ArticleHuman genetics2020
Low-pass genome sequencing: a validated method in clinical cytogenetics.
Article in Human genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 68 citations in OpenAlex.
- Comparison of Medium-Coverage Whole-Genome Sequencing and Chromosomal Microarray in Prenatal Testing of Absence of Heterozygosity.Prenatal diagnosis · 2026Article
- Prenatal Tympanic Ring Anomaly Without Microtia: A Subtle Clue Toward Severe Early-Onset Monogenic Disorders.Prenatal diagnosis · 2026Article
- Prenatal Whole-Genome Sequencing for Fetal Anomalies: Diagnostic Performance, Challenges, and Clinical Implications.International journal of molecular sciences · 2026Review
- Clinical validation of artificial intelligence-assisted karyotyping on peripheral blood in a cytogenetic diagnostic laboratory.Human genetics · 2025Review
- Performance testing for the sensitivity and resolution of low-pass WGS for small CNV detection.BMC medical genomics · 2025Article
- Advancements in Prenatal Genetic Screening and Testing: Emerging Technologies and Evolving Applications.Diagnostics (Basel, Switzerland) · 2025Review
- Chromosomal quality control in hPSCs: A practical guide to SNP array analysis with GenomeStudio.Frontiers in cell and developmental biology · 2025Article
- Validation and depth evaluation of recurrent neural network-based ultra low-pass genome sequencing for the detection of absence of heterozygosity: A multi-centre study of 409 cases.Clinical and translational medicine · 2024Article
- Recurrent neural network for predicting absence of heterozygosity from low pass WGS with ultra-low depth.BMC genomics · 2024Article
- Improving CNV Detection Performance in Microarray Data Using a Machine Learning-Based Approach.Diagnostics (Basel, Switzerland) · 2023Article
- Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs.BMC medical genomics · 2023Article
- Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis.Diagnostics (Basel, Switzerland) · 2023Article
- Article
- The Burden and Benefits of Knowledge: Ethical Considerations Surrounding Population-Based Newborn Genome Screening for Hearing.International journal of neonatal screening · 2022Article
- Experience of Low-Pass Whole-Genome Sequencing-Based Copy Number Variant Analysis: A Survey of Chinese Tertiary Hospitals.Diagnostics (Basel, Switzerland) · 2022Article
- Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis.Diagnostics (Basel, Switzerland) · 2022Review
- Analysis of autosomal dominant genes impacted by copy number loss in 24,844 fetuses without structural abnormalities.BMC genomics · 2022Article
- Investigation of Chromosomal Structural Abnormalities in Patients With Undiagnosed Neurodevelopmental Disorders.Frontiers in genetics · 2022Article
- Copy Number Variation Analysis of Euploid Pregnancy Loss.Frontiers in genetics · 2022Article
- Low-pass genome sequencing-based detection of absence of heterozygosity: validation in clinical cytogenetics.Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
Corrections and comments
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Authors and funding
17 authors at 4 institutions in 2 countries.
Funding
Abstract
Clinically significant copy-number variants (CNVs) known to cause human diseases are routinely detected by chromosomal microarray analysis (CMA). Recently, genome sequencing (GS) has been introduced for CNV analysis; however, sequencing depth (determined by sequencing read-length and read-amount) is a variable parameter across different laboratories. Variating sequencing depths affect the CNV detection resolution and also make it difficult for cross-laboratory referencing or comparison. In this study, by using data from 50 samples with high read-depth GS (30×) and the reported clinically significant CNVs, we first demonstrated the optimal read-amount and the most cost-effective read-length for CNV analysis to be 15 million reads and single-end 50 bp (equivalent to a read-depth of 0.25-fold), respectively. In addition, we showed that CNVs at mosaic levels as low as 30% are readily detected, furthermore, CNVs larger than 2.5 Mb are also detectable at mosaic levels as low as 20%. Herein, by conducting a retrospective back-to-back comparison study of low-pass GS versus routine CMA for 532 prenatal, miscarriage, and postnatal cases, the overall diagnostic yield was 22.4% (119/532) for CMA and 23.1% (123/532) for low-pass GS. Thus, the overall relative improvement of the diagnostic yield by low-pass GS versus CMA was ~ 3.4% (4/119). Identification of cryptic and clinically significant CNVs among prenatal, miscarriage, and postnatal cases demonstrated that CNV detection at higher resolutions is warranted for clinical diagnosis regardless of referral indications. Overall, our study supports low-pass GS as the first-tier genetic test for molecular cytogenetic testing.
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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.