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Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis

Lieselot Deleye¹, Dieter De Coninck¹, Dieter Deforce¹

¹Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.

Methods in Molecular Biology (Clifton, N.J.)

|December 11, 2017

Abstract:

Shallow whole genome sequencing has recently been introduced for genome-wide detection of chromosomal copy number alterations (CNAs) in preimplantation genetic diagnosis (PGD), using only 4-7 trophectoderm cells biopsied from day-5 embryos. This chapter describes the complete method, starting from whole genome amplification (WGA) on isolated blastomere(s), up to data analysis for CNA detection. The process is described generically and can also be used to perform CNA analysis on a limited number of cells (down to a single cell) in other applications. This unique description also includes some tips and tricks to increase the chance of success.

Keywords:

Copy number alterations (CNAs)Massive parallel sequencing (MPS)Preimplantation genetic diagnosis (PGD)Shallow whole genome sequencing Whole genome amplification (WGA)

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Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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