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David S Cram

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https://www.readbyqxmd.com/read/28541280/a-quantitative-csmart-assay-for-noninvasive-prenatal-screening-of-autosomal-recessive-nonsyndromic-hearing-loss-caused-by-gjb2-and-slc26a4-mutations
#1
Mingyu Han, Zhifeng Li, Wenlu Wang, Shasha Huang, Yanping Lu, Zhiying Gao, Longxia Wang, Dongyang Kang, Linwei Li, Yiqian Liu, Mengnan Xu, David S Cram, Pu Dai
PurposeThe aim of this study was to assess the performance of a noninvasive prenatal screening (NIPS) assay for accurate fetal genotyping of pregnancies at genetic risk for autosomal recessive nonsyndromic hearing loss (ARNSHL).MethodsA total of 80 pregnant couples carrying known mutations in either the GJB2 or SLC26A4 genes associated with a risk for ARNSHL were recruited to the study. Fetal amniocyte samples were genotyped by invasive prenatal screening (IPS), whereas the cell-free fetal DNA present in maternal plasma samples was genotyped using a novel NIPS method based on circulating single-molecule amplification and resequencing technology (cSMART)...
May 25, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28303777/placental-up-regulation-of-leptin-and-arms2-is-associated-with-growth-discordance-in-monochorionic-diamniotic-twin-pregnancies
#2
Luming Sun, Jia Zhou, Kai Wang, Jian Wang, Ling Shang, Jianguang Zhang, Junqing Wu, David S Cram
Fetal growth discordance is a relatively common complication of monochorionic diamniotic (MCDA) twin pregnancies and is caused by a combination of maternal and placental factors. The aim of the study was to survey placental gene expression patterns and identify genes associated with growth discordance. Clinical samples comprised eight growth-discordant MCDA twin placentas (31+3-34+4 weeks gestational age) and six growth-concordant twin placentas (31+2-37 weeks gestational age). Gene expression libraries were constructed from placental biopsy samples and analyzed by RNA-sequencing...
April 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28247551/characterization-of-chromosomal-abnormalities-in-pregnancy-losses-reveals-critical-genes-and-loci-for-human-early-development
#3
Yiyun Chen, Justin Bartanus, Desheng Liang, Hongmin Zhu, Amy M Breman, Janice L Smith, Hua Wang, Zhilin Ren, Ankita Patel, Pawel Stankiewicz, David S Cram, Sau Wai Cheung, Lingqian Wu, Fuli Yu
Detailed characterization of chromosomal abnormalities, a common cause for congenital abnormalities and pregnancy loss, is critical for elucidating genes for human fetal development. Here, 2,186 product-of-conception samples were tested for copy-number variations (CNVs) at two clinical diagnostic centers using whole-genome sequencing and high-resolution chromosomal microarray analysis. We developed a new gene discovery approach to predict potential developmental genes and identified 275 candidate genes from CNVs detected from both datasets...
June 2017: Human Mutation
https://www.readbyqxmd.com/read/28152582/contribution-of-maternal-copy-number-variations-to-false-positive-fetal-trisomies-detected-by-noninvasive-prenatal-testing
#4
Xiya Zhou, Lili Sui, Yalan Xu, Yijun Song, Qingwei Qi, Jianguang Zhang, Hongmin Zhu, Huaiyu Sun, Feng Tian, Mengnan Xu, David S Cram, Juntao Liu
OBJECTIVE: The aim of the study was to determine the contribution and significance of maternal copy number variations (CNVs) to false-positive noninvasive prenatal testing (NIPT) trisomy results. METHODS: A total of 112 021 patients were referred for NIPT. Fetal aneuploidy testing was performed using low coverage massively parallel sequencing, and results reported as chromosome Z-scores. Copy number variation sequencing (CNV-Seq) was used to detect maternal DNA CNVs...
February 2, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27908601/corrigendum-to-a-pregnancy-with-discordant-fetal-and-placental-chromosome-18-aneuploidies-revealed-by-invasive-and-noninvasive-prenatal-diagnosis-reproductive-biomedicine-online-29-2014-136-139
#5
Chong Chen, David S Cram, Fanni Xie, Ping Wang, Xueqin Xu, Huanzheng Li, Zhuo Song, Di Chen, Jianguang Zhang, Shaohua Tang
No abstract text is available yet for this article.
February 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/27899642/the-ucsc-genome-browser-database-2017-update
#6
Cath Tyner, Galt P Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steve Heitner, Angie S Hinrichs, Donna Karolchik, Brian T Lee, Christopher M Lee, Parisa Nejad, Brian J Raney, Kate R Rosenbloom, Matthew L Speir, Chris Villarreal, John Vivian, Ann S Zweig, David Haussler, Robert M Kuhn, W James Kent
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27870944/application-of-single-molecule-amplification-and-resequencing-technology-for-broad-surveillance-of-plasma-mutations-in-patients-with-advanced-lung-adenocarcinoma
#7
Zheng Wang, Gang Cheng, Xiaohong Han, Xinlin Mu, Yuhui Zhang, Di Cui, Chang Liu, Li Zhang, Zaiwen Fan, Lingyun Ma, Li Yang, Jing Di, David S Cram, Yuankai Shi, Dongge Liu
Liquid biopsy to access the circulating tumor DNA is a promising surrogate for invasive tumor genotyping. We designed a multiplex assay based on circulating single-molecule amplification and resequencing technology (cSMART) to simultaneously detect and quantitate hot spot EGFR, KRAS, BRAF, ERBB2, and ALK plasma DNA variants in 103 patients with advanced lung adenocarcinoma. In validation studies using an analytical mutation standard, the sensitivity of the assay for EGFR mutation detection was at least 0.1% and specificity was 100%...
January 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27862068/development-and-validation-of-a-fetal-genotyping-assay-with-potential-for-noninvasive-prenatal-diagnosis-of-hereditary-hearing-loss
#8
Ying Chen, Yiqian Liu, Benjing Wang, Jun Mao, Ting Wang, Kan Ye, Yanlin Ye, David S Cram, Hong Li
OBJECTIVE: Inherited non-syndromic hearing loss (NSHL) is a common sensory disorder that afflicts otherwise healthy individuals. The aim of the study was to evaluate the performance of circulating single molecule amplification and re-sequencing technology (cSMART) for non-invasive prenatal testing (NIPT) of NSHL. METHOD: Neonatal inheritance of NSHL mutations was determined from bloodspots using SNaPshot genotyping. NIPT of cell-free DNA for fetal NSHL mutations in the GJB2, GJB3 and SLC26A4 genes was performed by a multiplex cSMART assay...
December 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27672536/next-generation-sequencing-coping-with-rare-genetic-diseases-in-china
#9
REVIEW
David S Cram, Daixing Zhou
With a population of 1.4 billion, China shares the largest burden of rare genetic diseases worldwide. Current estimates suggest that there are over ten million individuals afflicted with chromosome disease syndromes and well over one million individuals with monogenic disease. Care of patients with rare genetic diseases remains a largely unmet need due to the paucity of available and affordable treatments. Over recent years, there is increasing recognition of the need for affirmative action by government, health providers, clinicians and patients...
August 2016: Intractable & Rare Diseases Research
https://www.readbyqxmd.com/read/27485761/a-novel-msx1-intronic-mutation-associated-with-autosomal-dominant-non-syndromic-oligodontia-in-a-large-chinese-family-pedigree
#10
Jinjie Xue, Qingping Gao, Yanru Huang, Xiaoyu Zhang, Pu Yang, David S Cram, Desheng Liang, Lingqian Wu
BACKGROUND: Tooth agenesis is a common developmental dental anomaly. The aim of the study was to identify the causal genetic mutation in a four-generation Chinese family affected with non-syndromic autosomal dominant tooth agenesis. METHODS: Genome-wide scanning was performed using the Illumina Linkage-12 array. Genotyping of short tandem repeat markers was used to finely map the causative locus. Haplotype analysis and Sanger sequencing was performed to precisely locate the position and nature of the gene defect...
October 1, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27453960/a-multi-modal-intervention-for-activating-patients-at-risk-for-osteoporosis-apropos-rationale-design-and-uptake-of-online-study-intervention-material
#11
Maria I Danila, Ryan C Outman, Elizabeth J Rahn, Amy S Mudano, Tammi F Thomas, David T Redden, Jeroan J Allison, Fred A Anderson, Julia P Anderson, Peter M Cram, Jeffrey R Curtis, Liana Fraenkel, Susan L Greenspan, Andrea Z LaCroix, Sumit R Majumdar, Michael J Miller, Jeri W Nieves, Monika M Safford, Stuart L Silverman, Ethel S Siris, Daniel H Solomon, Amy H Warriner, Nelson B Watts, Robert A Yood, Kenneth G Saag
OBJECTIVE: To develop an innovative and effective educational intervention to inform patients about the need for osteoporosis treatment and to determine factors associated with its online uptake. METHODS: Postmenopausal women with a prior fracture and not currently using osteoporosis therapy were eligible to be included in the Activating Patients at Risk for OsteoPOroSis (APROPOS). Four nominal groups with a total of 18 racially/ethnically diverse women identified osteoporosis treatment barriers...
December 15, 2016: Contemporary Clinical Trials Communications
https://www.readbyqxmd.com/read/27409166/comprehensive-profiling-and-quantitation-of-oncogenic-mutations-in-non-small-cell-lung-carcinoma-using-single-molecule-amplification-and-re-sequencing-technology
#12
Shirong Zhang, Bing Xia, Hong Jiang, Limin Wang, Rujun Xu, Yanbin Shi, Jianguang Zhang, Mengnan Xu, David S Cram, Shenglin Ma
Activating and resistance mutations in the tyrosine kinase domain of several oncogenes are frequently associated with non-small cell lung carcinoma (NSCLC). In this study we assessed the frequency, type and abundance of EGFR, KRAS, BRAF, TP53 and ALK mutations in tumour specimens from 184 patients with early and late stage disease using single molecule amplification and re-sequencing technology (SMART). Based on modelling of EGFR mutations, the detection sensitivity of the SMART assay was at least 0.1%. Benchmarking EGFR mutation detection against the gold standard ARMS-PCR assay, SMART assay had a sensitivity and specificity of 98...
August 2, 2016: Oncotarget
https://www.readbyqxmd.com/read/27274452/two-stage-revision-anterior-cruciate-ligament-reconstruction-bone-grafting-technique-using-an-allograft-bone-matrix
#13
Jorge Chahla, Chase S Dean, Tyler R Cram, David Civitarese, Luke O'Brien, Samuel G Moulton, Robert F LaPrade
Outcomes of primary anterior cruciate ligament (ACL) reconstruction have been reported to be far superior to those of revision reconstruction. However, as the incidence of ACL reconstruction is rapidly increasing, so is the number of failures. The subsequent need for revision ACL reconstruction is estimated to occur in up to 13,000 patients each year in the United States. Revision ACL reconstruction can be performed in one or two stages. A two-stage approach is recommended in cases of improper placement of the original tunnels or in cases of unacceptable tunnel enlargement...
February 2016: Arthroscopy Techniques
https://www.readbyqxmd.com/read/27167073/clinical-application-of-next-generation-sequencing-in-preimplantation-genetic-diagnosis-cycles-for-robertsonian-and-reciprocal-translocations
#14
Wenke Zhang, Ying Liu, Li Wang, Hui Wang, Minyue Ma, Mengnan Xu, Xiaofei Xu, ZhiYing Gao, Jinliang Duan, David S Cram, Yuanqing Yao
PURPOSE: The purpose of this study was to apply next-generation sequencing (NGS) technology to identify chromosomally normal embryos for transfer in preimplantation genetic diagnosis (PGD) cycles for translocations. METHODS: A total of 21 translocation couples with a history of infertility and repeated miscarriage presented at our PGD clinic for 24-chromosome embryo testing using copy number variation sequencing (CNV-Seq). RESULTS: Testing of 98 embryo samples identified 68 aneuploid (69...
July 2016: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/27103944/molecular-characterization-of-a-novel-ring-6-chromosome-using-next-generation-sequencing
#15
Rui Zhang, Xuan Chen, Peiling Li, Xiumin Lu, Yu Liu, Yan Li, Liang Zhang, Mengnan Xu, David S Cram
BACKGROUND: Karyotyping is the gold standard cytogenetic method for detection of ring chromosomes. In this study we report the molecular characterization of a novel ring 6 (r6) chromosome in a six-year-old girl with severe mental retardation, congenital heart disease and craniofacial abnormalities. METHODS: Cytogenetic analysis was performed by conventional karyotyping. Molecular genetic analyses were performed using high-resolution chromosome microarray analysis (CMA) and next generation sequencing (NGS)...
2016: Molecular Cytogenetics
https://www.readbyqxmd.com/read/27084671/copy-number-variation-sequencing-based-prenatal-diagnosis-using-cell-free-fetal-dna-in-amniotic-fluid
#16
Qingwei Qi, Sijia Lu, Xiya Zhou, Fengxia Yao, Na Hao, Guangjun Yin, Wenhui Li, Junjie Bai, Ning Li, David S Cram
OBJECTIVE: The study aimed to determine whether cell-free fetal DNA (cffDNA) present in amniotic fluid supernatant can be used as a surrogate for amniocyte-based diagnosis of fetal chromosomal abnormalities. METHOD: Amniocentesis was performed on 28 high-risk pregnancies. Amniocytes and the cffDNA fraction were prepared from the amniotic fluid samples. Chromosomal analysis of amniocytes was performed by either karyotyping or single nucleotide polymorphism (SNP) arrays...
June 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27071701/a-comparative-study-of-egfr-oncogenic-mutations-in-matching-tissue-and-plasma-samples-from-patients-with-advanced-non-small-cell-lung-carcinoma
#17
COMPARATIVE STUDY
Xiaofei Chai, Pengfei Ren, Bing Wei, Jie Ma, Ling Mai, David S Cram, Yongping Song, Yongjun Guo
BACKGROUND: Plasma based EGFR mutation analysis is emerging as a viable alternative to tumour tissue genotyping for patients with non-small cell lung carcinoma (NSCLC). The purpose of the study was to determine the degree of concordance between EGFR genotypes derived from matching tissue and blood samples. METHODS: EGFR activating mutations L858R, exon 19 deletions, G719A/C/S and L861Q as well as resistance mutations T790M and exon 20 insertions were co-analysed in 61 matching tissue and blood biopsies collected from NCSLC patients...
June 1, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/26899834/molecular-analysis-of-dna-in-blastocoele-fluid-using-next-generation-sequencing
#18
Yixin Zhang, Na Li, Li Wang, Huiying Sun, Minyue Ma, Hui Wang, Xiaofei Xu, Wenke Zhang, Yingyu Liu, David S Cram, Baofa Sun, Yuanqing Yao
BACKGROUND: Preimplantation genetic testing (PGT) requires an invasive biopsy to obtain embryonic material for genetic analysis. The availability of a less invasive procedure would increase the overall efficacy of PGT. The aim of the study was to explore the potential of blastocoele fluid (BF) as an alternative source of embryonic DNA for PGT. METHODS: Collection of BF was performed by aspiration with a fine needle prior to vitrification. BF DNA was subjected to whole-genome amplification (WGA) and analyzed by high-resolution next-generation sequencing (NGS)...
May 2016: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/26833920/identification-of-copy-number-variations-associated-with-congenital-heart-disease-by-chromosomal-microarray-analysis-and-next-generation-sequencing
#19
Xiangyu Zhu, Jie Li, Tong Ru, Yaping Wang, Yan Xu, Ying Yang, Xing Wu, David S Cram, Yali Hu
OBJECTIVE: To determine the type and frequency of pathogenic chromosomal abnormalities in fetuses diagnosed with congenital heart disease (CHD) using chromosomal microarray analysis (CMA) and validate next-generation sequencing as an alternative diagnostic method. METHOD: Chromosomal aneuploidies and submicroscopic copy number variations (CNVs) were identified in amniocytes DNA samples from CHD fetuses using high-resolution CMA and copy number variation sequencing (CNV-Seq)...
April 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/26676536/detection-and-quantitation-of-chromosomal-mosaicism-in-human-blastocysts-using-copy-number-variation-sequencing
#20
Tida Ruttanajit, Sujin Chanchamroen, David S Cram, Kritchakorn Sawakwongpra, Wanwisa Suksalak, Xue Leng, Junmei Fan, Li Wang, Yuanqing Yao, Wiwat Quangkananurug
OBJECTIVE: Currently, our understanding of the nature and reproductive potential of blastocysts associated with trophectoderm (TE) lineage chromosomal mosaicism is limited. The objective of this study was to first validate copy number variation sequencing (CNV-Seq) for measuring the level of mosaicism and second, examine the nature and level of mosaicism in TE biopsies of patient's blastocysts. METHOD: TE biopy samples were analysed by array comparative genomic hybridization (CGH) and CNV-Seq to discriminate between euploid, aneuploid and mosaic blastocysts...
February 2016: Prenatal Diagnosis
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