Proband-independent haplotyping based on NGS-based long-read sequencing for detecting pathogenic variant carrier status in preimplantation genetic testing for monogenic diseases

Utilizing Long-Read Sequencing for Haplotype Construction and Prevention of Autosomal Dominant Polycystic Kidney Disease Transmission in Mosaicism Family

This study presents a case of autosomal dominant polycystic kidney disease (ADPKD) involving a mosaic microdeletion in the PKD1 gene and explores the application of long-read sequencing technologies for haplotype construction and preimplantation genetic testing (PGT). We report on a family where the proband was clinically diagnosed with PKD and found to have a partial deletion of the PKD1 gene because of the mosaic deletion mutation of PKD1 in the mother of the proband. Utilizing Oxford Nanopore long-read sequencing, we successfully constructed the haplotype of the deleted fragment region and identified an unaffected embryo for transplantation, resulting in a successful pregnancy. The prenatal genetic diagnosis confirmed the absence of deletion abnormalities in the fetus. Our findings underscore the significance of integrating advanced genomic technologies into clinical practice for PGT in ADPKD, particularly in cases involving partial deletion of X chromosome mosaic embryo transferred or complex structural variants. This approach not only prevents the transmission of ADPKD but also demonstrates the utility of long-read sequencing in overcoming the limitations of traditional PGT methods. Further research is warranted to evaluate the broader application of long-read sequencing for other monogenic disorders and to refine these techniques for enhanced diagnostic precision and clinical outcomes.

Reproductive Choices in Haemoglobinopathies: The Role of Preimplantation Genetic Testing

Haemoglobinopathies are among the most prevalent genetic disorders globally. In the context of these conditions, preimplantation genetic testing (PGT) plays a pivotal role in preventing genetic diseases in the offspring of carrier parents, reducing the need for pregnancy termination and enabling the selection of compatible sibling donors for potential stem cell transplantation in cases of thalassemia or sickle cell disease. This review explores the evolving role of PGT as a reproductive option for haemoglobinopathy carriers, tracing the development of PGT protocols from patient-specific to comprehensive testing enabled by advanced technologies like next-generation sequencing (NGS). We discuss key technical, biological, and practical limitations of PGT, as well as the ethical considerations specific to haemoglobinopathies, such as the complexity of interpreting genotypes. Emerging technologies, such as whole-genome sequencing, non-invasive PGT, and gene editing, hold significant promise for expanding applications but also raise new challenges that must be addressed. It will be interesting to explore how advancements in technology, along with the changing management of haemoglobinopathies, will impact reproductive choices. It is anticipated that continued research will improve genetic counseling for PGT for haemoglobinopathies, while a careful evaluation of ethical and societal implications is also required. Responsible and equitable implementation of PGT is essential for ensuring that all families at risk can make informed reproductive choices.

Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells

Long-read whole-genome sequencing (lrWGS) enhances haplotyping by providing more phasing information per read compared to short-read sequencing. However, its use for single-cell haplotype phasing remains underexplored. This proof-of-concept study examines lrWGS data from single cells for small variant (single nucleotide variant (SNV) and indel) and structural variation (SV) calling, as well as haplotyping, using the Genome in a Bottle (GIAB) Ashkenazi trio. lrWGS was performed on single-cell (1 cell) and multi-cell (10 cells) samples from the offspring. Chromosome-length haplotypes were obtained by leveraging both long reads and pedigree information. These haplotypes were further refined by replacing them with matched parental haplotypes. In single-cell and multi-cell samples, 92% and 98% of heterozygous SNVs, and 74% and 78% of heterozygous indels were accurately haplotyped. Applied to human embryos for preimplantation genetic testing (PGT), lrWGS demonstrated 100% consistency with array-based methods for detecting monogenic disorders, without requiring phasing references. Aneuploidies were accurately detected, with insights into the mechanistic origins of chromosomal abnormalities inferred from the parental unique allele fractions (UAFs). We show that lrWGS-based concurrent haplotyping and aneuploidy profiling of single cells provides an alternative to current PGT methods, with applications potential in areas such as cell-based prenatal diagnosis and animal and plant breeding.

ViLR: a novel virtual long read method for breakpoint identification and direct SNP haplotyping in de novo PGT-SR carriers without a proband

BACKGROUND

Despite the gradual application of third-generation long read sequencing (LRS) or reference embryo establishment to preimplantation genetic testing for structural rearrangement (PGT-SR) without familial involvement, there are still limitations to their extensive clinical application yet. This study developed a novel virtual NGS-based long read method (ViLR) and preliminarily evaluated its clinical feasibility of breakpoint characterization and direct SNP haplotyping for de novo chromosomal structural rearrangements (CSR).

METHODS

A total of 10 families with de novo CSR risk were enrolled in this study for ViLR analysis. In contrast to LRS, ViLR is a virtual long read solution that used the same barcoded labeling and assembly of different long gDNAs differently barcoded. Notably, ViLR could generate an average fragment length of over 30 Kb, with an N50 block size of up to 16 Mb in a single assay, allowing to achieve accurate breakpoint mapping and direct carrier's haplotyping. An approximately 2 Mbp region flanking upstream and downstream of each breakpoint was selected for informative SNP collection. Embryo haplotype determination was based on the established carriers' haplotypes after whole genome amplification and sequencing. To confirm PGT-SR results, we performed prenatal genetic diagnosis.

RESULTS

This study achieved an average mapping rate of 99.5%, > 90% coverage depth (> 10X), an average number of effective barcode (> 5 kb length) counts of 11,000,000 and an average fragment length of 40 kb, which generated sufficient informative SNPs for breakpoint characterization and haplotype phasing. ViLR analysis of 10 de novo PGT-SR carriers precisely identified breakpoints and haplotypes. Seven families obtained 18 euploid embryos, in which 10 were euploid/normal embryos, 7 were euploid/balanced carrier embryos, and the remaining one unknown was due to homologous recombination of the breakpoint region. Prenatal genetic diagnosis was performed for four women, and the outcomes coincided with the results from embryo PGT-SR. At the time of writing this paper, four healthy babies had been delivered uneventfully.

CONCLUSION

Here, we demonstrated the clinical potential of ViLR as a novel solution for breakpoint identification and direct SNP haplotyping in de novo PGT-SR families without proband involvement.

CLINICAL TRIAL NUMBER

Not applicable.

A precise and cost-efficient whole-genome haplotyping method without probands: preimplantation genetic testing analysis

RESEARCH QUESTION

Is there a precise and efficient haplotyping method to expand the application of preimplantation genetic testing (PGT)?

DESIGN

In this study, eight cell-line families and 18 clinical families including 99 embryos were used to construct whole-genome haplotyping based on link-read sequencing (Phbol-seq) and optimized analytical workflow with a correction algorithm. The correction algorithm was based on a differentiation of assembly errors and homologous recombination, in which the main feature of parental assembly error was that all embryos (embryo number ≥2) had breakpoints at the same chromosome position.

RESULTS

With Phbol-seq, parental assembly errors and homologous recombination were accurately distinguished and corrected. Using the link-reads (>25% long-reads were ≥30 kilobases [kb]), complete genome-wide parental haplotypes were constructed, and the consistency of the typing results of each chromosome with a conventional method requiring other family members was more than 95%. In addition, the length of N50 contigs was 11.03-16.2 million bases (mb), which was far beyond the N50 contigs from long-read sequencing (148-863 kb). The complete haplotype analysis of all embryos could be performed by Phbol-seq and revealed 100% concordance with the available diagnostic results obtained by the conventional method requiring other family members.

CONCLUSIONS

Phbol-seq has high clinical value as a precise and cost-efficient whole-genome haplotyping method without probands as part of PGT and other genetic research, which could promote the application of PGT to decrease the birth of children with genetic diseases and the development of linkage-related genetic research.

The current clinical applications of preimplantation genetic testing (PGT): acknowledging the limitations of biology and technology

INTRODUCTION

Preimplantation Genetic Testing (PGT) is a cutting-edge test used to detect genetic abnormalities in embryos fertilized through Medically Assisted Reproduction (MAR). PGT aims to ensure that embryos selected for transfer are free of specific genetic conditions or chromosome abnormalities, thereby reducing chances for unsuccessful MAR cycles, complicated pregnancies, and genetic diseases in future children.

AREAS COVERED

In PGT, genetics, embryology, and technology progress and evolve together. Biological and technological limitations are described and addressed to highlight complexity and knowledge constraints and draw attention to concerns regarding safety of procedures, clinical validity, and utility, extent of applications and overall ethical implications for future families and society.

EXPERT OPINION

Understanding the genetic basis of diseases along with advanced technologies applied in embryology and genetics contribute to faster, cost-effective, and more efficient PGT. Next Generation Sequencing-based techniques, enhanced by improved bioinformatics, are expected to upgrade diagnostic accuracy. Complicating findings such as mosaicism, mt-DNA variants, variants of unknown significance, or variants related to late-onset or polygenic diseases will however need further appraisal. Emphasis on monitoring such emerging data is crucial for evidence-based counseling while standardized protocols and guidelines are essential to ensure clinical value and respect of Ethical, Legal and Societal Issues.