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

Geng, Qian1; Cui, Xiaoli2; Zhang, Yaqi2; Zhang, Lijuan2; Zhang, Cai2; Wang, Kai2; Chen, Jianguo2; Zhu, Qingyan2; Xie, Jiansheng1; Xu, Zhiyong1; Liu, Yang1; Zhang, MengMeng2; Ding, Lijie2; Zhang, Wenyong3,4; Yang, Chuanchun2

2019-11-13

10.1007/s10815-019-01588-6

JOURNAL OF ASSISTED REPRODUCTION AND GENETICS   影响因子和分区

1058-0468

1573-7330

PurposeTo 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).MethodsThe 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.ResultsTwo 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.ConclusionsOur 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.

Single-nucleotide polymorphism Heterozygous mutation Quadratic curve Z test Triploid Uniparental disomy

SCI

英语

其他

Genetics & Heredity ; Obstetrics & Gynecology ; Reproductive Biology

Genetics & Heredity ; Obstetrics & Gynecology ; Reproductive Biology

WOS:000496197200001

SPRINGER/PLENUM PUBLISHERS

CLINICAL MEDICINE

Web of Science

1.Shenzhen Matern & Child Healthcare Hosp, Shenzhen, Peoples R China
2.CheerLand Precis Biomed Co Ltd, Shenzhen, Guangdong, Peoples R China
3.Southern Univ Sci & Technol, Shenzhen, Peoples R China
4.Southern Univ Sci & Technol, CheerLand Inst Precis Med, Shenzhen, Guangdong Sheng, Peoples R China

Geng, Qian,Cui, Xiaoli,Zhang, Yaqi,et al. Screening of triploid with low-coverage whole-genome sequencing by a single-nucleotide polymorphism-based test in miscarriage tissue[J]. JOURNAL OF ASSISTED REPRODUCTION AND GENETICS,2019,36(12):2525-2531.

Geng, Qian.,Cui, Xiaoli.,Zhang, Yaqi.,Zhang, Lijuan.,Zhang, Cai.,...&Yang, Chuanchun.(2019).Screening of triploid with low-coverage whole-genome sequencing by a single-nucleotide polymorphism-based test in miscarriage tissue.JOURNAL OF ASSISTED REPRODUCTION AND GENETICS,36(12),2525-2531.

Geng, Qian,et al."Screening of triploid with low-coverage whole-genome sequencing by a single-nucleotide polymorphism-based test in miscarriage tissue".JOURNAL OF ASSISTED REPRODUCTION AND GENETICS 36.12(2019):2525-2531.