Karyomapping Proposed as Alternative to Preimplantation Genetic Diagnosis for Evaluation of IVF Embryos

British researchers have suggested that karyomapping is a viable and cost-effective method for detecting a wide range of genetic diseases in IVF (in vitro fertilization) embryos.

Preimplantation Genetic Diagnosis (PGD) of single gene defects by genetic analysis of single or small numbers of cells in biopsy specimens from IVF embryos is clinically well-established. However, PGD for monogenic disorders (resulting from a single defective gene) is expensive, time-consuming, and requires the tailoring of a specific test for each couple and/or disorder.

Targeted haplotyping by multiplex fluorescent polymerase chain reaction (PCR) of closely linked or intragenic short tandem repeat (STR) markers combined with direct mutation detection improves the accuracy of single cell analysis significantly and minimizes potential errors caused by undetected allele dropout or contamination. Allele dropout refers to the failure of one of the two alleles of a heterozygous locus to amplify. This makes a heterozygous cell appear homozygous at the affected locus, potentially leading to misdiagnosis.

Investigators at the University of Kent (United Kingdom) introduced Karyomapping as an alternative to traditional PGD analysis. A karyomap, unlike a karyotype, identifies the parental and grandparental origin of each chromosome and chromosome segment and is unique for every individual being defined by the independent segregation of parental chromosomes and the pattern of non-recombinant and recombinant chromosomes. Karyomapping, therefore, enables both genome wide linkage based analysis of inheritance and detection of chromosome imbalance where either both haplotypes from one parent are present (trisomy) or neither are present (monosomy/deletion).

The karyomap, as described in the current study, was derived from data obtained by PCR and genome-wide sequencing that identified single nucleotide polymorphisms (SNPs). Bead array data was imported directly into dedicated software for karyomapping (BlueFuse Multi, Version 4.0; Illumina [Little Chesterford, United Kingdom]). BlueFuse Multi displayed the detailed karyomaps for each parental chromosome as two rows of informative SNPs (colored dots) mapped to their physical location above and below a continuous haploblock bar, all of which were color coded to indicate the parental haplotype.

With genomic DNA samples, call rates of greater than 98% were generally achieved. With materials from single blastomeres and multiple-cell trophectoderm samples, call rates were significantly lower, in the 75%–95% range. Nonetheless, karyomap analysis of these samples was highly consistent, indicating few genotyping errors. Samples with call rates of less than 60% (for euploid samples), indicating failure of amplification, had a high incidence of erroneous heterozygous calls, which prevented reliable karyomap analysis. These samples were excluded from further analysis.

In the paper published in the January 6, 2015, online edition of the Journal of Assisted Reproduction and Genetics the authors provided proof-of-principle for the widespread clinical application of Karyomapping, first by adapting the protocol for clinical use in a regular PGD timeframe (24 hours) and secondly by detection of the autosomal dominant condition Marfan syndrome.

Related Links:
University of Kent
Illumina