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prenatal whole genome

Haley K Sullivan, Michelle Bayefsky, Paul G Wakim, Kathi Huddleston, Barbara B Biesecker, Sara Chandros Hull, Benjamin E Berkman
OBJECTIVE: To assess pregnant women's views and preferences on noninvasive prenatal whole genome sequencing. METHODS: A survey was offered to 805 pregnant women receiving prenatal care in practices affiliated with a large, tertiary care maternity hospital. Respondents were asked to envision undergoing prenatal whole genome sequencing and discuss their preferences and reasons for receiving different categories of genomic results, organized by actionability, severity, prevalence, and age of onset...
February 4, 2019: Obstetrics and Gynecology
Lesley Walker, Christopher M Watson, Sarah Hewitt, Laura A Crinnion, David T Bonthron, Kelly E Cohen
Molecular diagnostic investigations, following the identification of foetal abnormalities, are routinely performed using array comparative genomic hybridisation (aCGH). Despite the utility of this technique, contemporary approaches for the detection of copy number variation are typically based on next-generation sequencing (NGS). We sought to compare an in-house NGS-based workflow (CNVseq) with aCGH, for invasively obtained foetal samples from pregnancies complicated by foetal structural abnormality. DNA from 40 foetuses was screened using both 8 × 60 K aCGH oligoarrays and low-coverage whole genome sequencing...
February 3, 2019: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
Jenny Lord, Dominic J McMullan, Ruth Y Eberhardt, Gabriele Rinck, Susan J Hamilton, Elizabeth Quinlan-Jones, Elena Prigmore, Rebecca Keelagher, Sunayna K Best, Georgina K Carey, Rhiannon Mellis, Sarah Robart, Ian R Berry, Kate E Chandler, Deirdre Cilliers, Lara Cresswell, Sandra L Edwards, Carol Gardiner, Alex Henderson, Simon T Holden, Tessa Homfray, Tracy Lester, Rebecca A Lewis, Ruth Newbury-Ecob, Katrina Prescott, Oliver W Quarrell, Simon C Ramsden, Eileen Roberts, Dagmar Tapon, Madeleine J Tooley, Pradeep C Vasudevan, Astrid P Weber, Diana G Wellesley, Paul Westwood, Helen White, Michael Parker, Denise Williams, Lucy Jenkins, Richard H Scott, Mark D Kilby, Lyn S Chitty, Matthew E Hurles, Eamonn R Maher
BACKGROUND: Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting...
January 31, 2019: Lancet
Slavé Petrovski, Vimla Aggarwal, Jessica L Giordano, Melissa Stosic, Karen Wou, Louise Bier, Erica Spiegel, Kelly Brennan, Nicholas Stong, Vaidehi Jobanputra, Zhong Ren, Xiaolin Zhu, Caroline Mebane, Odelia Nahum, Quanli Wang, Sitharthan Kamalakaran, Colin Malone, Kwame Anyane-Yeboa, Russell Miller, Brynn Levy, David B Goldstein, Ronald J Wapner
BACKGROUND: Identification of chromosomal aneuploidies and copy number variants that are associated with fetal structural anomalies has substantial value. Although whole-exome sequencing (WES) has been applied to case series of a few selected prenatal cases, its value in routine clinical settings has not been prospectively assessed in a large unselected cohort of fetuses with structural anomalies. We therefore aimed to determine the incremental diagnostic yield (ie, the added value) of WES following uninformative results of standard investigations with karyotype testing and chromosomal microarray in an unselected cohort of sequential pregnancies showing fetal structural anomalies...
January 31, 2019: Lancet
Nosrat Ghaemi, Martha Ghahraman, Samaneh Noroozi Asl, Rahim Vakili, Fatemeh Fardi Golyan, Meysam Moghbeli, Mohammad Reza Abbaszadegan
BACKGROUND: Puberty can be considered the end point of a maturation process which is defined by the dynamic interactions of genes and environmental factors during prenatal and postnatal development. Kisspeptin/G protein-coupled receptor-54, is as an essential gatekeeper and regulator of GnRH neurons, and a key factor in initiation of puberty. Loss and gain of functional mutations in the GPR54 gene are associated with hypogonadotropic hypogonadism and precocious puberty, respectively. This study was designed to evaluate variations of GPR54 in familial precocious puberty...
January 11, 2019: Italian Journal of Pediatrics
Lennart Raman, Annelies Dheedene, Matthias De Smet, Jo Van Dorpe, Björn Menten
Shallow whole-genome sequencing to infer copy number alterations (CNAs) in the human genome is rapidly becoming the method par excellence for routine diagnostic use. Numerous tools exist to deduce aberrations from massive parallel sequencing data, yet most are optimized for research and often fail to redeem paramount needs in a clinical setting. Optimally, a read depth-based analytical software should be able to deal with single-end and low-coverage data-this to make sequencing costs feasible. Other important factors include runtime, applicability to a variety of analyses and overall performance...
December 19, 2018: Nucleic Acids Research
Vanessa Felice, Avinash Abhyankar, Vaidehi Jobanputra
Whole-exome sequencing (WES) has been used as a standard of care for postnatal diagnosis in the clinical setting in the past few years for children and adults with undiagnosed disease. Many rare disorders have been diagnosed through WES, which is less expensive than the traditional serial genetic testing where patients had previously spent years on an uninformative diagnostic odyssey. Seeking a diagnosis often entails enduring time consuming, and sometimes invasive procedures which may be associated with medical risks that are stressful for families and impose a heavy burden on the health-care system...
2019: Methods in Molecular Biology
Benjamin B Currall, Caroline W Antolik, Ryan L Collins, Michael E Talkowski
Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prenatal genome abnormalities. The two most ubiquitous traditional methods for prenatal SV assessment, karyotyping and chromosomal microarrays, do not provide sufficient resolution for some clinically actionable SVs. Standard whole-genome sequencing (WGS) overcomes shortcomings of traditional techniques by providing base-pair resolution of the entire accessible genome. However, while sequencing costs have continued to decline in recent years, conventional WGS costs remain high for most routine clinical applications...
2019: Methods in Molecular Biology
Ji Ping Peng, Hai Ming Yuan
Chromosomal microarray analysis (CMA) is a technique for screening numerical and structural abnormalities of chromosomes at the whole genome level. It is a routine tool for pediatric and prenatal genetic diagnoses. It has also been applied to investigate the genetic etiologies of miscarriages. In our study, we used the CMA technology to analyze the chromosomal variations of fetuses from miscarriages at the whole genome level, and to evaluate its clinical applications in studies of miscarriages. The CMA analyses were performed on 2600 miscarriage specimens, of which 2505 specimens (96...
September 20, 2018: Yi Chuan, Hereditas
Gordon K C Leung, Christopher C Y Mak, Jasmine L F Fung, Wilfred H S Wong, Mandy H Y Tsang, Mullin H C Yu, Steven L C Pei, K S Yeung, Gary T K Mok, C P Lee, Amelia P W Hui, Mary H Y Tang, Kelvin Y K Chan, Anthony P Y Liu, Wanling Yang, P C Sham, Anita S Y Kan, Brian H Y Chung
BACKGROUND: Whole-exome sequencing (WES) has become an invaluable tool for genetic diagnosis in paediatrics. However, it has not been widely adopted in the prenatal setting. This study evaluated the use of WES in prenatal genetic diagnosis in fetuses with structural congenital anomalies (SCAs) detected on prenatal ultrasound. METHOD: Thirty-three families with fetal SCAs on prenatal ultrasonography and normal chromosomal microarray results were recruited. Genomic DNA was extracted from various fetal samples including amniotic fluid, chorionic villi, and placental tissue...
October 25, 2018: BMC Medical Genomics
Liesbeth Vossaert, Qun Wang, Roseen Salman, Xinming Zhuo, Chunjing Qu, David Henke, Ron Seubert, Jennifer Chow, Lance U'ren, Brennan Enright, Jackie Stilwell, Eric Kaldjian, Yaping Yang, Chad Shaw, Brynn Levy, Ronald Wapner, Amy Breman, Ignatia Van den Veyver, Arthur Beaudet
OBJECTIVE: To gather additional data on the ability to detect subchromosomal abnormalities of various sizes in single fetal cells isolated from maternal blood, using low-coverage shotgun next-generation sequencing for cell-based noninvasive prenatal testing (NIPT). METHOD: Fetal trophoblasts were recovered from approximately 30 mL of maternal blood using maternal white blood cell depletion, density-based cell separation, immunofluorescence staining, and high-resolution scanning...
December 2018: Prenatal Diagnosis
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...
February 2019: 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
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