scholarly journals The prognostic significance of single‐nucleotide polymorphism array‐based whole‐genome analysis and uniparental disomy in myelodysplastic syndrome

2021 ◽  
Author(s):  
Yang Ou ◽  
Yan Yang ◽  
Hongbin Yu ◽  
Xin Zhang ◽  
Min Liu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Myelodysplastic Syndrome ◽  
Genome Analysis ◽  
Single Nucleotide Polymorphism Array ◽  
Prognostic Significance ◽  
Uniparental Disomy ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Whole Genome Analysis ◽  
Single Nucleotide

scholarly journals Screening of triploid with low-coverage whole-genome sequencing by a single-nucleotide polymorphism-based test in miscarriage tissue

2019 ◽  
Vol 36 (12) ◽  
pp. 2525-2531
Author(s):  
Qian Geng ◽  
Xiaoli Cui ◽  
Yaqi Zhang ◽  
Lijuan Zhang ◽  
Cai Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Uniparental Disomy ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Quadratic Curve ◽  
Low Coverage

Abstract Purpose To establish a single-nucleotide polymorphism-based analysis (SBA) method to identify triploidy in the miscarriage tissue by using low-coverage whole-genome sequencing (LC-WGS). Methods The method was established by fitting a quadratic curve model by counting the distribution of three heterozygous mutation content intervals. The triploid test result was mainly determined by the opening direction and the axis of symmetry of the quadratic curve, and Z test between the same batch samples was also used for auxiliary judgment. Results Two hundred thirteen diploid samples and 8 triploid samples were used for establishment of the analytical method and 203 unknown samples were used for blind testing. In the blind testing, we found 2 cases positive for triploidy. After chromosome microarray analysis (CMA) and mass spectrometry verification, we found that both samples were true positives. We randomly selected 5 samples from the negative samples for mass spectrometry verification, and the results showed that these samples were all true negatives. Conclusions Our method achieved accurate detection of triploidy in the miscarriage tissue and has the potential to detect more chromosomal abnormality types such as uniparental disomy (UPD) using a single LC-WGS approach.

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