Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts

Abstract

This study demonstrates that shallow whole genome sequencing can be applied efficiently for the detection of numerical and structural chromosomal aberrations in embryos, equaling or even exceeding the resolution of the routinely used microarrays.

The comparison of the performance of four whole genome amplification kits on ion proton platform in copy number variation detection

“…Ion Proton is one of the currently main NGS platforms and is widely applied to diverse fields, including exome sequencing, transcriptome sequencing, single-cell sequencing etc. [5][6][7][8][9], and especially it often occurs in clinical examination, such as noninvasive prenatal diagnosis [10] and preimplantation genetic screening [11].…”

Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing

“…In another study, SurePlex WGA proved its efficient amplification of DNA from 4–6 blastocyst cells for downstream MPS with a reliable detection of chromosomal aberrations down to 3 Mb4. Nevertheless, results show that the WGA representation bias is still a limiting factor in achieving higher resolution copy number profiles when starting from a single or a limited number of cells4. In order not to call over- or underamplified regions as CNAs, the read counts need to be averaged out in genomics windows of at least 0.5 Mb4, leading to a 3 Mb resolution for CNA detection (see also Methods section).…”

“…SurePlex amplified samples lead to accurate detection of CNA with a resolution of 3 Mb. In another study, SurePlex WGA proved its efficient amplification of DNA from 4–6 blastocyst cells for downstream MPS with a reliable detection of chromosomal aberrations down to 3 Mb4. Nevertheless, results show that the WGA representation bias is still a limiting factor in achieving higher resolution copy number profiles when starting from a single or a limited number of cells4.…”

“…Nevertheless, results show that the WGA representation bias is still a limiting factor in achieving higher resolution copy number profiles when starting from a single or a limited number of cells4. In order not to call over- or underamplified regions as CNAs, the read counts need to be averaged out in genomics windows of at least 0.5 Mb4, leading to a 3 Mb resolution for CNA detection (see also Methods section). With less representation bias, smaller windows and a higher resolution could be used.…”

“…With less representation bias, smaller windows and a higher resolution could be used. Accurate detection of CNAs from amplified DNA is of importance for applications such as pre-implantation genetic diagnosis (PGD) in which day-5 embryos are screened for CNA using of 3–7 trophectoderm cells4. Cell-based liquid biopsy both in cancer and prenatal diagnosis, is another emerging field where accurate, high resolution CNA detection starting from a limited number of cells is invaluable.…”