ArticleBMC medical genomics2019
BasePhasing: a highly efficient approach for preimplantation genetic haplotyping in clinical application of balanced translocation carriers.
Article in BMC medical genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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9 citing papers in PubMed, 1 synthesis or guideline pooled it, 20 citations in OpenAlex.
- Successful birth after preimplantation genetic testing for a couple with two different reciprocal translocations and review of the literature.Reproductive biology and endocrinology : RB&E · 2021Pooled it
- Clinical application of an Asian Screening Array-based preimplantation genetic testing workflow for various genetic disorders.Orphanet journal of rare diseases · 2026Article
- Generation of quartet reference materials for preimplantation genetic testing for structural rearrangements.BMC genomics · 2026Article
- ViLR: a novel virtual long read method for breakpoint identification and direct SNP haplotyping in de novo PGT-SR carriers without a proband.Reproductive biology and endocrinology : RB&E · 2025Article
- Susceptibility gene identification and risk evaluation model construction by transcriptome-wide association analysis for salt sensitivity of blood pressure.BMC genomics · 2024Article
- Retrospective Analysis of Meiotic Segregation Pattern and Reproductive Outcomes in Blastocysts from Robertsonian Preimplantation Genetic Testing Cycles.Reproductive sciences (Thousand Oaks, Calif.) · 2023Article
- Chromosomal Aberrations in Cattle.Genes · 2021Review
- A comprehensive and universal approach for embryo testing in patients with different genetic disorders.Clinical and translational medicine · 2021Article
- Meiotic Heterogeneity of Trivalent Structure and Interchromosomal Effect in Blastocysts With Robertsonian Translocations.Frontiers in genetics · 2021Article
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9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPreimplantation genetic testing (PGT) has already been applied in chromosomally balanced translocation carriers to improve the clinical outcome of assisted reproduction. However, traditional methods could not further distinguish embryos carrying a translocation from those with a normal karyotype prior to implantation.
methodsTo solve this problem, we developed a method named "Chromosomal Phasing on Base level" (BasePhasing), which based on Infinium Asian Screening Array-24 v1.0 (ASA) and a specially phasing pipeline. Firstly, by comparing the number of single nucleotide polymorphism (SNP) loci in different minor allele frequencies (MAFs) and in 2Mbp continuous windows of ASA chip and karyomap-12 chip, we verified whether ASA could be adopted for genome-wide haplotype linkage analysis. Besides, the whole gene amplification (WGA) of 3-10 cells of GM16457 cell line was used to verify whether ASA chip could be used for testing of WGA products. Finally, two balanced translocation families were utilized to carry out BasePhasing and to validate the feasibility of its clinical application.
resultsThe average number of SNP loci in each window of ASA (473.2) was twice of that of Karyomap-12 (201.2). The coincidence rate of SNP loci in genomic DNA and WGA products was about 97%. The 5.3Mbp deletion was detected positively in cell line GM16457 of both genomic DNA and WGA products, and haplotype linkage analysis was performed in genome wide successfully. In the two balanced translocation families, 18 blastocysts were analyzed, in which 8 were unbalanced and the other 10 were balanced or normal chromosomes. Two embryos were transferred back to the patients successfully, and prenatal cytogenetic analysis of amniotic fluid was performed in the second trimester. The results predicted by BasePhasing and prenatal diagnosis were totally consistent.
conclusionsInfinium ASA bead chip based BasePhasing pipeline shows good performance in balanced translocation carrier testing. With the characteristics of simple operation procedure and accurate results, we demonstrate that BasePhasing is one of the most suitable methods to distinguish between balanced and structurally normal chromosome embryos from translocation carriers in PGT at present.
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