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

Chow, Judy F.C.; Cheng, Heidi H.Y.; Lau, Esther Yuet Ying; Yeung, William S.B.; Ng, Ernest H.Y.

doi:10.1016/j.ygeno.2019.04.001

Cited by 36 publications

(37 citation statements)

References 27 publications

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“…This RT was located in a repetitive region, showing the limitations of short read sequence data, as short reads are not able to span repeats. On the other hand, long read sequencing is emerging as a strong technique for detection of RT in complex regions (10,11).…”

Section: Discussionmentioning

confidence: 99%

“…Currently, there are three types of sequence data that have been used for balanced RT detection in humans: long read, linked-read, and short read sequence data. Long read sequencing is a rather expensive technique at the moment, but has been most successful at detection of complex rearrangements and breakpoints located in repetitive elements, as well as for simple RT (10,11). Short reads sequencing is relatively cheap and performs well at detecting simple rearrangements (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Using Short Read Sequencing to Characterise Balanced Reciprocal Translocations in Pigs

Bouwman

Derks

Broekhuijse

et al. 2020

Preprint

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Background A balanced constitutional reciprocal translocation (RT) is a mutual exchange of terminal segments of two non-homologous chromosomes without any loss or gain of DNA in germline cells. Carriers of balanced RTs are viable individuals with no apparent phenotypical consequences. These animals produce, however, unbalanced gametes and show therefore reduced fertility and offspring with congenital abnormalities. This cytogenetic abnormality is usually detected using chromosome staining techniques. The aim of this study was to test the possibilities of using paired end short read sequencing for detection of balanced RTs in boars and investigate their breakpoints and junctions.Results Balanced RTs were recovered in a blinded analysis, using structural variant calling software DELLY, in 6 of the 7 carriers with 30 fold short read paired end sequencing. In 15 non-carriers we did not detect any RTs. Reducing the coverage to 20 fold, 15 fold and 10 fold showed that at least 20 fold coverage is required to obtain good results. One RT was not detected using the blind screening, however, a highly likely RT was discovered after unblinding. This RT was located in a repetitive region, showing the limitations of short read sequence data. The detailed analysis of the breakpoints and junctions suggested three junctions showing microhomology, three junctions with blunt-end ligation, and three micro-insertions at the breakpoint junctions. The RTs detected also showed to disrupt genes.Conclusions We conclude that paired end short read sequence data can be used to detect and characterize balanced reciprocal translocations, if sequencing depth is at least 20 fold coverage. However, translocations in repetitive areas may require large fragments or even long read sequence data.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Using Short Read Sequencing to Characterise Balanced Reciprocal Translocations in Pigs

Bouwman

Derks

Broekhuijse

et al. 2020

Preprint

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“…The direct detection of complex and/or larger gene rearrangements has so far been difficult since the exact breakpoints of the rearrangement are frequently unknown. High-resolution characterization of breakpoints located outside highly repetitive regions is now achievable with long-read nanopore sequencing [52].…”

Section: Pgt-m For De Novo Pathogenic Variantsmentioning

confidence: 99%

Preimplantation Genetic Testing for Monogenic Disorders

Rycke

Berckmoes

2020

Genes

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Preimplantation genetic testing (PGT) has evolved into a well-established alternative to invasive prenatal diagnosis, even though genetic testing of single or few cells is quite challenging. PGT-M is in theory available for any monogenic disorder for which the disease-causing locus has been unequivocally identified. In practice, the list of indications for which PGT is allowed may vary substantially from country to country, depending on PGT regulation. Technically, the switch from multiplex PCR to robust generic workflows with whole genome amplification followed by SNP array or NGS represents a major improvement of the last decade: the waiting time for the couples has been substantially reduced since the customized preclinical workup can be omitted and the workload for the laboratories has decreased. Another evolution is that the generic methods now allow for concurrent analysis of PGT-M and PGT-A. As innovative algorithms are being developed and the cost of sequencing continues to decline, the field of PGT moves forward to a sequencing-based, all-in-one solution for PGT-M, PGT-SR, and PGT-A. This will generate a vast amount of complex genetic data entailing new challenges for genetic counseling. In this review, we summarize the state-of-the-art for PGT-M and reflect on its future.

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“…However, CMA is not capable of identifying chromosomal breakpoint at the nucleotide level. Several techniques have been developed to map chromosome breakpoints to the kilo base-pair (kb) level [56][57][58][59][60][61][62] . However, these techniques are time-consuming, expensive, and do not provide enough information of the breakpoint-linked SNPs for haplotyping analysis 63 .…”

Section: Whole Genome Sequencing For Structural Variant and Chromosommentioning

confidence: 99%

Development of cytogenomics for prenatal diagnosis: from chromosomes to single nucleotides: a review

Chan

Kan

2019

Hong Kong Journal of Gynaecology, Obstetrics and Midwifery

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Prenatal diagnosis encompasses traditional cytogenetics and molecular-based techniques. In the new era of genomics, challenge to prenatal diagnosis has led to revised diagnostic strategies. In this review, we discuss the application of chromosomal microarray and a new prenatal diagnosis workflow in the public setting in Hong Kong. Using this prenatal diagnosis workflow, up to 40% of fetuses with structural anomalies can be identified with an underlying genetic aetiology, leaving the majority of cases undiagnosed. With the advancement of next generation sequencing, we are able to tackle the challenge of investigating chromosomal changes to single nucleotide variant level. Therefore, we also discuss whole exome sequencing, whole genome sequencing, and long-read sequencing, as well as their limitations and prenatal applications. This DNA-based technology should be evaluated for prenatal clinical application in Hong Kong.

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

Cited by 36 publications

References 27 publications

Using Short Read Sequencing to Characterise Balanced Reciprocal Translocations in Pigs

Using Short Read Sequencing to Characterise Balanced Reciprocal Translocations in Pigs

Preimplantation Genetic Testing for Monogenic Disorders

Development of cytogenomics for prenatal diagnosis: from chromosomes to single nucleotides: a review

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