the CNV resolution to be tailored according to laboratory requirements and sample sequencing depth and coverage.

Automatic and manual copy number calling of whole chromosome and sub-chromosome copy number events, including detailed information on the position and size of each event.

• Avila Perez, C., Parnell, L., Florensa Bargallo, M., Herreros Cuesta, J., Larreategui Laiseca, Z., Prados Dodd, N., Ruiz Perez, M., & Wells, D. (2023). P-731: The accuracy of truly non-invasive PGT using spent culture media is insufficient to justify routine clinical use. Human Reproduction, 38(Supplement_1), dead093. 1050.
• Banu, M., Pathan, A. A. K., & Chaitanya, K. V. (2023). Diagnostics for Genetically Inherited Disorders: From Cytogenetics to Genomics Technologies-A Review. Biomedical and Pharmacology Journal, 16(2).
• Cheng, H. Y. H., Chow, J. F. C., Lam, K. K. W., Lai, S. F., Yeung, W. S. B., & Ng, E. H. Y. (2023). Randomised double-blind controlled trial of non-invasive preimplantation genetic testing for aneuploidy in in vitro fertilisation: a protocol paper. BMJ Open, 13(7), e072557.
• Curnow, E., Ryan, G. L., & Yu, B. (2023). Discordant non-invasive PGT-A results and clinical outcome. Fertility and Sterility, 120(4), e276.
• Spath, K., Costa-Borges, N., Nikitos, E., Kostaras, K., Calderón, G. C., Psathas, P., & Wells, D. (2023). P-730: Detection of mitochondrial reversal following meiotic spindle transfer: a finding of importance for mitochondrial replacement therapies used for the purpose of avoiding…. Human Reproduction, 38 (Supplement_1), dead093. 1049.
• Sonehara, H., Matsumoto, R., Nakayama, N., Kobanawa, M., Numata, K., Kawasaki, A., & Shozu, M. (2022). Aneuploidy and sex concordance rate between cell-free DNA analysis from spent culture media of preimplantation embryo and DNA from whole embryo with respect to different…. Reproductive Medicine and Biology, 21(1), e12493.