ArticlePloS one2014
PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Molecular Genetic Analysis and Prenatal Diagnosis of a Family With MECP2 Duplication Syndrome.Journal of clinical laboratory analysis · 2026Article
- Identification a rare chromosomal translocation 45,X, der(Y;15)(q11.2;q11.2) in an azoospermic patient using C-MoKa.Molecular cytogenetics · 2026Article
- Performance testing for the sensitivity and resolution of low-pass WGS for small CNV detection.BMC medical genomics · 2025Article
- ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing.Bioinformatics (Oxford, England) · 2025Article
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- A Chinese patient with Rothmund-Thomson syndrome.Molecular genetics & genomic medicine · 2024Article
- Retrospective study revealed integration of CNV-seq and karyotype analysis is an effective strategy for prenatal diagnosis of chromosomal abnormalities.Frontiers in genetics · 2024Article
- 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
- Clinical and Genetic Characteristics of a Cohort with Distal Vaginal Atresia.International journal of molecular sciences · 2022Article
- Genetic Diagnostic Yield and Novel Causal Genes of Congenital Heart Disease.Frontiers in genetics · 2022Article
- Low-pass genome sequencing: a validated method in clinical cytogenetics.Human genetics · 2020Article
- Detection of chromosomal abnormalities in spontaneous miscarriage by low‑coverage next‑generation sequencing.Molecular medicine reports · 2020Article
- Comprehensive genetic diagnosis of acute myeloid leukemia by next-generation sequencing.Haematologica · 2019Article
- 46,XX Testicular Disorders of Sex Development WithFrontiers in genetics · 2019Article
- Next-generation sequencing identified genetic variations in families with fetal non-syndromic atrioventricular septal defects.International journal of clinical and experimental pathology · 2018Article
- Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach.Genetics in medicine : official journal of the American College of Medical Genetics · 2016Article
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- Investigation of copy number variation in children with conotruncal heart defects.Arquivos brasileiros de cardiologia · 2015Article
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopy number variations (CNVs) represent an important type of genetic variation that deeply impact phenotypic polymorphisms and human diseases. The advent of high-throughput sequencing technologies provides an opportunity to revolutionize the discovery of CNVs and to explore their relationship with diseases. However, most of the existing methods depend on sequencing depth and show instability with low sequence coverage. In this study, using low coverage whole-genome sequencing (LCS) we have developed an effective population-scale CNV calling (PSCC) method. METHODOLOGY/PRINCIPAL
findingsIn our novel method, two-step correction was used to remove biases caused by local GC content and complex genomic characteristics. We chose a binary segmentation method to locate CNV segments and designed combined statistics tests to ensure the stable performance of the false positive control. The simulation data showed that our PSCC method could achieve 99.7%/100% and 98.6%/100% sensitivity and specificity for over 300 kb CNV calling in the condition of LCS (∼2×) and ultra LCS (∼0.2×), respectively. Finally, we applied this novel method to analyze 34 clinical samples with an average of 2× LCS. In the final results, all the 31 pathogenic CNVs identified by aCGH were successfully detected. In addition, the performance comparison revealed that our method had significant advantages over existing methods using ultra LCS. CONCLUSIONS/SIGNIFICANCE: Our study showed that PSCC can sensitively and reliably detect CNVs using low coverage or even ultra-low coverage data through population-scale sequencing.
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