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prenatal whole genome

Huayu Luo, Qizhi Xiao, Wen Su, Shuxia Chen, Min Jiang, Gefei Xiao
OBJECTIVE: To analyze a fetus with abnormal cardiac ultrasound by using various techniques and explore its genotype-phenotype correlation. METHODS: Lymphocytes derived from umbilical cord blood sample were subjected to G-banding analysis. Short tandem repeats quantitative fluorescence PCR (STR-QF-PCR) was used for analysis of fetal DNA as an auxiliary test. Low-coverage whole genome sequencing (WGS) was used to detect chromosomal deletion/duplication which exceeded 100 kb in size...
October 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Siyang Liu, Shujia Huang, Fang Chen, Lijian Zhao, Yuying Yuan, Stephen Starko Francis, Lin Fang, Zilong Li, Long Lin, Rong Liu, Yong Zhang, Huixin Xu, Shengkang Li, Yuwen Zhou, Robert W Davies, Qiang Liu, Robin G Walters, Kuang Lin, Jia Ju, Thorfinn Korneliussen, Melinda A Yang, Qiaomei Fu, Jun Wang, Lijun Zhou, Anders Krogh, Hongyun Zhang, Wei Wang, Zhengming Chen, Zhiming Cai, Ye Yin, Huanming Yang, Mao Mao, Jay Shendure, Jian Wang, Anders Albrechtsen, Xin Jin, Rasmus Nielsen, Xun Xu
We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1...
October 4, 2018: Cell
Hefan Miao, Jiapeng Zhou, Qi Yang, Fan Liang, Depeng Wang, Na Ma, Bodi Gao, Juan Du, Ge Lin, Kai Wang, Qianjun Zhang
Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and genetic counseling. One possible reason is the limited ability to detect disease causal structural variants (SVs) from short reads sequencing technologies. Long reads sequencing can produce longer reads (typically 1000 bp or longer), therefore offering greatly improved ability to detect SVs that may be missed by short-read sequencing...
2018: Hereditas
Matthew S Hestand, Mark Bessem, Peter van Rijn, Renee X de Menezes, Daoud Sie, Ingrid Bakker, Elles M J Boon, Erik A Sistermans, Marjan M Weiss
An important factor in quality control of non-invasive prenatal screening (NIPS) or testing (NIPT) is a sufficient percentage of fetal DNA to avoid false-negative results. Here we evaluate 14,379 shallow whole-genome sequenced diagnostic NIPS samples, as well as negative controls, for both technical and biological factors that can influence fetal fraction and its assessment. Technically, bioinformatics analyses can have a profound impact on fetal fraction determination. We found best performance for fetal fraction determination with the Y chromosome based tool DEFRAG for male fetuses and the count based tool SeqFF for female fetuses...
September 25, 2018: European Journal of Human Genetics: EJHG
Ruth Horn, Michael Parker
The Prenatal Assessment of Genome and Exomes (PAGE) project is a UK-wide study aiming to gain a better understanding of genetic variants causing developmental problems during pregnancy. A further aim of the study is to provide an evidence-base for the introduction of prenatal whole genome and exome sequencing (PWGES) into prenatal diagnostics provided by the NHS, which is expected in 2018. This paper presents the findings of a qualitative interview study undertaken with 20 health professionals and researchers involved in the PAGE project, and explores their implications for understandings of 'good practice' in the uses of prenatal genomics clinically...
2018: PloS One
Shaomei Yu, Jiancheng Han, Shuang Gao, Xiaowei Liu, Xiaoyan Gu, Ye Zhang, Lin Sun, Yihua He
OBJECTIVE: The purpose of this study was to analyze the fetal echocardiographic features and the associated anomalies of prenatal aortopulmonary window (APW). METHODS: We retrospectively reviewed the fetal echocardiographic database (n = 24 000) in our hospital between May 2012 and December 2017. The general clinical information, fetal echocardiographic features, and the associated anomalies in patients with APW were analyzed. Four patients had undergone whole genome sequencing using fetal tissues...
September 7, 2018: Echocardiography
Sarah Harris, Kelly Gilmore, Emily Hardisty, Anne Drapkin Lyerly, Neeta L Vora
OBJECTIVE: Ethical and counseling challenges are expected with the introduction of prenatal whole exome sequencing. In this study, we describe specific challenges identified through the UNC-Chapel Hill Prenatal Exome Sequencing Study. METHODS: Participants were a subset of women participating in the fetal exome study, which has enrolled 73 mother-father-fetus trios in pregnancies diagnosed with structural anomalies and normal standard genetic testing results. In this descriptive study, cases were reviewed by members of the research team, including a bioethicist, to identify counseling challenges...
September 1, 2018: Prenatal Diagnosis
Yingying Wu, Fangfang Qi, Dan Song, Zitian He, Zejie Zuo, Yunjie Yang, Qiongliang Liu, Saisai Hu, Xiao Wang, Xiaona Zheng, Junhua Yang, Qunfang Yuan, Juntao Zou, Kaihua Guo, Zhibin Yao
BACKGROUND: Prenatal infection is a substantial risk factor for neurodevelopmental disorders such as autism in offspring. We have previously reported that influenza vaccination (VAC) during early pregnancy contributes to neurogenesis and behavioral function in offspring. RESULTS: Here, we probe the efficacy of VAC pretreatment on autism-like behaviors in a lipopolysaccharide (LPS)-induced maternal immune activation (MIA) mouse model. We show that VAC improves abnormal fetal brain cytoarchitecture and lamination, an effect associated with promotion of intermediate progenitor cell differentiation in MIA fetal brain...
August 13, 2018: Journal of Neuroinflammation
Xiaoyun Wei, Zheng Ao, Lin Cheng, Zhaobo He, Qinqin Huang, Bo Cai, Lang Rao, Qianfang Meng, Zixiang Wang, Yue Sun, Wei Liu, Yuanzhen Zhang, Shishang Guo, Feng Guo, Xing-Zhong Zhao
Non-invasive prenatal diagnostics (NIPD) has been an emerging field for prenatal diagnosis research. Carrying the whole genome coding of the fetus, fetal nucleated red blood cells (FNRBCs) have been pursued as a surrogate biomarker traveling around in maternal blood. Here, by combining a unique microbead-based centrifugal separation and enzymatic release, we demonstrated a novel method for FNRBC isolation from the blood samples. First, the gelatin-coated silica microbeads were modified with FNRBC-specific antibody (anti-CD147) to capture the target cells in the blood samples...
October 26, 2018: Nanotechnology
Makoto Nakabayashi, Akihiro Kawashima, Rika Yasuhara, Yosuke Hayakawa, Shingo Miyamoto, Chiaki Iizuka, Akihiko Sekizawa
The discovery of circulating tumour DNA molecules created a paradigm shift in tumour biomarkers as predictors of recurrence. Non-invasive prenatal testing (NIPT) to detect circulating cell-free foetal DNA in maternal plasma is increasingly recognised as a valuable substitute to perceive foetal copy number variation (CNV). This study aimed to determine whether the copy number detection in plasma samples using NIPT platform could be used as a prognostic biomarker in patients with gynaecological cancer. We conducted a prospective study using samples containing preoperative plasma from 100 women with gynaecological cancers...
July 25, 2018: Scientific Reports
Stefan Frey, Anna Eichler, Valeska Stonawski, Jennifer Kriebel, Simone Wahl, Sabina Gallati, Tamme W Goecke, Peter A Fasching, Matthias W Beckmann, Oliver Kratz, Gunther H Moll, Hartmut Heinrich, Johannes Kornhuber, Yulia Golub
Prenatal alcohol exposure (PAE) is known to elicit a broad range of systemic effects, including neurophysiological alterations that result in adverse behavioral and cognitive outcomes. However, molecular pathways underlying these long-term intrauterine effects remain to be investigated. Here, we tested a hypothesis that PAE may lead to epigenetic alterations to the DNA resulting in attentional and cognitive alterations of the children. We report the results of the study that included 156 primary school children of the Franconian Cognition and Emotion Studies (FRANCES) cohort which were tested for an objective marker of PAE, ethyl glucuronide (EtG) in meconium at birth...
2018: Frontiers in Behavioral Neuroscience
Rhiannon Mellis, Natalie Chandler, Lyn S Chitty
The advent of affordable and rapid next-generation sequencing has been transformative for prenatal diagnosis. Sequencing of cell-free DNA in maternal plasma has enabled the development of not only a highly sensitive screening test for fetal aneuploidies, but now definitive noninvasive prenatal diagnosis for monogenic disorders at an early gestation. Sequencing of fetal exomes offers broad diagnostic capability for pregnancies with unexpected fetal anomalies, improving the yield and accuracy of diagnoses and allowing better counseling for parents...
August 2018: Expert Review of Molecular Diagnostics
Shannon M Rego, Michael P Snyder
High-throughput sequencing has dramatically improved our ability to determine and diagnose the underlying causes of human disease. The use of whole-genome and whole-exome sequencing has facilitated faster and more cost-effective identification of new genes implicated in Mendelian disease. It has also improved our ability to identify disease-causing mutations for Mendelian diseases whose associated genes are already known. These benefits apply not only in cases in which the objective is to assess genetic disease risk in adults and children, but also for prenatal genetic testing and embryonic testing...
June 29, 2018: Cold Spring Harbor Perspectives in Medicine
Emilie Abraham, Sophie Rousseaux, Lydiane Agier, Lise Giorgis-Allemand, Jörg Tost, Julien Galineau, Agnès Hulin, Valérie Siroux, Daniel Vaiman, Marie-Aline Charles, Barbara Heude, Anne Forhan, Joel Schwartz, Florent Chuffart, Ekaterina Bourova-Flin, Saadi Khochbin, Rémy Slama, Johanna Lepeule
BACKGROUND: Air pollution exposure represents a major health threat to the developing foetus. DNA methylation is one of the most well-known molecular determinants of the epigenetic status of cells. Blood DNA methylation has been proven sensitive to air pollutants, but the molecular impact of air pollution on new-borns has so far received little attention. OBJECTIVES: We investigated whether nitrogen dioxide (NO2 ), particulate matter (PM10 ), temperature and humidity during pregnancy are associated with differences in placental DNA methylation levels...
September 2018: Environment International
Nicholas B Larson, Chen Wang, Jie Na, Ross A Rowsey, William Edward Highsmith, Nicole L Hoppman, Jean-Pierre Kocher, Eric W Klee
The recent advances in next-generation sequencing (NGS) technologies have enabled the development of effective high-throughput noninvasive prenatal screening (NIPS) assays for fetal genetic abnormalities using maternal circulating cell-free DNA (ccfDNA). An important NIPS quality assurance is quantifying the fetal proportion of the sampled ccfDNA. For methods using allelic read count ratios from targeted sequencing of single-nucleotide polymorphisms (SNPs), systematic biases and errors may reduce accuracy and diminish assay performance...
September 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Constantia Aristidou, Athina Theodosiou, Andria Ketoni, Mads Bak, Mana M Mehrjouy, Niels Tommerup, Carolina Sismani
Background: Precise characterization of apparently balanced complex chromosomal rearrangements in non-affected individuals is crucial as they may result in reproductive failure, recurrent miscarriages or affected offspring. Case presentation: We present a family, where the non-affected father and daughter were found, using FISH and karyotyping, to be carriers of a three-way complex chromosomal rearrangement [t(6;7;10)(q16.2;q34;q26.1), de novo in the father]. The family suffered from two stillbirths, one miscarriage, and has a son with severe intellectual disability...
2018: Molecular Cytogenetics
Muhammad Aman Khan, Aman Ullah, Muhammad Naeem
Autosomal recessive osteopetrosis is a severe fatal disorder with an average incidence of around 1:250,000. It is diagnosed soon after birth or within the 1st year of life with severe symptoms of abnormal bone remodelling. This study was aimed to identify the underlying genetic cause of the disease in a Pakistani family segregating infantile malignant osteopetrosis in autosomal recessive pattern. Whole exome sequencing of the proband was performed using the 51 Mb SureSelect V4 library kit and sequenced using the Illumina HiSeq2500 sequencing system...
June 20, 2018: Molecular Biology Reports
Emily Lostchuck, Alice Poulton, Jane Halliday, Lisa Hui
OBJECTIVES: To assess trends in ultrasound-indicated prenatal diagnostic testing over the past two decades, in the context of rapidly-changing practices in aneuploidy screening and chromosome analysis. METHODS: Retrospective analysis of ultrasound-indicated amniocenteses and chorionic villus sampling from the Australian state of Victoria from 1994-2016. Ultrasound-indicated prenatal diagnostic testing included those performed for: fetal structural abnormality, fetal death, fetal growth restriction, abnormal amniotic fluid volume, genetic "soft marker", or unspecified ultrasound abnormality...
June 6, 2018: Ultrasound in Obstetrics & Gynecology
Nasibeh Karimi, Reza Alibakhshi, Shekoufeh Almasi
Background: Cystic fibrosis (CF) is one of the most common autosomal recessive disorders in Caucasian population. The incidence of disorder varies among different religious, ethnic and geographical isolates. The aim of this study was to identify the spectrum and the frequency of known and unknown disease-causing mutations in Iranian CF patients. Methods: Genomic DNA was extracted from peripheral whole blood with a QIAamp DNA Mini-Kit. Mutation analysis was done in the CFTR gene including complete coding region and intron/exon boundaries using a direct sequencing method...
January 2018: Journal of Reproduction & Infertility
Sau W Cheung, Weimin Bi
In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus...
June 2018: Expert Review of Molecular Diagnostics
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