The uncertainty of copy number variants: pregnancy decisions and clinical follow-up.

BACKGROUND: Next-generation sequencing for copy number variants is often used as a follow-up investigation of unusual fetal ultrasound results and is capable of detecting copy number variations with a resolution of ∼0.1 Mb. In a prenatal setting, observation and subsequent management of pregnancies with a fetal variant of uncertain significance remains problematic for counseling. OBJECTIVE: This study aimed to follow the decision-making processes in pregnancies with a fetal variant of uncertain significance and prospectively assess copy number variation interpretations and implications under the newer 2020 American College of Medical Genetics and Genomics guidelines. STUDY DESIGN: In a single prenatal unit, prospective chromosome testing using copy number variation sequencing for 8030 fetuses with unexpected noninvasive findings identified 139 pregnancies with a copy number variation classified as a variant of uncertain significance according to the 2015 American College of Medical Genetics and Genomics guidelines current at the time. Parent-of-origin testing was subsequently performed to determine if the copy number variation was inherited or de novo. All couples were offered specialized genetic counseling to assist in pregnancy management decisions. For the continued pregnancies that reached term, newborns were clinically assessed for evidence of any disease at 0 to 10 months and/or at 2 to 4 years of age. RESULTS: Of the 139 variants of uncertain significance found, most (78%) were inherited with no evidence of disease in the carrier parent. On the basis of primary ultrasound findings combined with results from noninvasive prenatal screening tests, most inherited variant of uncertain significance pregnancies were continued, whereas most pregnancies involving de novo variants of uncertain significance were terminated. From clinical follow-up of the 113 live births, only 5 showed any evidence of a phenotype that was not apparently related to the original variant of uncertain significance. Prospective reanalysis of the 139 variants of uncertain significance using recent 2020 American College of Medical Genetics and Genomics guidelines changed the status of 24 variants of uncertain significance, with 15 reclassified as benign and 9 as pathogenic. However, the 5 children born with an inherited variant of uncertain significance reclassified as pathogenic showed no evidence of a disease phenotype on clinical follow-up. CONCLUSION: The severity of fetal ultrasound findings combined with results from parent-of-origin testing were the key drivers in pregnancy management decisions for patients. According to birth outcomes from continued pregnancies, most variants of uncertain significance proved to be apparently benign in nature and potentially of low risk of adverse disease outcome. There was a discordance rate of 17% for variant of uncertain significance scoring between the 2015 and 2020 American College of Medical Genetics and Genomics guidelines for defining a variant of uncertain significance, suggesting that difficulties remain for predicting true pathogenicity. Nonetheless, with increasing knowledge of population copy number variation polymorphisms, and a more complete assessment for alternative genetic causes, patients having prenatal assessments should feel less anxious when a fetal variant of uncertain significance is identified.

Variant haplophasing by long-read sequencing: a new approach to preimplantation genetic testing workups.

OBJECTIVE: To apply long-read, third-generation sequencing as a part of a general workup strategy for performing structural rearrangement (PGT-SR) and monogenic disease (PGT-M) embryo testing. DESIGN: Prospective study. SETTING: In vitro fertilization unit. PATIENT(S): Couples presenting for PGT-SR (n = 15) and PGT-M (n = 2). INTERVENTION(S): Blastocyst biopsy with molecular testing for translocation breakpoints or mutations (targets). MAIN OUTCOME MEASURE(S): Detailed, parental-phased, single-nucleotide polymorphism (SNP) profiles around targets for selection of informative polymorphic markers to simplify and facilitate clinical preimplantation genetic testing (PGT) designs that enable discrimination between carrier and noncarrier embryos. RESULT(S): High definition of chromosome breakpoints together with closely phased polymorphic markers was achieved for all 15 couples presenting for PGT-SR. Similarly, for the two couples presenting for PGT-M, tightly linked informative markers around the mutations were also simply identified. Three couples with translocations t(1;17)(q21;p13), t(3;13)(p25;q21.2), and t(12;13)(q23;q22) proceeded with PGT-SR, requesting preferential identification of noncarrier embryos for transfer. Following selection of a set of informative SNPs linked to breakpoints, we successfully performed PGT-SR tests, resulting in ongoing pregnancies with a noncarrier fetus for all couples. Similarly, with the use of tests based on informative SNPs linked to the parental mutations, one couple proceeded with PGT-M for maple syrup urine disease, resulting in an ongoing pregnancy with a disease-free fetus. CONCLUSION(S): For couples contemplating clinical PGT, variant haplophasing around the target reduces the workup process by enabling rapid selection of closely linked informative markers for patient-specific test design.

Third-generation sequencing: any future opportunities for PGT?

PURPOSE: To investigate use of the third-generation sequencing (TGS) Oxford Nanopore system as a new approach for preimplantation genetic testing (PGT). METHODS: Embryos with known structural variations underwent multiple displacement amplification to create fragments of DNA (average ~ 5 kb) suitable for sequencing on a nanopore. RESULTS: High-depth sequencing identified the deletion interval for the relatively large HBA1/2--SEA alpha thalassemia deletion. In addition, STRs were able to be identified in the primary sequence data for potential use in conventional PGT-M linkage confirmation. Sequencing of amplified embryo DNA carrying a translocation enabled balanced embryos to be identified and gave the precise identification of translocation breakpoints, offering the opportunity to differentiate carriers from non-carrier embryos. Low-pass sequencing gave reproducible profiles suitable for simple identification of whole-chromosome and segmental aneuploidies. CONCLUSION: TGS on the Oxford Nanopore is a possible alternative and versatile approach to PGT with potential for performing economical workups where the long read sequencing information can be used for assisting in a traditional PGT workup to design an accurate and reliable test. Additionally, application of TGS has the possibility of providing combined PGT-A/SR or in selected stand-alone PGT-M cases involving pathogenic deletions. Both of these applications offer the opportunity for simultaneous aneuploidy detection to select either balanced embryos for transfer or additional carrier identification. The low cost of the instrument offers new laboratories economical entry into onsite PGT.

Single-Molecule Sequencing: A New Approach for Preimplantation Testing and Noninvasive Prenatal Diagnosis Confirmation of Fetal Genotype.

We investigated the potential of next-generation sequencing (NGS) as an alternative method for preimplantation genetic testing of monogenic disease (PGT-M) with human leukocyte antigen (HLA) matching and for noninvasive prenatal diagnosis follow-up. The case involved parents who were carriers of the Fanconi anemia complementation group G (FANCG) 260delG mutation. After clinical PGT using conventional short tandem repeat and mutation analysis, two euploid disease-free embryos were transferred, resulting in a twin pregnancy. Using the original embryo whole genome amplification products from 10 embryos, NGS confirmed the genotypes of the eight nontransferred embryos for both mutation status and HLA combination. NGS also confirmed that the two transferred embryos, which resulted in a twin pregnancy, were euploid, Fanconi disease free, and HLA matched to their sick sibling. At 15 weeks' gestation, noninvasive prenatal diagnosis of the maternal cell-free DNA determined fetal fractions of 14% and 6.6% for twins 1 and 2, respectively. The maternal plasma FANCG 260delG mutation ratio was measured at 46.2%, consistent with the presence of a carrier fetus and a normal fetus. These findings provide proof of concept that NGS has clinical utility as a safe and effective PGT-M method for embryo genotyping as well as more complex direct HLA matching. In addition, NGS can be used to confirm the original PGT-M and HLA matching embryo results in early pregnancy without the need for invasive prenatal diagnosis.

Clinical application of single-molecule optical mapping to a multigeneration FSHD1 pedigree.

INTRODUCTION: Facioscapulohumeral muscular dystrophy 1 (FSHD1) is a relatively common autosomal dominant adult muscular dystrophy with variable disease penetrance. The disease is caused by shortening of a D4Z4 repeat array located near the telomere of chromosome 4 at 4q35. This causes activation of a dormant gene DUX4, permitting aberrant DUX4 expression which is toxic to muscles. Molecular diagnosis of FSHD1 by Southern blot hybridization or FISH combing is difficult and time consuming, requiring specialist laboratories. As an alternative, we apply a novel approach for the diagnosis of FSHD1 utilizing single-molecule optical mapping (SMOM). METHODS: Long DNA molecules with BssS1 enzyme marking were subjected to SMOM on the Bionano Genomics platform to determine the number of D4Z4 repeats. Southern blot and molecular combing were used to confirm the FSHD1 haplotypes. RESULTS: In a study of a five-generation FSHD1 pedigree, SMOM correctly diagnosed the disease and normal haplotypes, identifying the founder 4qA disease allele as having 4 D4Z4 repeat units. Southern blot and molecular combing analysis confirmed the SMOM results for the 4qA disease and 4qB nondisease alleles. CONCLUSION: Based on our findings, we propose that SMOM is a reliable and accurate technique suitable for the molecular diagnosis of FSHD1.

Preferential selection and transfer of euploid noncarrier embryos in preimplantation genetic diagnosis cycles for reciprocal translocations.

OBJECTIVE: To develop and validate a new strategy to distinguish between balanced/euploid carrier and noncarrier embryos in preimplantation genetic diagnosis (PGD) cycles for reciprocal translocations and to successfully achieve a live birth after selective transfer of a noncarrier embryo. DESIGN: Retrospective and prospective study. SETTING: In vitro fertilization (IVF) units. PATIENT(S): Eleven patients undergoing mate pair sequencing for identification of translocation breakpoints, followed by clinical PGD cycles. INTERVENTION(S): Embryo biopsy with 24-chromosome testing to determine carrier status of balanced/euploid embryos. MAIN OUTCOME MEASURE(S): Definition of translocation breakpoints and polymerase chain reaction (PCR) diagnostic primers, correct diagnosis of euploid embryos for carrier status, and a live birth with a normal karyotype after transfer of a noncarrier embryo. RESULT(S): In 9 of 11 patients (82%), translocation breakpoints were successfully identified. In four patients with a term PGD pregnancy established with a balanced/euploid embryo of unknown carrier status, the correct carrier status was retrospectively determined, matching with the cytogenetic karyotype of the resulting newborns. In a prospective PGD cycle undertaken by a patient with a 46,XY,t(7;14)(q22;q24.3) translocation, the four balanced/euploid embryos identified comprised three carriers and one noncarrier. Transfer of the noncarrier embryo resulted in birth of a healthy girl who was subsequently confirmed with a normal 46,XX karyotype. CONCLUSION(S): The combination of mate pair sequencing and PCR breakpoint analysis of balanced reciprocal translocation derivatives is a novel, reliable, and accurate strategy for distinguishing between carrier and noncarrier balanced/euploid embryos. The method has potential application in clinical PGD cycles for patients with reciprocal translocations or other structural rearrangements.

Prenatal diagnosis of chromosomal mosaicism in over 1600 cases using array comparative genomic hybridization as a first line test.

OBJECTIVE: The aim of this study was to assess the detection of chromosomal mosaicism in chorionic villus (CVS) and amniotic fluid (AF) samples using array comparative genomic hybridization (aCGH) and quantitative fluorescent polymerase chain reaction. METHODS: All patients undergoing invasive prenatal testing by aCGH at a specialist prenatal screening service were included in the study. A total of 1609 samples (953 CVS and 656 AF) underwent quantitative fluorescent polymerase chain reaction and targeted aCGH without concurrent conventional G-banded karyotyping. RESULTS: Chromosomal mosaicism was detected in 20 of the 1609 cases (1.24%); of which 17 were derived from 953 CVS (1.78%), and three from 656 AF (0.46%). Mosaicism was observed at a level as low as 9%. Four cases were likely confined placental mosaicism, 12 were likely true fetal mosaicism, and four cases were unable to be classified into either group. CONCLUSIONS: This study demonstrates that the use of aCGH as a first line test is able to identify chromosomal mosaicism down to 9%, which is lower than the level reliably detected using standard cytogenetic analysis. aCGH avoids the disadvantages of culturing, which include culture bias, artifact, and culture failure.

The genetic screening of preimplantation embryos by comparative genomic hybridisation.

Comparative genomic hybridization (CGH) is an indirect DNA-based test which allows for the accurate analysis of aneuploidy involving any of the 24 types of chromosomes present (22 autosomes and the X and Y sex chromosomes). Traditionally, embryos have been screened using fluorescence in situ hybridization (FISH)--a technique that was limited in the number of chromosomes able to be identified in any one sample. Early CGH reports on aneuploidy in preimplantation embryos showed that any of the 24 chromosomes could be involved and so FISH methods were going to be ineffective in screening out abnormal embryos. Our results from routine clinical application of array CGH in preimplantation genetic diagnosis (PGD) patients confirm previous reports on patterns of chromosomal contribution to aneuploidy. The pregnancy outcomes following embryo transfer also indicate that despite the requirement to freeze embryos, rates are encouraging, and successful ongoing pregnancies can be achieved.

What next for preimplantation genetic screening (PGS)? Experience with blastocyst biopsy and testing for aneuploidy.

Blastocysts more commonly have a normal karyotype than cleavage-stage embryos do. Moreover, blastocysts have also made a metabolic transition from catabolism and recycling of the oocyte's reserves and resources, processes that fuel the first 3 days of cleavage. Although not all blastocysts are karyotypically equal, it is still to be determined to what extent a mosaic karyotype might be a normal feature among embryos, both at the cleavage stage and the blastocyst stage--and when looking for karyotypic abnormalities by embryo biopsy might help the chance of implantation rather than harm it. It is also still impractical to look at all the chromosomes that can, through their aneuploidy, stand in the way of successful embryonic and fetal development. We report a randomized clinical trial of blastocyst biopsy followed by preimplantation genetic screening (PGS) for aneuploidy using 5-colour FISH. The trial was suspended and then terminated early when we were unable to show an advantage for PGS. If we are correct in assuming that mitotic non-disjunction is common by the stage of the blastocyst (and that it is much less ominous than meiotic non-disjunction), then further studies of effective PGS of blastocysts for aneuploidy require methods of analysis that cover all the chromosomes and can differentiate the triallelic and monoallelic states of meiotically derived aneuploidies from the biallelic state of mitotic aneuploidies.

Pregnancies and live births after trophectoderm biopsy and preimplantation genetic testing of human blastocysts.

OBJECTIVE: To compare multiple-cell trophectoderm biopsy for preimplantation genetic diagnosis (PGD) from day-5 blastocysts with previously published experience with day-3 cleavage-stage embryos. DESIGN: Retrospective review of laboratory and clinical experience. SETTING: Sydney IVF, a private clinic in Australia. PATIENT(S): Preimplantation genetic diagnosis (PGD) patients age < 44 years with at least one IVF blastocyst suitable for biopsy, recruited from January 2002 through August 2004. INTERVENTION(S): Biopsy of trophectoderm from blastocysts on day 5 or 6, with same-day PGD for mutation testing, translocation testing, aneuploidy screening or sex selection. Spare, normal biopsied blastocysts were cryostored for possible later transfer. MAIN OUTCOME MEASURE(S): Fetal heart-positive pregnancy rate and accumulating live birth rate after adding results from biopsied fresh and frozen blastocysts for particular couples. RESULT(S): In 231 started PGD treatment cycles, unambiguous results were obtained from 974 of 1,050 biopsied blastocysts (93%); all blastocysts survived the biopsy procedure by reconstitution of their blastocele. One hundred nineteen women (median age, 36 years) have had 127 blastocysts transferred fresh (fetal heart-positive implantation rate, 41%). Of 146 blastocysts cryostored, 27 have been thawed (all with > 50% cell survival) and 24 transferred (implantation rate, 26%). To date, 53 pregnancies have been delivered or are ongoing, with an additional 4 clinical miscarriages (7%) and 6 subclinical miscarriages (total miscarriage rate, including biochemical pregnancies, 16%). There were no twin pregnancies. CONCLUSION(S): With technically appropriate blastocyst culture and freezing, blastocyst biopsy and cryostorage and later transfer of biopsied blastocysts is shown to be a practical and probably preferable path to preimplantation genetic testing of embryos compared with cleavage-stage embryo biopsy, being accompanied by a high implantation rate (and hence more conducive to elective single embryo transfer) and by a low rate of twinning and miscarriage.

Moving to blastocyst biopsy for preimplantation genetic diagnosis and single embryo transfer at Sydney IVF.

Developments at Sydney IVF in the successful culture of blastocysts, combined with day 5 or 6 blastocyst biopsy and blastocyst cryostorage after biopsy, permit up to five or six cells to be genetically tested, leaving the inner cell mass intact and enabling embryos to be electively transferred one at a time. These advantages can be obtained without diminishing the chance of pregnancy compared with cleavage-stage biopsy and testing.