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array comparative hybridization

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https://www.readbyqxmd.com/read/28814329/severe-persistent-pulmonary-hypertension-of-the-newborn-and-dysmorphic-features-in-neonate-with-a-deletion-involving-twist1-and-phf14-a-case-report
#1
Carina Schinagl, Guro Reinholt Melum, Olaug Kristin Rødningen, Kathrine Bjørgo, Jannicke Hanne Andresen
BACKGROUND: Persistent pulmonary hypertension is a well-known disease of the newborn that in most cases responds well to treatment with nitric oxide and treatment of any underlying causes. Genetic causes of persistent pulmonary hypertension of the newborn are rare. The TWIST1 gene is involved in morphogenetics, and deletions are known to cause Saethre-Chotzen syndrome. Deletions of PHF14 have never been reported in neonates, but animal studies have shown a link between severe defects in lung development and deletions of this gene...
August 17, 2017: Journal of Medical Case Reports
https://www.readbyqxmd.com/read/28814070/hpv-genotype-specific-persistence-and-potential-risk-factors-among-korean-women-results-from-a-2-year-follow-up-study
#2
Cecile Ingabire, Min Kyung Lim, Young-Joo Won, Jin-Kyoung Oh
Purpose: High-risk human papilloma virus (HPV) infection progression should be considered a critical factor for preventing cervical cancer, although most infections are transient and rarely persist. This study aimed to examine the specific types of HPV infections, their change patterns, and the potential risk factors among Korean women. Materials and Methods: We included 4,588 women who visited hospitals in Busan and Suwon for cervical cancer screening, and 1,224 of these women attended a 2-year follow-up...
August 17, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28810831/application-of-a-bayesian-non-linear-model-hybrid-scheme-to-sequence-data-for-genomic-prediction-and-qtl-mapping
#3
Tingting Wang, Yi-Ping Phoebe Chen, Iona M MacLeod, Jennie E Pryce, Michael E Goddard, Ben J Hayes
BACKGROUND: Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some traits, the most accurate genomic predictions are achieved with non-linear Bayesian methods. However, as the number of variants and the size of the reference population increase, the computational time required to implement these Bayesian methods (typically with Monte Carlo Markov Chain sampling) becomes unfeasibly long...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28806950/precision-medicine-approaches-to-lung-adenocarcinoma-with-concomitant-met-and-her2-amplification
#4
Doo-Yi Oh, Kyungsoo Jung, Ji-Young Song, Seokhwi Kim, Sang Shin, Yong-Jun Kwon, Ensel Oh, Woong-Yang Park, Sang Yong Song, Yoon-La Choi
BACKGROUND: Patient-derived xenograft (PDX) models are important tools in precision medicine and for the development of targeted therapies to treat cancer patients. This study aimed to evaluate our precision medicine strategy that integrates genomic profiling and preclinical drug-screening platforms, in order to personalize cancer treatments using PDX models. METHODS: We performed array-comparative genomic hybridization, microarray, and targeted next-generation sequencing analyses, in order to determine the oncogenic driver mutations...
August 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28805617/molecular-cytogenetic-characterization-of-a-duplication-of-15q24-2-q26-2-associated-with-anencephaly-and-neural-tube-defect
#5
Chih-Ping Chen, Chen-Yu Chen, Schu-Rern Chern, Peih-Shan Wu, Shin-Wen Chen, Shih-Ting Lai, Chen-Chi Lee, Chien-Wen Yang, Wayseen Wang
OBJECTIVE: We present molecular cytogenetic characterization of a duplication of 15q24.2-q26.2 associated with anencephaly and neural tube defect (NTD). CASE REPORT: A 35-year-old pregnant woman was found to have a fetus with anencephaly by prenatal ultrasound at 12 weeks of gestation. The pregnancy was subsequently terminated, and a malformed fetus was delivered with anencephaly. Cytogenetic analysis of the cultured placental tissues revealed a karyotype of 46,XX,dup(15) (q24...
August 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28805616/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of-mosaicism-for-a-small-supernumerary-marker-chromosome-derived-from-chromosome-16
#6
Chih-Ping Chen, Tsang-Ming Ko, Schu-Rern Chern, Peih-Shan Wu, Shin-Wen Chen, Shih-Ting Lai, Chien-Wen Yang, Chen-Wen Pan, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome (sSMC) derived from chromosome 16. CASE REPORT: A 28-year-old woman underwent amniocentesis at 17 weeks of gestation because of abnormal maternal serum screening for Down syndrome. Amniocentesis revealed a karyotype of 47,XY,+mar[5]/46,XY[9]. Parental karyotypes were normal. Prenatal ultrasound findings were unremarkable. Array comparative genomic hybridization (aCGH) analysis of cultured amniocytes revealed a de novo 16% gene dosage increase of 16q11...
August 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28805612/detection-of-paternal-uniparental-disomy-9-in-a-neonate-with-prenatally-detected-mosaicism-for-a-small-supernumerary-marker-chromosome-9-and-a-supernumerary-ring-chromosome-9
#7
Chih-Ping Chen, Ming Chen, Liang-Kai Wang, Schu-Rern Chern, Peih-Shan Wu, Shin-Wen Chen, Shih-Ting Lai, Shun-Ping Chang, Chien-Wen Yang, Chen-Wen Pan, Wayseen Wang
OBJECTIVE: We present the association of paternal uniparental disomy (UPD) 9 with mosaicism for a small supernumerary marker chromosome 9 [sSMC(9)] and a supernumerary ring chromosome 9 [r(9)]. MATERIALS AND METHODS: A 38-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XY,+mar [25]/48,XY,+mar,+r(9) [4]/47,XY,+r(9) [1]/46,XY [6]. The parental karyotypes were normal. Array comparative genomic hybridization (aCGH) of cultured amniocytes revealed a result of de novo 9p13...
August 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28805610/validation-of-a-high-throughput-and-robust-technique-bacs-on-beads-assay-karyolite-bobs-for-pre-implantation-aneuploidy-screening
#8
Grace Wing Shan Kong, Yanlin Ma, Jian Ou, Yvonne Ka Yin Kwok, Wei Wang, Queenie Sum Yee Yeung, Cherry Kit Man Wong, Qi Li, Wen Xu, Weiying Lu, Hong Li, Tin Chiu Li, Kwong Wai Choy
OBJECTIVE: This study aims to validate the BACs-on-Beads (BoB) technology as a robust and high throughput method for pre-implantation genetic screening (PGS) for aneuploidy. MATERIAL AND METHODS: The performances with respect to the sensitivity, specificity, success rate and detection rate of this technique from new BoBs technology and traditional array chromosomal genomic hybridization (aCGH) were compared. And the use of BoBs as a screening tool for euploid embryos in PGS was evaluated...
August 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28804721/corrigendum-to-comparative-study-of-exome-copy-number-variation-estimation-tools-using-array-comparative-genomic-hybridization-as-control
#9
Yan Guo, Quanhu Sheng, David C Samuels, Brian Lehmann, Joshua A Bauer, Jennifer Pietenpol, Yu Shyr
[This corrects the article DOI: 10.1155/2013/915636.].
2017: BioMed Research International
https://www.readbyqxmd.com/read/28802496/molecular-melanoma-diagnosis-update-gene-fusion-genomic-hybridization-and-massively-parallel-short-read-sequencing
#10
REVIEW
Ursula E Lang, Iwei Yeh, Timothy H McCalmont
Molecular evaluation of melanocytic tumors can be diagnostically useful to confirm malignancy or benignancy. Molecular tools are ancillary and supplemental to histopathologic evaluation and do not replace conventional microscopy. Immunohistochemistry, fluorescence in situ hybridization, array comparative genomic hybridization, and massively parallel short-read sequencing, often referred to as next-generation sequencing, each provide varied (and often incomplete) additional information, and careful planning is necessary if tissue is limited...
September 2017: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/28798363/defining-quantification-methods-and-optimizing-protocols-for-microarray-hybridization-of-circulating-micrornas
#11
Anna Garcia-Elias, Leonor Alloza, Eulàlia Puigdecanet, Lara Nonell, Marta Tajes, Joao Curado, Cristina Enjuanes, Oscar Díaz, Jordi Bruguera, Julio Martí-Almor, Josep Comín-Colet, Begoña Benito
MicroRNAs (miRNAs) have emerged as promising biomarkers of disease. Their potential use in clinical practice requires standardized protocols with very low miRNA concentrations, particularly in plasma samples. Here we tested the most appropriate method for miRNA quantification and validated the performance of a hybridization platform using lower amounts of starting RNA. miRNAs isolated from human plasma and from a reference sample were quantified using four platforms and profiled with hybridization arrays and RNA sequencing (RNA-seq)...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790112/burden-and-profile-of-somatic-mutation-in-duodenal-adenomas-from-patients-with-familial-adenomatous-and-mutyh-associated-polyposis
#12
Laura Elizabeth Thomas, Joanna J Hurley, Elena Meuser, Sian Jose, Kevin E Ashelford, Matthew Mort, Shelley Idziaszczyk, Julie Maynard, Helena Leon Brito, Manon Harry, Angharad Walters, Meera Raja, Sarah Jane Walton, Sunil Dolwani, Geraint T Williams, Meleri Morgan, Morgan Moorghen, Susan K Clark, Julian R Sampson
Duodenal polyposis and cancer are important causes of morbidity and mortality in familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP). This study aimed to comprehensively characterize somatic genetic changes in FAP and MAP duodenal adenomas to better understand duodenal tumorigenesis in these disorders.<br /><br />Experimental Design: Sixty-nine adenomas were biopsied during endoscopy in 16 FAP and 10 MAP patients with duodenal polyposis. Ten FAP and 10 MAP adenomas and matched blood DNA samples were exome sequenced, 42 further adenomas underwent targeted sequencing and 47 were studied by array comparative genomic hybridization...
August 8, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28777864/-genetic-analysis-and-prenatal-diagnosis-for-a-pregnant-woman-with-an-unbalanced-t-1-2-t-6-7-translocation-and-intellectual-disability
#13
Yinhong Zhang, Bicheng Yang, Xinhua Tang, Shu Chen, Rui Yu, Jing He, Jie Su, Shu Zhu, Baosheng Zhu
OBJECTIVE: To provide genetic analysis for a pregnant woman with chromosomal translocations and intellectual disability, and to provide prenatal diagnosis for her fetus. METHODS: Routine G-banding was performed to analyze the karyotypes of the woman and her fetus. Copy number variants were determined with array comparative genomic hybridization (array-CGH). RESULTS: The pregnant woman has carried an apparently balanced translocation involving chromosomes 1, 2, 6 and 7, with a karyotype of 46, XX, t(1;2) (p22;p23), t(6;7) (q21;p15)...
August 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28777857/-application-of-chromosomal-karyotyping-analysis-and-array-cgh-for-fetal-abnormalities-detected-by-ultrasonography
#14
Yousheng Wang, Bin Tang, Li Guo, Hanbiao Chen, Jian Lu, Aihua Yin
OBJECTIVE: To assess the value of chromosomal karyotyping and array-based comparative genomic hybridization for the diagnosis of fetus with abnormalities detected by ultrasonography. METHODS: Umbilical cord blood samples were derived from 1 603 pregnant women. The samples were cultured for routine G-banding karyotype analysis. Among these, 792 samples have further subjected to array CGH analysis. RESULTS: Among the 1 603 fetuses, 117 (7.30%) were found with chromosomal abnormalities...
August 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28777848/-phenotypic-and-genetic-analysis-of-four-patients-with-13q33-q34-microdeletion
#15
Huanhuan Wang, Bing Xiao, Xing Ji, Jingmin Zhang, Ying Cao, Lin Ni, Hui Ye, Lixiao Shen
OBJECTIVE: To explore the correlation between 13q33-q34 microdeletion and clinical phenotype. METHODS: Routine chromosomal banding was performed to analyze the karyotype, while array-based comparative genomic hybridization (aCGH array) and single nucleotide polymorphism array(SNP array) were employed to investigate the genome copy number variations. RESULTS: The karyotype of patient 1 was 46, XY, 9qh+,13qs. Patient 2 showed 46, XX, der (13)...
August 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28766492/mody3-renal-cysts-and-dandy-walker-variants-with-a-microdeletion-spanning-the-hnf1a-gene
#16
Hiro Matsukura, Mariko Nagamori, Kazushi Miya, Tohru Yorifuji
Heterozygous hepatocyte nuclear factor-1-α gene (<italic>HNF1A</italic>) mutations are the most common cause of maturity-onset diabetes of the young (MODY), but they rarely involve extrahepatic manifestations. Renal cysts and diabetes syndrome can be caused by <italic>HNF1B</italic> mutations. No association between MODY3 and Dandy-Walker variants (DWV) has been reported. <italic>HNF1A</italic> mutations might be responsible for renal malformations. In a Japanese girl with glycosuria, developmental delay, mental retardation, renal cysts, and DWV, the <italic>HNF1B</italic> gene had no mutations...
September 2017: Clinical Nephrology
https://www.readbyqxmd.com/read/28764467/spectral-analysis-of-bistatic-scattering-from-underwater-elastic-cylinders-and-spheres
#17
Aaron M Gunderson, Aubrey L España, Philip L Marston
Far field sound scattering from underwater elastic spheres and finite cylinders is considered over the full range of scattering angles. Three models for the frequency response of the scattered field are evaluated: a hybrid finite element/propagation simulation for a finite cylinder with broadside illumination, an approximate solution for the finite cylinder, and the exact solution for a sphere. The cylinder models are shown to give comparable results, attesting to the strength of the finite cylinder approximate solution...
July 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28758373/fetal-cerebral-ventricular-dilatation-etiopathogenic-study-of-130-observations
#18
Sihem Darouich, Lucile Boutaud, Bettina Bessières, Maryse Bonnière, Jelena Martinovic, Charlotte Mechler, Caroline Alby, Jean-Pierre Bernard, Philippe Roth, Yves Ville, Valerie Malan, Michel Vekemans, Tania Attié-Bitach, Férechté Encha-Razavi
BACKGROUND: Fetal cerebral ventricular dilatation (CVD) is a common abnormal prenatal finding that often predicts a poor prognosis. The etiology involves both genetic and nongenetic factors with diverse pathogenic mechanisms. We describe the neuropathological features of CVD in a large cohort of fetuses. The goals are to determine the physiopathological mechanisms and etiologies. METHODS: We retrospectively analyzed a series of 130 fetuses examined at the Necker University Hospital following termination of pregnancy between January 2000 and December 2014...
July 31, 2017: Birth defects research
https://www.readbyqxmd.com/read/28752839/development-and-validation-of-a-novel-clinical-fluorescence-in-situ-hybridization-assay-to-detect-jak2-and-pd-l1-amplification-a-fluorescence-in-situ-hybridization-assay-for-jak2-and-pd-l1-amplification
#19
Meixuan Chen, Mariacarla Andreozzi, Barbara Pockaj, Michael T Barrett, Idris Tolgay Ocal, Ann E McCullough, Maria E Linnaus, James M Chang, Jennifer H Yearley, Lakshmanan Annamalai, Karen S Anderson
The amplification of chromosome 9p24.1 encoding PD-L1, PD-L2, and JAK2 has been reported in multiple types of cancer and is associated with poor outcome, upregulation of PD-L1, and activation of the JAK/STAT pathway. We have developed a novel fluorescence in situ hybridization assay which combines 3 probes mapping to 9p24.1 with a commercial chromosome 9 centromere (CEN9) probe for detection of the JAK2/9p24.1 amplification. JAK2 fluorescence in situ hybridization was compared with array-based comparative genomic hybridization in 34 samples of triple negative breast cancer tumor...
July 28, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28751446/gene-copy-number-estimation-from-targeted-next-generation-sequencing-of-prostate-cancer-biopsies-analytic-validation-and-clinical-qualification
#20
George Seed, Wei Yuan, Joaquin Mateo, Suzanne Carreira, Claudia Bertan, Maryou Lambros, Gunther Boysen, Roberta Ferraldeschi, Susana Miranda, Ines Figueiredo, Ruth Riisnaes, Mateus Crespo, Daniel Nava Rodrigues, Eric Talevich, Dan R Robinson, Lakshmi P Kunju, Yi-Mi Wu, Robert Lonigro, Shahneen Sandhu, Arul Chinnayan, Johann S de Bono
Abstract <p>Purpose</p> <p>Precise detection of copy number aberrations (CNAs) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next generation sequencing (NGS) is inexpensive, high throughput and easily feasible, allowing single nucleotide variant calls, but CNA estimation from this remains challenging..</p> <p>Experimental Design</p> <p>We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration resistant prostate cancer biopsies, and used capture based whole exome sequencing (WES), array comparative genomic hybridization (aCGH), and fluorescent in situ hybridization (FISH) to explore the viability of this approach...
July 27, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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