STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification...

Area of Science:

• Genomics
• Molecular Biology
• Biotechnology

Background:

• Liquid biopsies and non-invasive prenatal testing (NIPT) require sensitive single-cell genetic analysis.
• Rare and fragile cells in circulation pose significant challenges for genetic analysis.
• Cell stabilization and unbiased whole genome amplification (WGA) are crucial for overcoming these challenges.

Purpose of the Study:

• To evaluate the performance of four WGA methods (Ampli1, DOPlify, PicoPLEX, REPLI-g) on single or limited cells.
• To assess DNA suitability for short tandem repeat (STR) profiling and copy number variant (CNV) analysis.
• To determine method efficacy after 24-hour Streck Cell-Free DNA BCT preservation.

Main Methods:

• Single or limited cells were preserved using Streck Cell-Free DNA BCT for 24 hours.
• DNA was amplified using four different WGA methods: Ampli1, DOPlify, PicoPLEX, and REPLI-g.
• Shallow whole genome massively parallel sequencing (MPS) was performed, followed by STR profiling and CNV analysis.

Main Results:

• Ampli1, DOPlify, and PicoPLEX demonstrated successful amplification and suitability for both STR and CNV analyses.
• REPLI-g WGA method yielded unsuitable DNA for STR profiling and CNV analysis after cell preservation.
• Minor performance differences were observed among the successful WGA methods.

Conclusions:

• Ampli1, DOPlify, and PicoPLEX are suitable WGA methods for genetic analysis of preserved rare cells.
• REPLI-g is not recommended for WGA of cells preserved with Streck Cell-Free DNA BCT.
• Optimized WGA is essential for advancing liquid biopsy and NIPT applications.