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1. Prenatal detection and molecular cytogenetic characterization of Xp deletion and Xq duplication: a case report and literature review

Author

Qing Lin, Chunya Liang, Bole Du, Lijiao Li, Hong Li, Xiaolan Mai, Sheng Li, Wenyu Xu, Cunzhen Wu, and Mi Zeng

Subjects
Noninvasive prenatal screening, Prenatal diagnosis, Chromosome microarray analysis, Xp22.33p22.32 deletion, Xq27.1q28 duplication, Internal medicine, RC31-1245, Genetics, QH426-470
Abstract

Abstract Background Copy number variation (CNV) of X chromosome can lead to a variety of neonatal abnormalities, especially for male fetuses. In recent years, due to the high sensitivity and high specificity of NIPS, its application has gradually expanded from chromosome aneuploidy to CNV. Few prenatal cases involving the detection of Xq duplication and deletion by NIPS have been reported, but it is of great significance for genetic counseling. Case presentation A 36-year-old woman was referred for prenatal diagnosis and genetic counseling at 17 weeks of gestation because of abnormal result of noninvasive prenatal screening (NIPS). Multiple congenital malformations, hydrocephalus, and enlarged gallbladder were observed by prenatal ultrasound. Amniocentesis revealed the karyotype of the fetus as 46, XN, add(X) (p22.2) and the result of chromosomal microarray analysis was arr[hg19] Xq27.1q28(138,506,454–154896094) × 2 and arr[hg19] Xp22.33p22.32(168,551–5,616,964) × 1. CNV-seq showed that the mother shares a 16.42 Mb duplication in the Xq27.1-q28 region and a 2.97 Mb deletion in the Xp22.33-p22.32 region. After genetic counseling, the couple chose to terminate the pregnancy. Conclusion The combination of NIPS and CMA would be of values in detection of subchromosomal duplications and/or deletions at fetal stage. The detection of X chromosome aberration in a male fetus should give suspicion of the possibility of maternal inheritance.

Published
2024
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2. Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study

Author

Fuman Jiang, Weiqiang Liu, Longmei Zhang, Yulai Guo, Min Chen, Xiaojing Zeng, Yang Wang, Yufan Li, JiaJia Xian, BoLe Du, Yuhuan Xie, Shuming Ouyang, Sheng Li, Yinghong Yang, Chunsheng Zhang, Fei Luo, and Xiaofang Sun

Subjects
Medicine, Science
Abstract

Abstract Noninvasive prenatal testing (NIPT) for single gene disorders remains challenging. One approach that allows for accurate detection of the slight increase of the maternally inherited allele is the relative haplotype dosage (RHDO) analysis, which requires the construction of parental haplotypes. Recently, the nanopore sequencing technologies have become available and may be an ideal tool for direct construction of haplotypes. Here, we explored the feasibility of combining nanopore sequencing with the RHDO analysis in NIPT of β-thalassemia. Thirteen families at risk for β-thalassemia were recruited. Targeted region of parental genomic DNA was amplified by long-range PCR of 10 kb and 20 kb amplicons. Parental haplotypes were constructed using nanopore sequencing and next generation sequencing data. Fetal inheritance of parental haplotypes was classified by the RHDO analysis using data from maternal plasma DNA sequencing. Haplotype phasing was achieved in 12 families using data from 10 kb library. While data from the 20 kb library gave a better performance that haplotype phasing was achieved in all 13 families. Fetal status was correctly classified in 12 out of 13 families. Thus, targeted nanopore sequencing combined with the RHDO analysis is feasible to NIPT for β-thalassemia.

Published
2021
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3. Noninvasive prenatal diagnosis of β‐thalassemia by relative haplotype dosage without analyzing proband

Author

Haoxian Li, Bole Du, Fuman Jiang, Yulai Guo, Yang Wang, Chunsheng Zhang, Xiaojing Zeng, Yuhuan Xie, Shuming Ouyang, Yexing Xian, Min Chen, Weiqiang Liu, and Xiaofang Sun

Subjects
cell‐free fetal DNA, haplotype, noninvasive prenatal diagnosis, relative haplotype dosage, β‐thalassemia, Genetics, QH426-470
Abstract

Abstract Background β‐thalassemia is one of the most common monogenic diseases in the world. Southeast China is a highly infected area affected by four β‐thalassemia mutation types (HBB:c.‐78A>G, HBB:c.52A>T, HBB:c.126_129delCTTT, and HBB:c.316‐197C>T). Relative haplotype dosage (RHDO), a haplotype‐based approach, has shown promise as an application for noninvasive prenatal diagnosis (NIPD); however, additional family members (such as the proband) are required for haplotype construction. The abovementioned circumstances make RHDO‐based NIPD cost prohibitive; additionally, the genetic information of the proband is not always available. Thus, it is necessary to find a practical method to solve these problems. Methods Targeted sequencing was applied to sequence parental genomic DNA and cell‐free fetal DNA (cffDNA). Parental haplotypes were constructed with the SHAPEIT software based on the 1000 Genomes Project (1000G) Phase 3 v5 Southern Han Chinese (CHS) haplotype dataset. Single‐nucleotide polymorphisms (SNPs) in the target region were called and classified, and the fetal mutation inheritance status was deduced using the RHDO method. Results Construction of the parental haplotypes and detection of the inherited parental mutations were successfully achieved in five families, despite a suspected recombination event. The status of the affected fetuses is consistent with the results of traditional reverse dot blot (RDB) diagnosis. Conclusion This research introduced SHAPEIT into the classical RHDO workflow and proved that it is applicable to construct parental haplotypes without information from other family members.

Published
2019
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4. Feasibility Study of Semiconductor Sequencing for Noninvasive Prenatal Detection of Fetal Aneuploidy

Author

Feng Mu, Yu Liang, Wei Wang, Ling Yang, Jiucheng Liu, Sang Hua, Yuan Yuan, Kaiyan Feng, Xin Yi, Lili Ye, Caixia Liu, Bole Du, Yibin Hao, Fuman Jiang, and Xinjie Huang

Subjects
Chromosomes, Human, Pair 21, Library preparation, Clinical Biochemistry, Chromosome Disorders, Trisomy, Biology, Bioinformatics, Fetus, Pregnancy, medicine, Humans, Chromosomes, Human, Pair 13, Plasma dna, Biochemistry (medical), DNA, Sequence Analysis, DNA, Ion semiconductor sequencing, medicine.disease, Fetal aneuploidy, Semiconductors, Feasibility Studies, Female, Chromosomes, Human, Pair 18, Maternal Serum Screening Tests, Personal genomics
Abstract

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.

Published
2013
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5. Effects of Maternal and Fetal Characteristics on Cell-Free Fetal DNA Fraction in Maternal Plasma

Author

Tze Kin Lau, Wei Wang, Yuying Yuan, Jun Wang, KaiKai Liao, Lijun Zhou, Zhonglin Chen, Fuman Jiang, Lijian Zhao, Zhongyi Zhu, Fang Chen, Ya Gao, Yi Zhou, Guo Yulai, Bole Du, Yumei Hou, Hongyun Zhang, and Cong Yu

Subjects
Adult, Genetic Markers, Male, medicine.medical_specialty, Adolescent, Prenatal diagnosis, Gestational Age, Body Mass Index, Young Adult, Fetus, Predictive Value of Tests, Pregnancy, Prenatal Diagnosis, medicine, Humans, Genetic Testing, Twin Pregnancy, Retrospective Studies, business.industry, Obstetrics, Obstetrics and Gynecology, Gestational age, DNA, Middle Aged, medicine.disease, Aneuploidy, Cell-free fetal DNA, embryonic structures, Hypertension, Pregnancy, Twin, Gestation, Female, Trisomy, business
Abstract

To study factors that influence the concentration of cell-free fetal DNA (fetal fraction) using a large clinical data set of pregnancies with male fetus. A retrospective analysis of 23 067 pregnancies that received noninvasive prenatal testing from January 2012 to October 2013, including 22 650 normal singleton pregnancies (control group) and 417 pregnancies with aneuploidy, twin pregnancy, or various maternal conditions including preexisting hypertension, preexisting diabetes, hyperthyroidism, and carrier of the surface antigen of the hepatitis B virus (HBsAg; study group). Multiples of the median (MoM) analysis was performed in the control group to derive gestation and body mass index (BMI)-corrected fetal fraction. The effects of study group conditions on fetal fraction were examined by calculating the ratio of MoM (RMoM) values. Fetal fraction showed a positive correlation with gestational age (r2 = .10, P < .001) and increased rapidly after the 21 weeks of gestation (r2 = .26, P < .001). Negative association with maternal BMI was found with fetal fraction (r2 = .04, P < .001). In study group, fetal fraction was higher among pregnant women with a trisomy 21 fetus (RMoM = 1.24, P < .001) and lower among trisomy 18 (RMoM = 0.84, P < .001). A 1.6-fold incensement of fetal fraction was observed in twin fetuses comparing to singleton pregnancy (RMoM = 1.62, P < .001). Women with preexisting hypertension had significantly lower fetal fraction (RMoM = 0.85, P = .02). Preexisting diabetes, hyperthyroidism, or carrier of HBsAg did not affect fetal fraction. The fetal fraction was affected by fetal aneuploidy, maternal BMI, and the number of gestation. Maternal preexisting of hypertension appeared to reduce fetal fraction.

Published
2015

6. A reliable, high-resolution and high-throughput genotyping method for HLA-DRB1

Author

Hao Zeng, Lijun Zhou, Xianghua Chai, Yicou Xu, Huiling Li, Zhiheng Lan, Meizhen Zhou, Ling Yang, Changjian Huang, Zhongyi Zhu, Bole Du, Wei Wang, Jun Wang, Fan Yang, Zhonglin Chen, Yuying Yuan, Guo Yulai, and Fuman Jiang

Subjects
Genetics, Genotype, Genotyping Techniques, Histocompatibility Testing, Immunology, High-Throughput Nucleotide Sequencing, General Medicine, Human leukocyte antigen, Exons, Biology, DNA sequencing, Tissue Donors, Gene Frequency, Genetic Loci, Immunology and Allergy, Humans, Typing, Primer (molecular biology), Exome, HLA-DRB1, Genotyping, Alleles, DNA Primers, HLA-DRB1 Chains
Abstract

Human leukocyte antigen (HLA) DNA typing is an essential part to identify a donor who may be a good match for the patients who need haematopoietic stem cells from bone marrow. Thus, fetching quickly high-resolution genotype is very important at present. However, current HLA DNA typing methods especially for HLA-DRB1 generally yielded ambiguous typing results because of high degree of heterozygosity on exome region and primer pairs design limitations, which generally amplified only exon2 of HLA-DRB1 and the position of its primer pairs is on exome region. To solve this problem, we developed a reliable, high-resolution and high-throughput (RHH) sequence based typing approach for HLA-DRB1 through massively parallel paired-end sequencing. Several primer pairs were designed to amplify three exon regions, which are part of exon1, the whole region of exon2 and exon3 of HLA-DRB1, to genotyping for HLA-DRB1 by synthesis. 94 samples were included to analyze and the highly successful genotyping ratio (98.94%) and no ambiguous genotyping result demonstrated the accurate performance of our method for HLA-DRB1 genotyping.

Published
2014

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