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prenatal whole genome

Xiaoyun Wei, Zheng Ao, Lin Cheng, Zhaobo He, Qinqin Huang, Bo Cai, Lang Rao, Qian-Fang Meng, Zixiang Wang, Yue Sun, Wei Liu, Yuanzhen Zhang, Shi Shang Guo, Feng Guo, Xingzhong 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 whereas 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 blood samples. First, the gelatin-coated silica microbeads were modified with FNRBCs specific antibody (anti-CD147) to capture the target cells in blood samples...
August 8, 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...
July 18, 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...
June 22, 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
Tanja S Hartwig, Louise Ambye, Lene Werge, Martin Kenneth Weiergang, Pernille Nørgaard, Steen Sørensen, Finn Stener Jørgensen
OBJECTIVES: We have established an open source platform for non-invasive prenatal testing (NIPT) based on massively parallel whole-genome sequencing in a public setting. The objective of this study was to investigate factors of importance for correct interpretation of NIPT results to ensure a high sensitivity and specificity. STUDY DESIGN: This investigation is a retrospective case-control study performed in a public NIPT center. The study included 108 aneuploid cases and 165 euploid controls...
July 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
William J Lane, Connie M Westhoff, Nicholas S Gleadall, Maria Aguad, Robin Smeland-Wagman, Sunitha Vege, Daimon P Simmons, Helen H Mah, Matthew S Lebo, Klaudia Walter, Nicole Soranzo, Emanuele Di Angelantonio, John Danesh, David J Roberts, Nick A Watkins, Willem H Ouwehand, Adam S Butterworth, Richard M Kaufman, Heidi L Rehm, Leslie E Silberstein, Robert C Green
BACKGROUND: There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone...
June 2018: Lancet Haematology
Prince Antwi, Christopher S Hong, Daniel Duran, Sheng Chih Jin, Weilai Dong, Michael DiLuna, Kristopher T Kahle
Campomelic dysplasia is a rare skeletal dysplasia characterized by Pierre Robin sequence, craniofacial dysmorphism, shortening and angulation of long bones, tracheobronchomalacia, and occasionally sex reversal. The disease is due to mutations in SOX9 or chromosomal rearrangements involving the long arm of Chromosome 17 harboring the SOX9 locus. SOX9, a transcription factor, is indispensible in establishing and maintaining neural stem cells in the central nervous system. We present a patient with angulation of long bones and external female genitalia on prenatal ultrasound who was subsequently found to harbor the chromosomal abnormality 46, XY, t(6;17) (p21...
June 2018: Cold Spring Harbor Molecular Case Studies
Ilse Julia Broekaert, Kerstin Becker, Ingo Gottschalk, Friederike Körber, Jörg Dötsch, Holger Thiele, Janine Altmüller, Peter Nürnberg, Christoph Hünseler, Sebahattin Cirak
BACKGROUND: Protein-losing enteropathy (PLE) is characterised by gastrointestinal protein leakage due to loss of mucosal integrity or lymphatic abnormalities. PLE can manifest as congenital diarrhoea and should be differentiated from other congenital diarrhoeal disorders. Primary PLEs are genetically heterogeneous and the underlying genetic defects are currently emerging. OBJECTIVES: We report an infant with fatal PLE for whom we aimed to uncover the underlying pathogenic mutation...
April 16, 2018: Journal of Medical Genetics
Wan Sun, Yanjie Shen, Shan Shan, Liyun Han, Yang Li, Zheng Zhou, Zilin Zhong, Jianjun Chen
Oculocutaneous albinism (OCA) is a set of autosomal recessive disorders characterized by hypopigmented hair, skin and eyes. Homozygous or compound heterozygous mutations in the tyrosinase (TYR) gene can cause OCA1, which is the most common and severe subtype of albinism. In the present study, 17 patients with non‑syndromic OCA were enrolled from eight provinces of China and were non‑consanguineous, with the exception of Patient 4000301. Total genomic DNA was isolated from peripheral blood. Screening was performed for the whole exons and their flanking regions of the TYR gene using Sanger sequencing and the pathogenicity of variants was predicted using in silico analysis...
June 2018: Molecular Medicine Reports
Yang Xu, Qing-Lin Kang, Zhen-Lin Zhang
Sheldon-Hall syndrome is the most common type of distal arthrogryposis syndromes, also known as distal arthrogryposis 2B (DA2B). Sheldon-Hall syndrome is caused by mutations in the TPM2, TNNI2, TNNT3 or MYH3 gene and characterized by ulnar deviation, camptodactyly, overlapping fingers and scoliosis from birth. We investigated a Chinese family with multiple members who clinically presented with distal arthrogryposis of the hands. In total, 261 subjects including one proband and ten family members from the non-consanguineous Chinese family and 250 healthy volunteers were included and had their genomic DNA extracted...
May 2018: Neuromuscular Disorders: NMD
Martin Sauk, Olga Žilina, Ants Kurg, Eva-Liina Ustav, Maire Peters, Priit Paluoja, Anne Mari Roost, Hindrek Teder, Priit Palta, Nathalie Brison, Joris R Vermeesch, Kaarel Krjutškov, Andres Salumets, Lauris Kaplinski
Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts...
April 4, 2018: Scientific Reports
Katerina Honkova, Andrea Rossnerova, Jitka Pavlikova, Vlasta Svecova, Jiri Klema, Jan Topinka, Alena Milcova, Helena Libalova, Hyunok Choi, Milos Veleminsky, Radim J Sram, Pavel Rossner
Prenatal exposure to air pollution is associated with intrauterine growth restriction and low birth weight. Gene expression changes in newborns in relation to air pollution have not been sufficiently studied. We analyzed whole genome expression in cord blood leukocytes of 202 newborns from diverse localities of the Czech Republic, differing among other factors in levels of air pollution: the district of Karvina (characterized by higher concentration of air pollutants) and Ceske Budejovice (lower air pollution levels)...
June 2018: Environmental and Molecular Mutagenesis
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