A Rapid PCR-Free Next-Generation Sequencing Method for the Detection of Copy Number Variations in Prenatal Samples.
Xiya ZhouXiangbin ChenYulin JiangQingwei QiNa HaoChengkun LiuMengnan XuDavid S CramJuntao LiuPublished in: Life (Basel, Switzerland) (2021)
Next-generation sequencing (NGS) is emerging as a new method for the detection of clinically significant copy number variants (CNVs). In this study, we developed and validated rapid CNV-sequencing (rCNV-seq) for clinical application in prenatal diagnosis. Low-pass whole-genome sequencing was performed on PCR libraries prepared from amniocyte genomic DNA. From 10-40 ng of input DNA, PCR-free libraries consistently produced sequencing data with high unique read mapping ratios, low read redundancy, low coefficient of variation for all chromosomes and high genomic coverage. In validation studies, reliable and accurate CNV detection using PCR-free-based rCNV-seq was demonstrated for a range of common trisomies and sex chromosome aneuploidies as well as microdeletion and duplication syndromes. In reproducibility studies, CNV copy number and genomic intervals closely matched those defined by chromosome microarray analysis. Clinical testing of genomic DNA samples from 217 women referred for prenatal diagnosis identified eight samples (3.7%) with known chromosome disorders. We conclude that PCR-free-based rCNV-seq is a sensitive, specific, reproducible and efficient method that can be used in any NGS-based diagnostic laboratory for detection of clinically significant CNVs.
Keyphrases
- copy number
- real time pcr
- genome wide
- mitochondrial dna
- loop mediated isothermal amplification
- single cell
- dna methylation
- single molecule
- circulating tumor
- rna seq
- label free
- cell free
- pregnant women
- metabolic syndrome
- type diabetes
- skeletal muscle
- adipose tissue
- circulating tumor cells
- quantum dots
- artificial intelligence
- mass spectrometry
- computed tomography
- contrast enhanced
- bioinformatics analysis