ArticleGenome research2015
Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 58 citations in OpenAlex.
- Evidence for feasibility of fetal trophoblastic cell-based noninvasive prenatal testing.Prenatal diagnosis · 2016Trial
- Identification of cryptic breakpoints through single-tube long fragment read whole genome sequencing based on preimplantation genetic testing.NPJ genomic medicine · 2025Article
- Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing.Nature communications · 2024Article
- Novel off-Targeting Events Identified after Genome Wide Analysis of CRISPR-Cas Edited Pigs.The CRISPR journal · 2024Article
- Comprehensive de novo mutation discovery with HiFi long-read sequencing.Genome medicine · 2023Article
- Accurate Sequencing and Haplotyping from 10 Cells Using Long Fragment Read (LFR) Technology.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Polygenic risk score for embryo selection-not ready for prime time.Human reproduction (Oxford, England) · 2022Article
- Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing.Nucleic acids research · 2022Article
- Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing.International journal of molecular sciences · 2022Review
- Assessment of Birth Defects and Cancer Risk in Children Conceived via In Vitro Fertilization in the US.JAMA network open · 2020Article
- A whole-genome sequencing-based novel preimplantation genetic testing method for de novo mutations combined with chromosomal balanced translocations.Journal of assisted reproduction and genetics · 2020Article
- Review
- Genome sequencing of human in vitro fertilisation embryos for pathogenic variation screening.Scientific reports · 2020Article
- The evolving role of genetic tests in reproductive medicine.Journal of translational medicine · 2019Review
- Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
- Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting theFrontiers in pharmacology · 2019Article
- Novel Double Factor PGT strategy analyzing blastocyst stage embryos in a single NGS procedure.PloS one · 2018Article
- Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.Nature biotechnology · 2017Article
- Pure CTCs, advanced WGS, and precise personalized combination therapies.Oncoscience · 2017Article
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, the methods available for preimplantation genetic diagnosis (PGD) of in vitro fertilized (IVF) embryos do not detect de novo single-nucleotide and short indel mutations, which have been shown to cause a large fraction of genetic diseases. Detection of all these types of mutations requires whole-genome sequencing (WGS). In this study, advanced massively parallel WGS was performed on three 5- to 10-cell biopsies from two blastocyst-stage embryos. Both parents and paternal grandparents were also analyzed to allow for accurate measurements of false-positive and false-negative error rates. Overall, >95% of each genome was called. In the embryos, experimentally derived haplotypes and barcoded read data were used to detect and phase up to 82% of de novo single base mutations with a false-positive rate of about one error per Gb, resulting in fewer than 10 such errors per embryo. This represents a ∼ 100-fold lower error rate than previously published from 10 cells, and it is the first demonstration that advanced WGS can be used to accurately identify these de novo mutations in spite of the thousands of false-positive errors introduced by the extensive DNA amplification required for deep sequencing. Using haplotype information, we also demonstrate how small de novo deletions could be detected. These results suggest that phased WGS using barcoded DNA could be used in the future as part of the PGD process to maximize comprehensiveness in detecting disease-causing mutations and to reduce the incidence of genetic diseases.
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