Hidehito Inagaki

OBJECTIVE: Myotonic dystrophy type 1 (DM1) is an autosomal dominant neurodevelopmental disorder caused by CTG repeat expansion in the DMPK gene. Although the clinical classification of DM1 is determined by the CTG repeat length in DMPK, conventional sizing relies on Southern blotting, which is a suboptimal method in prenatal and PGD contexts as it requires large amounts of genomic DNA. We here evaluated the utility of nanopore long read sequencing (LRS) for DM1 diagnosis in these contexts. METHOD: LRS was performed with adaptive sampling or CRISPR/Cas9-mediated enrichment targeting DMPK. The use of whole genome amplified DNA (WGA-DNA) prepared with RepliG was also assessed. RESULTS: Adaptive sampling and Cas9-based LRS enabled detection of both the normal and expanded alleles. Further, LRS with CRISPR/Cas9-mediated enrichment improved efficiency and enabled accurate sizing of expanded CTG repeats exceeding 1000 units. In contrast, the use of whole genome amplified DNA prepared with RepliG did not permit reliable CTG repeat sizing, even when combined with adaptive sampling or CRISPR/Cas9. CONCLUSION: Nanopore sequencing can potentially replace Southern blotting for prenatal DM1 diagnosis, including repeat sizing. However, further improvement is needed for PGD using WGA-DNA.

INTRODUCTION: Alternative RNA splicing adds diverse variations to gene function, and its abnormalities are occasionally associated with the etiology of disease. We examined this possibility in pre-eclampsia. METHODS: We performed transcriptome analysis of placentas from pre-eclamptic and normotensive pregnancies and screened for disease-specific aberrant splicing. RESULTS: We identified aberrant splicing at exon 14 in the ZC3H4 gene. This in-frame exon is generally skipped in placentas from normal pregnancies but often observed in those from pre-eclampsia patients. The level of exon inclusion did not correlate with disease severity, such as blood pressure or fetal weight, but showed an association with the decrease in placental weight. Significantly, placental blood flow resistance measured by Doppler ultrasound correlated with the level of ZC3H4 exon 14 inclusion, suggesting that this retention leads to the onset and/or symptoms of pre-eclampsia. ZC3H4 is known to act on transcriptional regulation via suppression of lncRNA expression. Moreover, the SOD1 gene, encoding superoxide dismutase that eliminates toxic free superoxide radicals, was identified in the downstream gene group for ZC3H4. Indeed, the expression of SOD1 was found in this current study to be decreased in the pre-eclamptic placenta in correlation with the levels of ZC3H4 exon 14 retention. DISCUSSION: Aberrant splicing of ZC3H4 gene may induce excessive oxidative stress in the placenta via the downregulation of downstream SOD1 expression thereby leading to the onset and development of pre-eclampsia.

It is occasionally necessary to distinguish balanced reciprocal translocations from normal diploidy since balanced carriers can have reproductive problems or manifest other disease phenotypes. It is challenging to do this however using next generation sequencing (NGS) or microarray-based preimplantation genetic testing (PGT). In this study, discarded embryos were harvested from balanced reciprocal translocation carriers intending PGT that were determined to be unsuitable for transfer due to unbalanced translocations or translocation-unrelated aneuploidy. Two trophoectoderm biopsy samples were obtained from each single embryo. Whole genome amplification (WGA) was performed either by looping-based amplification (LBA) or multiple displacement amplification (MDA). NGS-based copy number variation (CNV) analysis as well as translocation-specific PCR was performed for each. We used embryo samples from t(8;22)(q24.13;q11.2) and t(11;22)(q23;q11.2) carriers since they are recurrent constitutional translocations that have nearly identical breakpoints even among independent unrelated families. CNV analysis was generally consistent between the two WGA methods. Translocation-specific PCR allowed us to detect each derivative chromosome in the MDA WGA samples but not with the LBA method, presumably due to coverage bias or the shorter sized WGA products. We successfully distinguished balanced reciprocal translocations from normal diploidy in normal samples with CNV analysis. A combination of CNV analysis and translocation-specific PCR using MDA-amplified WGA product can distinguish between balanced reciprocal translocation and normal diploidy in preimplantation genetic testing for structural rearrangements (PGT-SR).

Long-read sequencers are known for their effectiveness in detecting genomic structural variations (SV) and are becoming a standard approach for comprehensive genetic analysis. In preimplantation genetic testing (PGT) for SV carriers, information on breakpoint junctions is required to determine the carrier status in embryo selection. Long-read sequencers are employed for SV cases that are difficult to analyze with conventional cytogenetical methods and the detailed SV junction information they provide yields valuable insights. They can also analyze the single-nucleotide variations (SNVs) that surround SVs and thus provide further information on the carrier status for embryo selection. Despite these advantages of long-read sequencers however, they are prone to inaccuracy and have high testing costs. This review summarizes the advanced applications of long-read sequencers currently in preclinical workups and their integration into PGT. It also presents in-house clinical cases that highlight long-read sequencing in practice and discusses the prospects for this field.