ArticleProceedings of the National Academy of Sciences of the United States of America2021
Haplotype-aware inference of human chromosome abnormalities.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Reproductive outcomes of mosaic embryo transfers - rethinking the clinical relevance of contemporary mosaicism reporting in preimplantation genetic testing for aneuploidy.Current opinion in obstetrics & gynecology · 2026Review
- Novel biallelic MEI1 variants cause female infertility characterized by multiple pronuclei formation and aberrant embryonic development.Journal of ovarian research · 2025Article
- Identifying a rare mechanism: double parallel trisomy rescue leading to combined segmental and whole-chromosome mosaicism in an IVF-derived embryo.Journal of assisted reproduction and genetics · 2025Article
- Accurate identification of abnormal ploidy using an artificial intelligence model in preimplantation genetic testing.Human reproduction open · 2025Article
- A method for determining potential parental contamination: linkage disequilibrium-based log-likelihood ratio analysis for IVF-PGT.Reproductive biology and endocrinology : RB&E · 2024Article
- A single-cell transcriptome atlas of human euploid and aneuploid blastocysts.Nature genetics · 2024Article
- Recurrent neural network for predicting absence of heterozygosity from low pass WGS with ultra-low depth.BMC genomics · 2024Article
- Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos.Genome research · 2024Article
- Aligning genotyping and copy number data in single trophectoderm biopsies for aneuploidy prediction: uncovering incomplete concordance.Human reproduction open · 2024Article
- Identifying risk variants for embryo aneuploidy using ultra-low coverage whole-genome sequencing from preimplantation genetic testing.American journal of human genetics · 2023Article
- Mapping of meiotic recombination in human preimplantation blastocysts.G3 (Bethesda, Md.) · 2023Article
- Identifying parental and cell-division origins of aneuploidy in the human blastocyst.American journal of human genetics · 2023Article
- A comprehensive preimplantation genetic testing approach for SEA-type α-thalassemia by fluorescent gap-polymerase chain reaction combined with haplotype analysis.Frontiers in genetics · 2023Article
- Parental genomes segregate into distinct blastomeres during multipolar zygotic divisions leading to mixoploid and chimeric blastocysts.Genome biology · 2022Article
- Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Extra or missing chromosomes-a phenomenon termed aneuploidy-frequently arise during human meiosis and embryonic mitosis and are the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing for aneuploidy (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy, may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05 × and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.