Distinguishing between carrier and noncarrier embryos with the use of long-read sequencing in preimplantation genetic testing for reciprocal translocations.

Balanced reciprocal translocation carriers are usually phenotypically normal but are at an increased risk of infertility, recurrent miscarriage or having affected children. Preimplantation genetic testing on chromosomal structural rearrangement (PGT-SR) offers a way to screen against unbalanced embryos. Here, we demonstrated a new method to distinguish carrier from noncarrier embryos. Translocation breakpoints were first delineated by nanopore sequencing followed by polymerase chain reaction (PCR) across breakpoints. High-resolution breakpoint mapping was successful in all (9/9) balanced reciprocal translocation carriers. Retrospective analysis of their embryo biopsies with breakpoint PCR showed 100% concordant results with PGT-SR on trophectoderm biopsies (40/40) and 53% concordance on blastomere biopsies (8/15). The low concordant rate in blastomeres was due to failure in the amplification of derivative chromosomes involving large deletions. Breakpoint PCR also showed 100% concordant results with prenatal/postnatal outcomes on 5 pregnancies, indicating that our new method can accurately distinguish carrier from noncarrier embryos.

High-resolution mapping of reciprocal translocation breakpoints using long-read sequencing.

Long-read nanopore sequencing enables direct high-resolution breakpoint mapping on balanced carriers of reciprocal translocation. The mean sequencing depth on the translocated chromosomes to achieve accurate mapping of breakpoints ranged from 2.5-fold to 6.2-fold. To speed up determination of the breakpoints from long-read sequencing data, alignment reads on the translocated chromosomes were extracted before piped into NanoSV. Checking the position of breakpoints on Interactive Genomics Viewer (IGV) was crucial to successful design of breakpoint PCR primers, especially when large deletion was involved at the breakpoints. •Long-read sequencing enables accurate breakpoint mapping with base-pair resolution•Splitting bam files by translocated chromosomes drastically speeded up the breakpoint determination•IGV helps to identify the breakpoint positions and facilitate the design of breakpoint PCR primers.

Evaluation of preimplantation genetic testing for chromosomal structural rearrangement by a commonly used next generation sequencing workflow.

OBJECTIVES: To evaluate the applicability of a commonly used next generation sequencing workflow in detecting unbalanced meiotic segregation products for reciprocal translocation and inversion carriers. STUDY DESIGN: All preimplantation genetic testing treatment cycles performed for reciprocal translocation or inversion carriers from 2012 to April 2017 were included. Three hundreds and forty-two archived whole genome amplified DNA, which had previously analyzed by array comparative genomic hybridization (aCGH), were retrospectively analyzed by next generation sequencing (NGS). Concordance on overall diagnosis and segmental aneuploidies related to the translocation/inversion breakpoints between aCGH and NGS were determined. RESULTS: Retrospective analysis of 287 blastomere biopsies and 55 trophectoderm (TE) biopsies showed that the concordance rate on the overall diagnosis between aCGH and NGS on abnormal samples was 100% (266/266), irrespective to the type of biopsy. The concordance rates of normal biopsies were 98.4% (61/62) on blastomere and 78.6% (11/14) on TE biopsies. NGS detected a de novo segmental aneuploidy on one blastomere biopsy and three possible low level mosaic aneuploidies on 3 TE biopsies, which were previously concluded as euploid by aCGH. Using the karyotype of reciprocal translocation/inversion carriers, size of anticipated segmental aneuploidies could be calculated and be used to predict the applicability of NGS before proceeding to treatment. CONCLUSION: This is the first report to evaluate the applicability of a commercial NGS-based workflow for preimplantation testing for reciprocal translocations/inversions. Our study demonstrated that NGS can diagnose unbalanced translocation/inversion products with the same efficiency as aCGH. The applicability of NGS, with respect to individual karyotype, can be predicted before proceeding to treatment.

Experience of more than 100 preimplantation genetic diagnosis cycles for monogenetic diseases using whole genome amplification and linkage analysis in a single centre.

OBJECTIVE: To report the outcomes of more than 100 cycles of preimplantation genetic diagnosis for monogenetic diseases. DESIGN: Case series. SETTING: Tertiary assisted reproductive centre in Hong Kong, where patients needed to pay for the cost of preimplantation genetic diagnosis on top of standard in-vitro fertilisation charges. PATIENTS: Patients undergoing preimplantation genetic diagnosis for monogenetic diseases at the Centre of Assisted Reproduction and Embryology, Queen Mary Hospital-The University of Hong Kong between 1 August 2007 and 30 April 2014 were included. INTERVENTIONS: In-vitro fertilisation, intracytoplasmic sperm injection, embryo biopsy, and preimplantation genetic diagnosis. MAIN OUTCOME MEASURES: Ongoing pregnancy rate and implantation rate. RESULTS: Overall, 124 cycles of preimplantation genetic diagnosis were initiated in 76 patients, 101 cycles proceeded to preimplantation genetic diagnosis, and 92 cycles had embryo transfer. The ongoing pregnancy rate was 28.2% per initiated cycle and 38.0% per embryo transfer, giving an implantation rate of 35.2%. There were 16 frozen-thawed embryo transfer cycles in which, following preimplantation genetic diagnosis, cryopreserved embryos were replaced resulting in an ongoing pregnancy rate of 37.5% and implantation rate of 30.0%. The cumulative ongoing pregnancy rate was 33.1%. The most frequent indication for preimplantation genetic diagnosis was thalassaemia, followed by neurodegenerative disorder and cancer predisposition. There was no misdiagnosis. CONCLUSIONS: Preimplantation genetic diagnosis is a reliable method to prevent couples conceiving fetuses severely affected by known genetic disorders, with ongoing pregnancy and implantation rates similar to those for in-vitro fertilisation for routine infertility treatment.

Comparison between fluorescent in-situ hybridisation and array comparative genomic hybridisation in preimplantation genetic diagnosis in translocation carriers.

OBJECTIVES: To compare the pregnancy outcome of the fluorescent in-situ hybridisation and array comparative genomic hybridisation in preimplantation genetic diagnosis of translocation carriers. DESIGN: Historical cohort. SETTING: A teaching hospital in Hong Kong. PATIENTS: All preimplantation genetic diagnosis treatment cycles performed for translocation carriers from 2001 to 2013. RESULTS: Overall, 101 treatment cycles for preimplantation genetic diagnosis in translocation were included: 77 cycles for reciprocal translocation and 24 cycles for Robertsonian translocation. Fluorescent in-situ hybridisation and array comparative genomic hybridisation were used in 78 and 11 cycles, respectively. The ongoing pregnancy rate per initiated cycle after array comparative genomic hybridisation was significantly higher than that after fluorescent in-situ hybridisation in all translocation carriers (36.4% vs 9.0%; P=0.010). The miscarriage rate was comparable with both techniques. The testing method (array comparative genomic hybridisation or fluorescent in-situ hybridisation) was the only significant factor affecting the ongoing pregnancy rate after controlling for the women's age, type of translocation, and clinical information of the preimplantation genetic diagnosis cycles by logistic regression (odds ratio=1.875; P=0.023; 95% confidence interval, 1.090-3.226). CONCLUSION: This local retrospective study confirmed that comparative genomic hybridisation is associated with significantly higher pregnancy rates versus fluorescent in-situ hybridisation in translocation carriers. Array comparative genomic hybridisation should be the technique of choice in preimplantation genetic diagnosis cycles in translocation carriers.

Array comparative genomic hybridization analyses of all blastomeres of a cohort of embryos from young IVF patients revealed significant contribution of mitotic errors to embryo mosaicism at the cleavage stage.

BACKGROUND: Embryos produced by in vitro fertilization (IVF) have a high level of aneuploidy, which is believed to be a major factor affecting the success of human assisted reproduction treatment. The aneuploidy rate of cleavage stage embryos based on 1-2 biopsied blastomeres has been well-reported, however, the true aneuploidy rate of whole embryos remain unclear because of embryo mosaicism. To study the prevalence of mosaicism in top quality IVF embryos, surplus embryos donated from young patients (aged 28-32) in the assisted reproduction program at Queen Mary Hospital, Hong Kong were used. METHODS: Thirty-six good quality day 2 embryos were thawed. Out of the 135 blastomeres in these embryos, 121 (89.6%) survived thawing. Twelve of these embryos without lysed blastomeres and which cleaved to at least seven cells after a 24-h culture were dissembled into individual blastomeres, which were analysed by array comparative genomic hybridization and microsatellite marker analysis by fluorescent PCR. RESULTS: Out of 12 day-3 embryos, 2 (16.7%) were normal, 3 (25%) were diploid/aneuploidy with <38% abnormality, 4 (33.3%) were diploid/aneuploidy mosaic with > =38% abnormality, and three (25%) were mosaic aneuploids. Conclusive chromosomal data were obtained from a high percentage of blastomeres (92.8%, 90/97). Microsatellite marker analysis performed on blastomeres in aneuploid embryos enabled us to reconstruct the chromosomal status of the blastomeres in each cleavage division. The results showed the occurrence of meiotic errors in 3 (25%) of the studied embryos. There were 16 mitotic errors (18.8%, 16/85) in the 85 mitotic divisions undertaken by the studied embryos. The observed mitotic errors were mainly contributed by endoreduplication (31.3%, 5/16), non-disjunction (25%, 4/16) and anaphase lagging (25%, 4/16). Chromosome breakages occurred in 6 divisions (7.1%, 6/85). CONCLUSIONS: Mosaicism occurs in a high percentage of good-quality cleavage stage embryos and mitotic errors contribute significantly to the abnormality.

Preimplantation genetic diagnosis using combined strategies on a breast cancer patient with a novel genomic deletion in BRCA2.

PURPOSE: To perform Preimplantation Genetic Diagnosis (PGD) on a paternal Brca2 unknown mutation carrier with early-onset breast cancer, whose paternal grandmother and mother had breast cancer at 60s. METHOD: Elucidating the linkage via single sperm haplotyping on patient's carrier brother, and identifying the genomic deletion via BLAST followed by PCR screening. PGD was subsequently conducted. RESULT: The mutant allele was found by using 4 microsatellite and 2 intragenic SNP markers. Recombination was detected in 8% of sperms. BLAST was utilized to locate putative hairpin structure(s), followed by PCR screening with seven sets of primers. A novel 2,596 bp deletion containing exon 15 ~ 16 was identified. Due to the severity of phenotype and the integrity of exon 11 encoding RAD51 binding domain, and the fact that the patient's mother also had breast cancer at her 60s, we speculate a possible coexistence of maternal breast cancer risk allele(s). Embryo biopsy was performed on day 3. Unaffected morula and blastocyst were replaced on day 5, resulting in a singleton livebirth. A breast lump appeared in the patient after delivery without the presence of malignant cells. CONCLUSION: Concerning the assisted reproductive option for breast cancer patients, the possibility of coexistence of multiple familial risk alleles and the significance of each mutation to the phenotype should be evaluated. To eliminate misdiagnosis resulting from recombination and/or allelic drop-out, both direct mutation detection and linkage analysis approaches may be necessary. BLAST is a very useful and cost-effective tool for identifying large genomic deletion.

Live birth following double-factor pre-implantation genetic diagnosis for both reciprocal translocation and alpha-thalassaemia.

We report a live birth from a couple with two genetic diseases, namely: reciprocal translocation carrier and alpha-thalassaemia trait, following pre-implantation genetic diagnostic tests. This is the first case in Hong Kong in which the technique of using one blastomere biopsy for two diseases was established, using array comparative genomic hybridisation and polymerase chain reaction.

Role of baseline antral follicle count and anti-Mullerian hormone in the index stimulation cycle of IVF treatment in predicting outcome of subsequent frozen-thawed embryo transfers.

This retrospective cohort study aims at determining whether baseline antral follicle count (AFC) and serum anti-Mullerian hormone (AMH) level in the index stimulation cycle predict live-birth outcome in subsequent frozen-thawed embryo transfer (FET) cycles. We studied 500 women undergoing the first IVF cycle who had embryo(s) cryopreserved. The main outcome measures were live-birth in the first FET cycle and cumulative live-birth in all the FETs combined after the same stimulation cycle. Our results showed that baseline AFC and AMH level on the day before ovarian stimulation showed significant correlation. In the first FET cycle, AFC and AMH level were significantly higher in subjects attaining live-birth in the first FET cycle or cumulative live-birth from all FETs than those who did not. Both AMH and AFC were insignificant predictors of live-birth in the first FET cycle or cumulative live-birth after adjusting for age. The areas under the ROC curves for AMH, AFC and age were 0.654, 0.625 and 0.628, respectively, for predicting cumulative live-birth. In conclusion, we reported for the first time that baseline AFC and AMH in the index stimulation cycle have only modest predictive performance on cumulative live-birth in subsequent FET cycles.

Live birth rate, multiple pregnancy rate, and obstetric outcomes of elective single and double embryo transfers: Hong Kong experience.

OBJECTIVE: To compare the live birth rate, multiple pregnancy rate, and obstetric outcomes of elective single and double embryo transfers. DESIGN: Case series with internal comparisons. SETTING: University affiliated hospital, Hong Kong. PARTICIPANTS: Between October 2009 and December 2011, 206 women underwent their first in-vitro fertilisation cycle. Elective single embryo transfer was offered to women who were aged 35 years or below, and had endometrial thickness of 8 mm or more and at least two embryos of good quality. MAIN OUTCOME MEASURES: Live birth rate, multiple birth rate, and obstetric outcomes. RESULTS: Among the 206 eligible women, 74 underwent an elective single embryo transfer and 132 a double embryo transfer. The live birth rate was comparable in the two groups, being 39.2% in the elective single embryo transfer group and 43.2% in the double embryo transfer group, while the multiple pregnancy rate was significantly lower in the elective single embryo transfer group than the double embryo transfer group (6.9% vs 40.4%; P<0.001). Gestational ages and birth weights were comparable in the two groups. There was no significant difference between the two groups with respect to the rate of preterm delivery and antenatal complications (27.6% vs 43.9%, respectively; P>0.05). CONCLUSION: In this selected population, an elective single embryo transfer policy decreases the multiple pregnancy rate without compromising the live birth rate. The non-significant difference in antenatal complications may be related to the small sample size.

Frozen-thawed embryo transfer cycles.

OBJECTIVE: To review the outcomes of frozen-thawed embryo transfer cycles. DESIGN. Retrospective review. SETTING: Tertiary assisted reproduction centre, Hong Kong. PATIENTS: Subfertile patients undergoing frozen-thawed embryo transfer between July 2005 and December 2007. MAIN OUTCOME MEASURES: Clinical and ongoing pregnancy rates. RESULTS: A total of 983 frozen-thawed embryo transfer cycles performed during the study period were reviewed. The clinical pregnancy and ongoing pregnancy rates were 35% and 30%, respectively. Factors associated with successful outcome included younger maternal age (<=35 years) and 4 or more blastomeres at replacement, but not the method of insemination, the cause of subfertility, or the type of frozen-thawed embryo transfer cycle. The overall multiple pregnancy rate was 18%. For cycles with a single embryo replaced, embryos having 4-cell or higher stages at replacement gave an ongoing pregnancy rate of 25%, whereas those with less than 4 cells had a significantly lower ongoing pregnancy rate of 5% only. Blastomere lysis after thawing significantly reduced the clinical pregnancy and ongoing pregnancy rates of cycles with one embryo replaced. CONCLUSIONS: Clinical pregnancy and ongoing pregnancy rates of frozen-thawed embryo transfer cycles were 35% and 30%, respectively. Higher pregnancy rates were associated with younger maternal age (<=35 years), blastomere numbers of 4 or more, and no blastomere lysis after thawing.

Singleton birth after preimplantation genetic diagnosis for Huntington disease using whole genome amplification.

OBJECTIVE: To report a successful case of preimplantation genetic diagnosis (PGD) for Huntington disease using whole genome amplification. DESIGN: Case report. SETTING: University assisted reproduction unit. PATIENT(S): A couple with family history of Huntington disease: The husband was carrying the expanded allele of the IT15 gene, and the wife had the normal allele. INTERVENTION(S): Preimplantation genetic diagnosis with whole genome amplification for identification of genetically normal embryos. MAIN OUTCOME MEASURE(S): Live birth. RESULT(S): In an IVF cycle, 15 oocytes were retrieved, of which 13 were mature and 11 were fertilized. On day 3, embryo biopsy and PGD were performed on ten good-quality embryos. Multiple displacement amplification was conducted, followed by polymerase chain reaction with fluorescence primers. Three pairs of primers were used for the amplification of the IT15 gene at the: 1) trinucleotide expansion site; 2) trinucleotide expansion site plus the polymorphic site situated on its 3'-end; and 3) polymorphic marker located downstream of the trinucleotide repeats. Two normal blastocysts were replaced on day 5 and another two good-quality blastocysts were cryopreserved. The woman gave birth to a normal baby girl whose normal genetic status was confirmed by prenatal diagnosis. CONCLUSION(S): Whole genome amplification by multiple displacement amplification can be used for PGD of Huntington disease.

Mitochondrial DNA deletion in granulosa and cumulus oophorus cells.

The incidence of the 4,977-bp deletion in mitochondrial DNA (DeltamtDNA4977) in 73 pairs of granulosa and cumulus oophorus cells was studied with polymerase chain reaction (PCR), and was significantly higher in granulosa cells (GC) (67/73, 91%) than in cumulus oophorus cells (17/73, 23.3%), independent of the donors' age. In the cumulus oophorus cells, the oocyte morphology, the ooplasma diameter, and the proportion of oocytes fertilized normally were comparable between those with and without DeltamtDNA4977; whereas the oocyte diameter and the zona thickness were significantly higher in those with DeltamtDNA4977.

A prospective, randomized, double-blind study to compare two doses of recombinant human chorionic gonadotropin in inducing final oocyte maturity and the hormonal profile during the luteal phase.

CONTEXT: Different doses of human chorionic gonadotropin (hCG) have been used in various in vitro fertilization (IVF) treatment protocols to achieve final oocyte maturation. There is as yet no agreement on the optimum dose required. OBJECTIVES: The objective of this study was to compare the effectiveness of 250 and 500 microg recombinant hCG (r-hCG), which represented the lower and upper limits of the dose range, in inducing final oocyte maturation during IVF and intracytoplasmic sperm injection cycles. DESIGN: This was a prospective, randomized, double-blind study. SETTING: This study was performed at an IVF clinic in a teaching hospital. PATIENTS: Sixty patients with an indication for intracytoplasmic sperm injection were studied. INTERVENTION: The treatment dose used was 250 or 500 microg r-hCG. MAIN OUTCOME MEASURES: The percentage of metaphase II oocytes retrieved per patient, as an indicator of oocyte maturation, and the hormone profiles of the treatment cycle starting from the day of hCG up to hCG+10 d were the main outcome measures. RESULTS: The percentage of metaphase II oocytes was similar in the two groups (89.3% vs. 86.0%; P = 0.326) despite higher serum and follicular fluid hCG levels on hCG+2 and hCG+4 d, as was the follicular fluid to serum hCG ratio in the 500-microg r-hCG group. Serum estradiol and progesterone levels were comparable initially, but became significantly higher in the 500-microg r-hCG group on hCG+10 d. CONCLUSION: The two doses of r-hCG were equally effective in inducing final oocyte maturation. It remains unclear whether the higher midluteal estradiol and progesterone levels in the 500-microg r-hCG group confer any benefit.

Bioavailability of hCG after intramuscular or subcutaneous injection in obese and non-obese women.

BACKGROUND: Obese women require higher gonadotrophin doses for ovarian stimulation and to trigger ovulation. The bioavailability of a drug is affected by its route of administration. Herein, the bioavailability of hCG was compared after intramuscular (i.m.) or subcutaneous (s.c.) injection in obese and non-obese women. METHODS: Twenty four Chinese women, 12 with a body mass index (BMI) >/==" BORDER="0">28 kg/m(2) and 12 with a BMI of 20-25 kg/m(2) were recruited as the obese and non-obese groups respectively. A single hCG injection was given intramuscularly on one occasion, and subcutaneously on a second occasion, separated by 4 weeks. Blood samples were taken at intervals for the pharmacokinetic study of hCG. RESULTS: Examination of the hCG plasma concentration-time curve showed the area under the curve (AUC) and maximum concentration (C(max)) of hCG to be significantly higher after i.m. injection than after s.c. injection in both the obese and non-obese groups. However, the AUC and C(max) values in obese women were significantly lower than in non-obese women, irrespective of whether i.m. or s.c. dosing was employed. CONCLUSIONS: Intramuscular dosing of hCG provided better bioavailability than s.c. dosing, but bioavailability was significantly less in obese women than in non-obese women.