Analysis of five Duchenne muscular dystrophy exons and gender determination using conventional duplex polymerase chain reaction on single cells

Concordance of various chromosomal errors among different parts of the embryo and the value of re-biopsy in embryos with segmental aneuploidies

Chromosomal mosaicism detected during preimplantation genetic testing for aneuploidy (PGT-A) and its impact on embryo implantation have been widely discussed, and healthy live births from mosaic embryos were reported by many groups. On the other hand, only very few studies have focused on segmental chromosome aneuploidies and their clinical impact. Eighty-nine embryos with various PGT-A results (trophectoderm 1: TE1) were re-analysed using a second trophectoderm biopsy (TE2) and the rest of the embryo (RE) for testing. Of 19 euploid TE1 biopsies, 18 were concordant across TE2 and RE. Similarly, whole chromosomal aneuploidies were concordant in 59 of 62 TE1-TE2 and 58 TE1-RE. In contrast, from 31 segmental aneuploidies detected in TE1, only 15 were observed again in TE2 and 14 in RE. If a TE1 segmental abnormality appeared again in TE2, it was almost always present in RE (17/18) as well. Moreover, when a TE1 segmental abnormality was not detected in TE2, in 12 out of 13 cases RE was also unaffected. Similarly, only 1 of 26 TE1 whole chromosome mosaics were repeated in TE2 and 7 in RE. Our study confirms that euploid and whole chromosomal aneuploidy results are highly predictive of the embryo. In contrast, mosaicism has a very low concordance rate. Most importantly, re-biopsy of embryos with segmental aneuploidies demonstrated that they are mostly not uniform across the embryo. Finally, in the case of segmental aneuploidy, the second biopsy enables an accurate prediction of the real status of the embryo and could be offered to patients undergoing PGT-A.

Karyomapping and how is it improving preimplantation genetics?

INTRODUCTION

Preimplantation genetic diagnosis and screening (PGD/PGS) has been applied clinically for >25 years however inherent drawbacks include the necessity to tailor each case to the trait in question, and that technology to detect monogenic and chromosomal disorders respectively is fundamentally different. Areas covered: The area of preimplantation genetics has evolved over the last 25 years, adapting to changes in technology and the need for more efficient, streamlined diagnoses. Karyomapping allows the determination of inheritance from the (grand)parental haplobocks through assembly of inherited chromosomal segments. The output displays homologous chromosomes, crossovers and the genetic status of the embryos by linkage comparison, as well as chromosomal disorders. It also allows for determination of heterozygous SNP calls, avoiding the risks of allele dropout, a common problem with other PGD techniques. Manuscripts documenting the evolution of preimplantation genetics, especially those investigating technologies that would simultaneously detect monogenic and chromosomal disorders, were selected for review. Expert commentary: Karyomapping is currently available for detection of single gene disorders; ~1000 clinics worldwide offer it (via ~20 diagnostic laboratories) and ~2500 cases have been performed. Due an inability to detect post-zygotic trisomy reliably however and confounding problems of embryo mosaicism, karyomapping has yet to be applied clinically for detection of chromosome disorders.

Trophoblast retrieval and isolation from the cervix (TRIC) for noninvasive prenatal screening at 5 to 20 weeks of gestation

OBJECTIVE

To use trophoblast cells accumulating in the endocervical canal at the beginning of pregnancy for noninvasive prenatal testing.

DESIGN

Prospective, double-blinded test for fetal gender.

SETTING

Academic medical center.

PATIENT(S)

Fifty-six women with singleton pregnancies at gestational age 5-20 weeks.

INTERVENTION(S)

Isolation of fetal cells from resident maternal cells in endocervical specimens using anti-human leukocyte antigen G coupled to magnetic nanoparticles; cell phenotyping immunofluorescently with a panel of trophoblast subtype-specific proteins; DNA integrity assessment with terminal dUTP nick-end labeling (TUNEL); and polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) to detect sex chromosomes in individual cells.

MAIN OUTCOME MEASURE(S)

Trophoblast phenotype, TUNEL index, and percentage male cells.

RESULT(S)

The women were given a routine Papanicolaou test; fetal genders were verified from medical records. Recovery after immunomagnetic isolation averaged 746±59 cells across gestational age, with 99% expressing chorionic gonadotropin, whereas the depleted cell fraction expressed none. The isolated cells had an extravillous trophoblast phenotype and intact nuclear DNA (>95%). Fetal gender was determined in 20 specimens without error by PCR. The FISH analysis of isolated cells from male specimens validated their fetal origin.

CONCLUSION(S)

Noninvasive prenatal testing is feasible beginning at a gestational age of 5 weeks.

Preimplantation genetic diagnosis for BRCA1 exon 13 duplication mutation using linked polymorphic markers resulting in a live birth

BACKGROUND

The risk of breast cancer associated with inheriting a BRCA1 mutation is extremely high, in addition, there is a 50% chance of transmitting this familial cancer mutation to any offspring.

METHODS

A 31-year-old woman with a strong maternal family history of early onset of breast cancer had experienced 3 years of primary infertility. Presymptomatic testing confirmed the woman had inherited a 6 kb duplication of exon 13 (ins6KbEx13) in BRCA1 from her mother. Neither gamete donation or adoption were acceptable options for this infertile couple, and as termination of pregnancy after prenatal diagnosis following in vitro fertilization (IVF) was not ethically acceptable, preimplantation genetic diagnosis (PGD) was sought. A single-cell PCR protocol for PGD for the breast and ovarian cancer predisposing BRCA1 exon 13 duplication mutation was developed which involved amplification of three specific gene regions, including the BRCA1 mutation (ins6KbEx13), an intragenic marker (D17S855) and a flanking marker (D17S1185).

RESULTS

In the first cycle of IVF, three embryos were analyzed and two were determined to be at low risk of having inherited the maternal BRCA1 mutation. Following the transfer of both embryos on day 5, a singleton pregnancy resulted. Declining confirmatory prenatal diagnosis, a male baby was subsequently delivered at term.

CONCLUSIONS

Successful PGD for BRCA1 resulted in the delivery of a live-born male. PGD using linked polymorphic markers provides an alternate option for reproduction for couples with or at risk of having inherited a BRCA1 mutation.

An efficient and reliable DNA extraction method for preimplantation genetic diagnosis: a comparison of allele drop out and amplification rates using different single cell lysis methods

OBJECTIVE

To evaluate methods of DNA extraction from single cells for their suitability to amplify and provide a correct diagnosis of target disease genes.

DESIGN

Experimental study.

SETTING

University hospital laboratory.

PATIENT(S)

Two normal adult male and female blood donors.

INTERVENTION(S)

Exon 51 of the dystrophin gene and the ZFX/ZFY gene were amplified from single lymphocytes using nested PCR. Five different methods of DNA extraction were tested (lysis in distilled water with freezing and thawing using liquid nitrogen, lysis in distilled water, alkaline lysis buffer, Proteinase K/sodium dodecyl sulfate (SDS) buffer, and N-lauroylsarcosine salt solution).

MAIN OUTCOME MEASURE(S)

Allele drop out and amplification rate.

RESULT(S)

The amplification efficiency from single unaffected lymphocytes was 89.0% using the liquid nitrogen method, 88.1% with the distilled water lysis method, 97.5% with the alkaline lysis buffer method, 91.5% with the Proteinase K/SDS lysis buffer method, and 84.8% using the N-lauroylsarcosine salt solution method. The mean allele drop out rate was 16.7%, 43.9%, 2.0%, 9.8%, and 18.9%, respectively, for each lysis method using single male lymphocytes as a template.

CONCLUSION(S)

Based on these results, DNA extraction using an alkaline lysis buffer results in more efficient rates of DNA amplification and less allele drop out than the other methods of DNA extraction tested. This method is suitable for the lysis of single cells in clinical preimplantation genetic diagnosis.

Preimplantation genetic diagnosis for Duchenne muscular dystrophy by multiple displacement amplification

OBJECTIVE

To evaluate the use of multiple displacement amplification (MDA) in preimplantation genetic diagnosis (PGD) for female carriers with Duchenne muscular dystrophy (DMD).

DESIGN

MDA was used to amplify a whole genome of single cells. Following the setup on single cells, the test was applied in two clinical cases of PGD. One mutant exon, six short tandem repeats (STR) markers within the dystrophin gene, and amelogenin were incorporated into singleplex polymerase chain reaction (PCR) assays on MDA products of single blastomeres.

SETTING

Center for reproductive medicine in First Affiliated Hospital, Sun Yat-sen University, China.

PATIENT(S)

Two female carriers with a duplication of exons 3-11 and a deletion of exons 47-50, respectively.

INTERVENTION(S)

The MDA of single cells and fluorescent PCR assays for PGD.

MAIN OUTCOME MEASURE(S)

The ability to analyze single blastomeres for DMD using MDA.

RESULT(S)

The protocol setup previously allowed for the accurate diagnosis of each embryo. Two clinical cases resulted in a healthy girl, which was the first successful clinical application of MDA in PGD for DMD.

CONCLUSION(S)

We suggest that this protocol is reliable to increase the accuracy of the PGD for DMD.

Preimplantation genetic diagnosis (PGD) for Duchenne muscular dystrophy (DMD) by triplex-nested PCR

OBJECTIVES

Duchenne muscular dystrophy (DMD) is a lethal X-linked recessive disorder with an incidence of approximately 1 in 3500 males, caused by mutation in the DMD gene. About 2/3 of DMD cases are caused by gross DMD gene deletion mutations. The purpose of this study was to develop a series of single-cell multiplex-nested PCR protocols for preimplantation genetic diagnosis (PGD) of the most prevalent DMD deletions.

METHODS

The protocols were developed on single blood leukocytes from normal males and females and patients with known DMD gene deletion. In the first reaction, 2 of 11 different primer sets (exons 4, 8, 12, 13, 17, 46, 47, 49, 50, 52 and intron 52) were used to allow the simultaneous amplification of different DMD loci and the SRY gender marker, in a single triplex-nested polymerase chain reaction (PCR). Aliquots of this reaction were then subjected to nested PCR in which each locus was amplified individually. Following the successful establishment of single-cell triplex-nested PCR in single leukocytes, the technique was employed in five clinical PGD cases.

RESULTS

For each DMD locus, more than 50 single leukocytes from healthy controls and more than 100 single leukocytes from affected individuals with known deletions were analyzed. Amplification efficiency for each tested locus was 98-100%. The false-negative rates for each analysis taken separately was <1%. Taken together, however, the results of the triplex-nested PCR analysis had a false-negative rate of 0%. No contamination was detected in all wash-drop blanks tested. We subsequently performed 18 PGD cycles in 5 DMD carriers. A total of 156 embryos were biopsied and successfully analyzed. Of these, 39 affected embryos were detected and 50 unaffected embryos were transferred (mean = 2.9 +/- 1.1 embryos per cycle). These resulted in three biochemical pregnancies and three clinical pregnancies, all of which have culminated in the birth of normal offspring.

CONCLUSION

Triplex-nested PCR using 2 of 11 DMD loci and the SRY gender marker allow PGD for >90% of DMD families with known deletions. These protocols are associated with a high amplification efficiency and accuracy.

Well-devised quantification analysis for duplication mutation of Duchenne muscular dystrophy aimed at preimplantation genetic diagnosis

PURPOSE

Preimplantation genetic diagnosis (PGD) has been performed for deletion and point mutation type of Duchenne muscular dystrophy (DMD). Our aim was to develop a PGD technique, not yet established, to directly detect duplication mutation instead of substitute diagnosis similar to gender determination.

METHODS

Our method is based on comparative quantification using conventional duplex PCR, real-time PCR and gender determination. We evaluated this method in single lymphocytes from a duplication type of DMD patient and a normal male.

RESULTS

There was a significant difference in the mean values of the ratios (the mutation locus/a normal reference): mean value +/- SE was 1.84 +/- 0.15 in the duplication patient, and 1.00 +/- 0.09 in the normal male (p < 0.001).

CONCLUSION

It is suggested that our comparative quantification method could be a new option in PGD for carriers with duplication mutation who wish to have an unaffected son.

Singleton births after routine preimplantation genetic diagnosis using exclusion testing (D4S43 and D4S126) for Huntington’s disease

OBJECTIVE

To develop exclusion testing protocols for Huntington's disease (HD) linkage markers suitable for use in a clinical preimplantation genetic diagnosis (PGD) setting for couples in whom a partner was at 50% risk of inheriting HD, but who choose not to undergo presymptomatic mutation testing.

DESIGN

Preimplantation genetic diagnosis using exclusion testing.

SETTING

In vitro fertilization clinic.

PATIENT(S)

Three couples with family histories of HD, two couples opposed to direct mutation testing.

INTERVENTION(S)

Development of single-cell polymerase chain reaction tests for PGD for the HD mutation and two HD gene-flanking markers (D4S43 and D4S126), allowing the identification of an individual embryo as being at either low or high risk for developing HD without being diagnostic of the presence of the mutation.

MAIN OUTCOME MEASURE(S)

D4S43, D4S126, and HD mutation.

RESULT(S)

After PGD for HD, couple 1 gave birth to a healthy girl after a frozen embryo transfer, and genetic status was confirmed by prenatal diagnosis to be very low risk for developing HD. Couple 2 gave birth to a healthy boy after their second cycle of PGD, and couple 3, after a third cycle, gave birth to a boy with congenital heart defects, which were successfully corrected with surgery at age 5 days. Both couples 2 and 3 declined prenatal testing, and therefore relinquished the opportunity to confirm the PGD.

CONCLUSION(S)

Preimplantation genetic diagnosis for HD using exclusion testing resulted in three live singleton births after six oocyte recovery procedures. The diagnostic protocol provided couples the opportunity to minimize the likelihood of disease transmission to their children, without the requirement for predictive testing.

Preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) was introduced at the beginning of the 1990s as an alternative to prenatal diagnosis, to prevent termination of pregnancy in couples with a high risk for offspring affected by a sex-linked genetic disease. At that time, embryos obtained in vitro were tested to ascertain their sex, and only female embryos were transferred. Since then, techniques for genetic analysis at the single-cell level, involving assessment of first and second polar bodies from oocytes or blastomeres from cleavage-stage embryos, have evolved. Fluorescence in-situ hybridisation (FISH) has been introduced for the analysis of chromosomes and PCR for the analysis of genes in cases of monogenic diseases. In-vitro culture of embryos has also improved through the use of sequential media. Here, we provide an overview of indications for, and techniques used in, PGD, and discuss results obtained with the technique and outcomes of pregnancies. A brief review of new technologies is also included.

Single cell multiplex PCR amplification of five dystrophin gene exons combined with gender determination

Large deletions in the dystrophin gene account for > 60% of mutations responsible for Duchenne muscular dystrophy (DMD). We have developed a genetic test that can be used directly for the preimplantation genetic diagnosis (PGD) of a majority of couples at risk of transmitting DMD. The test, a double nested multiplex polymerase chain reaction assay for the amplification of exons 8, 19, 45, 47 and 51 allows the detection of over 70% of all DMD deletions. Amelogenin sequences on the X and the Y chromosomes were also co-amplified to provide a correlation between embryo gender and deletion status. The setting up of reliable single cell assays for preimplantation genetic diagnosis is delicate and time consuming. Assays have to be validated on a large number of single cells for each specific mutation to assess efficiency and accuracy before being applied clinically. The multiplex procedure permitted the validation of all tested loci in the same series of isolated lymphocytes rather than in separate series for each exon. One hundred single lymphocytes, 50 female and 50 male cells, were analysed with an overall amplification rate of 98% and an amplification failure of 2% per exon. We suggest that this test is reliable, easy to set up and much preferable to a mere sex determination with the selective transfer of female embryos.