In the early 2000s, the discovery of a DNA polymerase isolated from a bacteriophage revolutionised our ability to amplify the whole genome of single or small numbers of cells. For the first time, it became possible to generate micrograms of DNA for genome-wide genetic analysis. At the same time, with advances in DNA sequencing of the human genome, a new class of abundant DNA markers was identified in which at specific positions, the nucleotide present in the DNA sequence could vary between one of two or three bases and was often different from one person to the next. Millions of these so-called single nucleotide polymorphisms (SNPs) are scattered across the genome on all chromosomes. Microarrays were developed to genotype 10s then 100s of thousands of these SNPs and this approach played an important role in tracking down disease genes and genetic contributions to common multifactorial diseases.
In 2003, believing in the potential of these markers, we began working on microarray-based SNP genotyping of DNA amplified from single or small numbers cells biopsied from human preimplantation embryos for preimplantation genetic testing of inherited diseases. This culminated in 2010, with the publication of a method for SNP genotyping and ‘karyomapping’ of the four parental chromosomes present in single or small numbers of embryo cells biopsied from human embryos (1). Karyomapping uses linkage analysis of disease genes to the parental SNP markers across each chromosome and is universally applicable to any monogenic disease. In addition, karyomapping identifies meiotic trisomies, monosomies and deletions and can be used for structural chromosome rearrangements, including distinguishing embryos with normal chromosomes and balanced translocation carriers. Thus, it can be used for preimplantation genetic testing for monogenic disease, structural rearrangements (PGT-M/SR/A) and any combination of these abnormalities. It was validated for use with monogenic disease in 2014 (2) and remains the most informative and cost-effective approach for preimplantation genetic testing.
Here, a series of guides are presented on the use of karyomapping for PGT with some examples of the kinds of abnormalities which occur in early human development, using various software programmes and macros to visualise the karyomaps at a chromosome level.
(1) Handyside AH, Harton GL, Mariani B, Thornhill AR, Affara N, Shaw M-A and Griffin DK (2010) Karyomapping: a universal method for genome wide analysis of genetic disease based on mapping crossovers between parental haplotypes. Journal of Medical Genetics 47 651–658.
(2) Natesan SA, Bladon AJ, Coskun S, Qubbaj W, Prates R, Munne S, Coonen E, Dreesen JCFM, Stevens SJC, Paulussen ADC et al. (2014) Genome-wide karyomapping accurately identifies the inheritance of single-gene defects in human preimplantation embryos in vitro. Genetics in Medicine 16 838-45.