Noninvasive prenatal detection of hemoglobin Bart hydrops fetalis via maternal plasma dispensed with parental haplotyping using the semiconductor sequencing platform

2020 ◽  
Vol 222 (2) ◽  
pp. 185.e1-185.e17
Author(s):  
Jiexia Yang ◽  
Chun-fang Peng ◽  
Yiming Qi ◽  
Xing-qiang Rao ◽  
Fangfang Guo ◽  
...  
Keyword(s):  
Maternal Plasma ◽  
Hydrops Fetalis ◽  
Sequencing Platform ◽  
Prenatal Detection ◽  
Semiconductor Sequencing

scholarly journals Feasibility Study of Semiconductor Sequencing for Noninvasive Prenatal Detection of Fetal Aneuploidy

2013 ◽  
Vol 59 (5) ◽  
pp. 846-849 ◽  
Author(s):  
Yuan Yuan ◽  
Fuman Jiang ◽  
Sang Hua ◽  
Bole Du ◽  
Yibin Hao ◽  
...  
Keyword(s):  
Maternal Plasma ◽  
Trisomy 13 ◽  
Personal Genome ◽  
Plasma Dna ◽  
Sequencing Technology ◽  
Fetal Aneuploidy ◽  
Prenatal Detection ◽  
Semiconductor Sequencing ◽  
Sequencing Platforms ◽  
Fetal Aneuploidies

BACKGROUND Noninvasive prenatal detection of common fetal aneuploidies with cell-free DNA from maternal plasma has been achieved with high-throughput next-generation sequencing platforms. Turnaround times for previously tested platforms are still unsatisfactory for clinical applications, however, because of the time spent on sequencing. The development of semiconductor sequencing technology has provided a way to shorten overall run times. We studied the feasibility of using semiconductor sequencing technology for the noninvasive detection of fetal aneuploidy. METHODS Maternal plasma DNA from 13 pregnant women, corresponding to 4 euploid, 6 trisomy 21 (T21), 2 trisomy 18 (T18), and 1 trisomy 13 (T13) pregnancies, were sequenced on the Ion Torrent Personal Genome Machine sequencer platform with 318 chips. The data were analyzed with the T statistic method after correcting for GC bias, and the T value was calculated as an indicator of fetal aneuploidy. RESULTS We obtained a mean of 3 524 401 high-quality reads per sample, with an efficiency rate of 77.9%. All of the T21, T13, and T18 fetuses could be clearly distinguished from euploid fetuses, and the time spent on library preparation and sequencing was 24 h. CONCLUSIONS Semiconductor sequencing represents a suitable technology for the noninvasive prenatal detection of fetal aneuploidy. With this platform, sequencing times can be substantially reduced; however, a further larger-scale study is needed to determine the imprecision of noninvasive fetal aneuploidy detection with this system.

scholarly journals Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA

2015 ◽  
Vol 112 (47) ◽  
pp. 14670-14675 ◽  
Author(s):  
Ai-hua Yin ◽  
Chun-fang Peng ◽  
Xin Zhao ◽  
Bennett A. Caughey ◽  
Jie-xia Yang ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Genetic Diagnosis ◽  
Maternal Plasma ◽  
Sequencing Depth ◽  
Comparative Genomic ◽  
Plasma Dna ◽  
Cell Free Dna ◽  
Sequencing Platform ◽  
Free Dna ◽  
Semiconductor Sequencing

Noninvasive prenatal testing (NIPT) using sequencing of fetal cell-free DNA from maternal plasma has enabled accurate prenatal diagnosis of aneuploidy and become increasingly accepted in clinical practice. We investigated whether NIPT using semiconductor sequencing platform (SSP) could reliably detect subchromosomal deletions/duplications in women carrying high-risk fetuses. We first showed that increasing concentration of abnormal DNA and sequencing depth improved detection. Subsequently, we analyzed plasma from 1,456 pregnant women to develop a method for estimating fetal DNA concentration based on the size distribution of DNA fragments. Finally, we collected plasma from 1,476 pregnant women with fetal structural abnormalities detected on ultrasound who also underwent an invasive diagnostic procedure. We used SSP of maternal plasma DNA to detect subchromosomal abnormalities and validated our results with array comparative genomic hybridization (aCGH). With 3.5 million reads, SSP detected 56 of 78 (71.8%) subchromosomal abnormalities detected by aCGH. With increased sequencing depth up to 10 million reads and restriction of the size of abnormalities to more than 1 Mb, sensitivity improved to 69 of 73 (94.5%). Of 55 false-positive samples, 35 were caused by deletions/duplications present in maternal DNA, indicating the necessity of a validation test to exclude maternal karyotype abnormalities. This study shows that detection of fetal subchromosomal abnormalities is a viable extension of NIPT based on SSP. Although we focused on the application of cell-free DNA sequencing for NIPT, we believe that this method has broader applications for genetic diagnosis, such as analysis of circulating tumor DNA for detection of cancer.

The Gene Mutation Spectrum of Breast Cancer Analyzed by Semiconductor Sequencing Platform

2018 ◽  
Vol 26 (1) ◽  
pp. 491-497 ◽  
Author(s):  
Yanhui Liu ◽  
Bo Yang ◽  
Xiaoyan Zhang ◽  
Quanfei Huang ◽  
Hailiang Liu
Keyword(s):  
Breast Cancer ◽  
Gene Mutation ◽  
Mutation Spectrum ◽  
Sequencing Platform ◽  
Semiconductor Sequencing

scholarly journals Non-invasive prenatal detection of achondroplasia using circulating fetal DNA in maternal plasma

2010 ◽  
Vol 28 (2) ◽  
pp. 167-172 ◽  
Author(s):  
Ji Hyae Lim ◽  
Mee Jin Kim ◽  
Shin Young Kim ◽  
Hye Ok Kim ◽  
Mee Jin Song ◽  
...  
Keyword(s):  
Maternal Plasma ◽  
Non Invasive ◽  
Prenatal Detection ◽  
Fetal Dna ◽  
Circulating Fetal Dna

scholarly journals Noninvasive Prenatal Detection of Trisomy 21 by an Epigenetic–Genetic Chromosome-Dosage Approach

2010 ◽  
Vol 56 (1) ◽  
pp. 90-98 ◽  
Author(s):  
Yu K Tong ◽  
Shengnan Jin ◽  
Rossa WK Chiu ◽  
Chunming Ding ◽  
KC Allen Chan ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Genetic Markers ◽  
Blood Cells ◽  
Trisomy 21 ◽  
Maternal Blood ◽  
Maternal Plasma ◽  
Plasma Samples ◽  
Prenatal Detection ◽  
Fetal Dna ◽  
Noninvasive Prenatal Diagnosis

Abstract Background: The use of fetal DNA in maternal plasma for noninvasive prenatal diagnosis of trisomy 21 (T21) is an actively researched area. We propose a novel method of T21 detection that combines fetal-specific epigenetic and genetic markers. Methods: We used combined bisulfite restriction analysis to search for fetal DNA markers on chromosome 21 that were differentially methylated in the placenta and maternal blood cells and confirmed any target locus with bisulfite sequencing. We then used methylation-sensitive restriction endonuclease digestion followed by microfluidics digital PCR analysis to investigate the identified marker. Chromosome-dosage analysis was performed by comparing the dosage of this epigenetic marker with that of the ZFY (zinc finger protein, Y-linked) gene on chromosome Y. Results: The putative promoter of the HLCS (holocarboxylase synthetase) gene was hypermethylated in the placenta and hypomethylated in maternal blood cells. A chromosome-dosage comparison of the hypermethylated HLCS and ZFY loci could distinguish samples of T21 and euploid placental DNA. Twenty-four maternal plasma samples from euploid pregnancies and 5 maternal plasma samples from T21 pregnancies were analyzed. All but 1 of the euploid samples were correctly classified. Conclusions: The epigenetic–genetic chromosome-dosage approach is a new method for noninvasive prenatal detection of T21. The epigenetic part of the analysis can be applied to all pregnancies. Because the genetic part of the analysis uses paternally inherited, fetal-specific genetic markers that are abundant in the genome, broad population coverage should be readily achievable. This approach has the potential to become a generally usable technique for noninvasive prenatal diagnosis.

Prenatal detection of fetal Down's syndrome from maternal plasma

The Lancet ◽  
2000 ◽  
Vol 356 (9244) ◽  
pp. 1819-1820 ◽  
Author(s):  
Leo LM Poon ◽  
Tse N Leung ◽  
Tze K Lau ◽  
YM Dennis Lo
Keyword(s):  
Down's Syndrome ◽  
Down’S Syndrome ◽  
Maternal Plasma ◽  
Prenatal Detection
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