Aneuploid Embryos & Preimplantation Genetic Testing

Aneuploid Embryos & Preimplantation Genetic Testing

Aneuploidy is the term associated with an abnormal number of chromosomes found in a cell within an early human embryo.  This term literally means not or without the correct number of chromosomes.  A genetically normal embryo is made up of cells that each contain 46 chromosomes, numbered 1-22 (autosomes) plus the sex chromosomes X and Y. Embryos with the correct number of chromosomes are also called euploid embryos.  Unfortunately, aneuploid embryos do not physically look any different than euploid embryos so without preimplantation genetic testing for aneuploidy (PGT-A), aneuploid embryos can and will be transferred and these embryos have been shown to fail implantation in about 96% of the cases1. It is therefore important to identify and selectively transfer euploid embryos which have been shown to have a very high chance of successful implantation and pregnancy.

As the graph (right) shows2, the incidence of embryo aneuploidy increases with maternal age from approximately 30% at age 30-34 up to almost 80% at age 41-42!  This is a major reason for the decreasing expectation of live birth per treatment cycle associated with maternal age. In this same chart you will notice that implantation rate does not decrease with maternal age when selectively transferring euploid embryos during IVF cycles.

  • PG-Seq™ Rapid Non-Invasive PGT Kit
    Optimized to test DNA from spent embryo culture media or blastocoelic fluid samples for non-invasive Preimplantation Genetic Testing.
  • PG-Seq™ Rapid Kit
    Accurately detects whole chromosome aneuploidy along with structural rearrangements such as unbalanced translocations and segmental errors from biopsies, with sample preparation taking only 3 hours using an efficient, streamlined workflow.
  • PG-Seq™ Kit 2.0
    An NGS workflow solution for PGT-A (Preimplantation Genetic Testing for Aneuploidy) and PGT-M (Preimplantation Genetic Testing for Monogenic Disorders) which includes the DOPlify® WGA kit, a library preparation kit which is used to prepare the WGA product for next generation sequencing and proprietary PG-Find software used to analyze the genome for chromosome aberrations as small as 5 MB.
PGT-A Rates

“More than 40% of healthy looking IVF embryos are aneuploid in women older than 35 years.”

Harton et al, Fert Steril Dec 2013, 100 (6): 1695-703

Preimplantation Genetic Testing-Aneuploidy

As this graph shows3, PGT-A and selective transfer of euploid embryos out performs no PGT-A as it relates to live birth rates.  Without PGT-A, implantation and pregnancy rates drop significantly as the female partner’s age increases.  In this data set, PGT-A cycles had a statistically significant increased pregnancy outcome for every age group compared to cycles without PGT-A.

Babies Transferred Embryos

The most significant recent advance to improve IVF success rates has been the introduction of 24 chromosome preimplantation genetic testing-aneuploidy (PGT-A).

The purpose of PGT-A is to identify embryos with the correct number of chromosomes for IVF transfer. PGT-A cannot correct aneuploid embryos; it can only identify those embryos that are not suitable for transfer.

Selecting only euploid embryos to transfer with PGT-A has been demonstrated to:

  • Reduce the time to pregnancy by reducing the number of cycles/transfers needed to become pregnant
  • Reduce the risk of miscarriage
  • Allow only the selection of euploid embryos for freezing, avoiding the expense of storing embryos unsuitable for transfer
  • Overcome the adverse effect of maternal age on IVF success by focusing on euploid embryos
  • Reduce the risk of multiple pregnancies from IVF

Check out our blog posts:

  • PGT Non Invasive

“PGS can increase the clinical pregnancy rate by around 50%.”

Yang et al. Molecular Cytogenetics 2012, 5: 24.

Preimplantation Genetic Testing for Monogenic Diseases (PGT-M)

Thousands of different single gene mutations, cancer predisposition genes, and now multi-factorial diseases can be screened in the early human embryo before transfer during an IVF cycle1. Having multiple cells to work with removes some of the potential issues that surrounded early attempts at single cell biopsy including reductions in allele drop-out (ADO) and preferential amplification (PA).  Allele drop-out arises in the early stages of amplification by polymerase chain reaction (PCR), where one allele of a heterozygote is not primed and products for this allele are not created.  In a heterozygote cell, this means that one allele will be missed which can lead to misdiagnosis as a homozygous embryo2.  Preferential amplification is similar to ADO except that some product is made for one allele while more product is made for the other allele.  Again, depending on the down-stream method of analysis chosen, this can lead to errant results and potential misdiagnosis. Dreesen’s and colleagues have published a thorough review of misdiagnosis during PGT-M (PGD)3, and Warren and colleagues have shown how using the PG-Seq™ kit with TSE lessens or eliminates the issues of PA and ADO4.

Although a PGT-M result may indicate that an embryo is unaffected by a monogenic disease, standard PGT-M methods are unable to assess aneuploidy.  Depending on the age of the female patient, somewhere between 44% and 75% of these transferred embryos may be aneuploid.  A robust method combining WGA along with gene-specific primers in a single reaction to allow both aneuploidy detection (PGT-A) and monogenic disease detection (PGT-M) would be a great leap forward for patients undergoing PGT-M.

Combining PGT-A and PGT-M has proved to be difficult without some concessions from either test.  Many labs perform combined PGT-A and PGT-M by following their normal WGA methods for PGT-A to a certain point, and then split the WGA into 2 different samples and process each of them separately (personal communication).  This system usually creates enough reads for PGT-A analysis and enough PCR product for downstream PGT-M testing, however splitting the WGA products into separate aliquots creates a few obvious issues, including the chance for sample switches/failed amplification, preferential amplification, and increased allele drop out (ADO) rates.  In addition, if the lab wants to use next generation sequencing (NGS) technology for all downstream analysis then this splitting typically creates samples with different bar codes so the sample would need to be analyzed separately for PGT-A and PGT-M, which adds to the cost.

The target sequence enrichment (TSE) protocol from PerkinElmer allows for linkage-based analysis of most gene mutations using SNP haplotyping along with detailed analysis of aneuploidy in all 23 chromosomes simultaneously.  This method uses whole genome amplification (WGA) to allow low pass sequencing coverage to detect aneuploidy down to approximately 10 MB in size along with TSE to specifically and reliably amplify the SNP set for each specific patient set.  This method allows for PGT-M with no allele drop out or preferential amplification for the gene mutation or associated SNPs and PGT-A analysis all in a single tube and in a single economical sequencing run.


  1. De Rycke M, Goossens V, Kokkali G, Meijer-Hoogeveen M, Coonen E, Moutou C. EHSRE PGD Consortium data collection XIV-XV: cycles from January 2011 to December 2012 with pregnancy follow-up to October 2013. Hum Reprod. 2017 32(10):1974-1994.
  2. Findlay I, Ray P, Quirke P, Rutherford A, Lilford R. Allelic drop-out and preferential amplification in single cells and human blastomeres: implications for preimplantation diagnosis of sex and cystic fibrosis. Hum Reprod. 1995 Jun:10(6):1609-18.
  3.  Dreesen J, Destouni A, Kourlaba G, Degn B, Mette WC, Carvalho F, Moutou C, Sengupta S, Shanjal S, Renwick P, Davies S, Kanavakis E, Harton G, Traeger-Synodinos J. Evaluation of PCR-based preimplantation genetic diagnosis applied to monogenic diseases: a collaborative ESHRE PGD consortium study. Eur J Hum Genet. 2014 Aug;22(8):1012-8.
  4. Warren K, Protopsaltis S, Jasper M. DOPlify®, Target Sequence Enrichment and Allele Dropout-is there a benefit? PGD-IS International Society Annual Meeting 2018. Bangkok Thailand.
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For research use only. Not for use in diagnostic procedures.

  1. Comprehensive chromosome screening is highly predictive of the reproductive potential of human embryos: a prospective, blinded, nonselection study. Scott RT Jr, Ferry K, Su J, Tao X, Scott K, Treff NR. Fertility and Sterility 2012 Apr:97(4):870-5
  2. Diminished effect of maternal age on implantation after preimplantation genetic diagnosis with array comparative genomic hybridization. Harton GL, Munné S, Surrey M, Grifo J, Kaplan B, McCulloh DH, Griffin DK, Wells D; PGD Practitioners Group. Fertility and Sterility 2013 Dec;100(6):1695-703
  3. McCulloh D., 8th Annual Southwestern Embryology Summit, 2019. Mesa, AZ
  4. Selection of single blastocysts for fresh transfer via standard morphology assessment alone and with array CGH for good prognosis IVF patients: results from a randomized pilot study. Yang Z, Liu J, Collins GS, Salem SA, Liu X, Lyle SS, Peck AC, Sills ES, Salem RD. Molecular Cytogenetics 2012 May 2;5(1):24