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David cram

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
David A Clunie, Don K Dennison, Dawn Cram, Kenneth R Persons, Mark D Bronkalla, Henri Rik Primo
This white paper explores the technical challenges and solutions for acquiring (capturing) and managing enterprise images, particularly those involving visible light applications. The types of acquisition devices used for various general-purpose photography and specialized applications including dermatology, endoscopy, and anatomic pathology are reviewed. The formats and standards used, and the associated metadata requirements and communication protocols for transfer and workflow are considered. Particular emphasis is placed on the importance of metadata capture in both order- and encounter-based workflow...
October 2016: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
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
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
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...
July 7, 2016: Oncotarget
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
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
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
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
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
Yijun Song, Xiya Zhou, Saiqiong Huang, Xiaohong Li, Qingwei Qi, Yulin Jiang, Yiqian Liu, Chengcheng Ma, Zhifeng Li, Mengnan Xu, David S Cram, Juntao Liu
BACKGROUND: Calculation of the fetal DNA fraction (FF) is important for reliable and accurate noninvasive prenatal testing (NIPT) for fetal genetic abnormalities. The aim of the study was to develop and validate a novel method for FF determination. METHODS: FF was calculated using the chromosome Y (ChrY) sequence read assay and by circulating single molecule amplification and re-sequencing technology of 76 autosomal SNPs. RESULTS: By Pearson correlation for FF (4...
May 1, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
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
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
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
Henry G Fein, T Brooks Vaughan, Harvey Kushner, David Cram, Dat Nguyen
BACKGROUND: Overweight and obesity are common among patients with Cushing's syndrome (CS) and may persist in some patients even after ostensibly curative surgery, contributing to cardiometabolic dysfunction and increased cardiovascular risk. Mifepristone, a selective glucocorticoid receptor antagonist, was effective in controlling hyperglycemia in a 24-week trial of adults (N = 50) with endogenous CS and associated type 2 diabetes mellitus/impaired glucose tolerance or hypertension who had failed or were not candidates for surgery (SEISMIC, Study of the Efficacy and Safety of Mifepristone in the Treatment of Endogenous Cushing's Syndrome)...
2015: BMC Endocrine Disorders
Lu-Ming Sun, Ying Li, Gang Zou, Fenghe Zhou, Xiaoping Lei, David S Cram, Dick Oepkes, Junqing Wu
OBJECTIVE: In monochorionic diamniotic (MCDA) twin pregnancies, unequal placental sharing does not always lead to adverse outcomes. The aim of this study is to investigate how unequal placental sharing may be compensated by placental anatomical changes. METHODS: Between January 2012 and July 2013, a total of 60 uncomplicated MCDA pregnancies ending in live birth of healthy twins were studied. Placentas were divided into two groups; an equally shared placenta group (placenta territory discordance ≤ 25%, N = 40) and an unequally shared placenta group (placenta territory discordance >25%, N = 20)...
2016: Journal of Maternal-fetal & Neonatal Medicine
Jingmei Ma, David S Cram, Jianguang Zhang, Ling Shang, Huixia Yang, Hong Pan
BACKGROUND: Non-invasive prenatal testing (NIPT) is currently used as a frontline screening test to identify fetuses with common aneuploidies. Occasionally, incidental NIPT results are conveyed to the clinician suggestive of fetuses with rare chromosome disease syndromes. We describe a child with trisomy 9 (T9) mosaicism where the prenatal history reported a positive NIPT result for T9 that was unconfirmed by conventional prenatal diagnosis. METHODS: NIPT was performed by low coverage whole genome plasma DNA sequencing...
2015: Molecular Cytogenetics
Jacob A Cram, Li C Xia, David M Needham, Rohan Sachdeva, Fengzhu Sun, Jed A Fuhrman
Interactions among microbes and stratification across depths are both believed to be important drivers of microbial communities, though little is known about how microbial associations differ between and across depths. We have monitored the free-living microbial community at the San Pedro Ocean Time-series station, monthly, for a decade, at five different depths: 5 m, the deep chlorophyll maximum layer, 150 m, 500 m and 890 m (just above the sea floor). Here, we introduce microbial association networks that combine data from multiple ocean depths to investigate both within- and between-depth relationships, sometimes time-lagged, among microbes and environmental parameters...
December 2015: ISME Journal
Junmei Fan, Li Wang, Hui Wang, Minyue Ma, Shufang Wang, Zhongyu Liu, Genming Xu, Jianguang Zhang, David S Cram, Yuanqing Yao
Next-generation sequencing is emerging as a reliable and accurate technology for pre-implantation genetic diagnosis (PGD) of aneuploidies and translocations. The aim of this study was to extend the clinical utility of copy number variation sequencing (CNV-Seq) to the detection of small pathogenic copy number variations (CNVs) associated with chromosome disease syndromes. In preliminary validation studies, CNV-Seq was highly sensitive and specific for detecting small CNV in whole-genome amplification products from three replicates of one and five cell samples, with a resolution in the order of 1-2 Mb...
July 2015: Reproductive Biomedicine Online
Na Li, Li Wang, Hui Wang, Minyue Ma, Xiaohong Wang, Yi Li, Wenke Zhang, Jianguang Zhang, David S Cram, Yuanqing Yao
Reliable and accurate pre-implantation genetic diagnosis (PGD) of patient's embryos by next-generation sequencing (NGS) is dependent on efficient whole genome amplification (WGA) of a representative biopsy sample. However, the performance of the current state of the art WGA methods has not been evaluated for sequencing. Using low template DNA (15 pg) and single cells, we showed that the two PCR-based WGA systems SurePlex and MALBAC are superior to the REPLI-g WGA multiple displacement amplification (MDA) system in terms of consistent and reproducible genome coverage and sequence bias across the 24 chromosomes, allowing better normalization of test to reference sequencing data...
April 20, 2015: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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