ArticlePloS one2013
A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed.
- Female reproductive tract-on-a-chip for selecting sperm with ultra-low DNA fragmentation index.Microsystems & nanoengineering · 2026Article
- Meiotic gene variants contribute to recurrent blastulation failure.Human reproduction open · 2026Article
- Whole-Genome Amplification on Single Circulating Trophoblast Cell.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing.International journal of molecular sciences · 2022Review
- Single-cell RNA sequencing technologies and applications: A brief overview.Clinical and translational medicine · 2022Review
- Simultaneous detection of genomic imbalance in patients receiving preimplantation genetic testing for monogenic diseases (PGT-M).Frontiers in genetics · 2022Article
- Risk Factors Affecting Alternate Segregation in Blastocysts From Preimplantation Genetic Testing Cycles of Autosomal Reciprocal Translocations.Frontiers in genetics · 2022Article
- Detecting Selection on Segregating Gene Duplicates in a Population.Journal of molecular evolution · 2021Article
- Article
- D-karyo-A New Prenatal Rapid Screening Test Detecting Submicroscopic CNVs and Mosaicism.Diagnostics (Basel, Switzerland) · 2021Article
- Improved clinical outcomes of preimplantation genetic testing for aneuploidy using MALBAC-NGS compared with MDA-SNP array.BMC pregnancy and childbirth · 2020Article
- DNA copy number profiling using single-cell sequencing.Briefings in bioinformatics · 2018Article
- Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms.Scientific reports · 2018Article
- Beyond Enumeration: Functional and Computational Analysis of Circulating Tumor Cells to Investigate Cancer Metastasis.Frontiers in medicine · 2018Review
- Single cell sequencing: a distinct new field.Clinical and translational medicine · 2017Review
- Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications.BMC cancer · 2017Article
- Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.Nucleic acids research · 2017Article
- Next-generation molecular diagnosis: single-cell sequencing from bench to bedside.Cellular and molecular life sciences : CMLS · 2017Review
- Current Progresses of Single Cell DNA Sequencing in Breast Cancer Research.International journal of biological sciences · 2017Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Copy number variations (CNVs), a common genomic mutation associated with various diseases, are important in research and clinical applications. Whole genome amplification (WGA) and massively parallel sequencing have been applied to single cell CNVs analysis, which provides new insight for the fields of biology and medicine. However, the WGA-induced bias significantly limits sensitivity and specificity for CNVs detection. Addressing these limitations, we developed a practical bioinformatic methodology for CNVs detection at the single cell level using low coverage massively parallel sequencing. This method consists of GC correction for WGA-induced bias removal, binary segmentation algorithm for locating CNVs breakpoints, and dynamic threshold determination for final signals filtering. Afterwards, we evaluated our method with seven test samples using low coverage sequencing (4∼9.5%). Four single-cell samples from peripheral blood, whose karyotypes were confirmed by whole genome sequencing analysis, were acquired. Three other test samples derived from blastocysts whose karyotypes were confirmed by SNP-array analysis were also recruited. The detection results for CNVs of larger than 1 Mb were highly consistent with confirmed results reaching 99.63% sensitivity and 97.71% specificity at base-pair level. Our study demonstrates the potential to overcome WGA-bias and to detect CNVs (>1 Mb) at the single cell level through low coverage massively parallel sequencing. It highlights the potential for CNVs research on single cells or limited DNA samples and may prove as a promising tool for research and clinical applications, such as pre-implantation genetic diagnosis/screening, fetal nucleated red blood cells research and cancer heterogeneity analysis.
Indexed as
Identifiers
What OpenQuestion holds
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.