Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis

Lieselot Deleye; Dieter De Coninck; Dieter Deforce; Filip Van Nieuwerburgh

doi:10.1007/978-1-4939-7514-3_3

Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis

Methods Mol Biol. 2018:1712:27-42. doi: 10.1007/978-1-4939-7514-3_3.

Authors

Lieselot Deleye¹, Dieter De Coninck¹, Dieter Deforce¹, Filip Van Nieuwerburgh²

Affiliations

¹ Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
² Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium. Filip.VanNieuwerburgh@UGent.be.

PMID: 29224066
DOI: 10.1007/978-1-4939-7514-3_3

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).

MeSH terms

Blastomeres
DNA Copy Number Variations / genetics*
Embryo, Mammalian
Female
Genome, Human*
Genome-Wide Association Study / methods*
High-Throughput Nucleotide Sequencing
Humans
Pregnancy
Preimplantation Diagnosis / methods*
Single-Cell Analysis
Statistics as Topic
Whole Genome Sequencing / methods*