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https://www.readbyqxmd.com/read/29457755/novel-approach-for-ces1-genotyping-integrating-single-nucleotide-variants-and-structural-variation
#1
Ditte Bjerre, Henrik Berg Rasmussen
AIM: Development of a specific procedure for genotyping of CES1A1 (CES1) and CES1A2, a hybrid of CES1A1 and the pseudogene CES1P1. MATERIALS & METHODS: The number of CES1A1 and CES1A2 copies and that of CES1P1 were determined using real-time PCR. Long range PCRs followed by secondary PCRs allowed sequencing of single nucleotide variants in CES1A1 and CES1A2. Results & conlusion: A procedure consisting of two main steps was developed. Its first main step, the copy number determination, informed about presence of CES1A2 ...
February 19, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29455582/nonvisualization-of-fetal-gallbladder-in-microarray-era-a-retrospective-cohort-study-and-review-of-the-literature
#2
Sagi-Dain Lena, Singer Amihood, Yarin Hadid, Sharony Reuven, Chana Vinkler, Bar-Shira Anat, Reeval Segel, Ben Shachar Shay, Maya Idit
OBJECTIVE: To examine the frequency of abnormal Chromosomal Microarray (CMA) analyses among fetuses with isolated nonvisualization of fetal gallbladder. METHODS: Data from CMA analyses performed due to isolated nonvisualization of fetal gallbladder between January 2013 and September 2016 were retrospectively acquired from a computerized database of the Israeli Ministry of Health. The results were compared to the rate for clinically significant CMA findings in general population, based on a large cohort of 5541 pregnancies undergoing CMA due to maternal request, and a systematic review of 9272 cases with normal ultrasound...
February 18, 2018: Journal of Maternal-fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/29455159/a-case-of-paternal-uniparental-isodisomy-for-chromosome-7-associated-with-overgrowth
#3
Akie Nakamura, Koji Muroya, Hiroko Ogata-Kawata, Kazuhiko Nakabayashi, Keiko Matsubara, Tsutomu Ogata, Kenji Kurosawa, Maki Fukami, Masayo Kagami
BACKGROUND: Paternal uniparental disomy for chromosome 7 (upd(7)pat) is extremely rare, and only four cases have been previously reported. As these cases were accompanied by autosomal-recessive disorders which are likely to be involved in growth restriction, the relevance of upd(7)pat to the overgrowth phenotype remains unclear. Here we describe one case of upd(7)pat with no additional genetic diseases, which may answer the question. METHODS: A 5-year-old Japanese boy presented with a tall stature of unknown causes...
February 17, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29451984/two-component-ferritin-nanoparticles-for-multimerization-of-diverse-trimeric-antigens
#4
Ivelin S Georgiev, Michael Gordon Joyce, Rita E Chen, Kwanyee Leung, Krisha McKee, Aliaksandr Druz, Joseph G Van Galen, Masaru Kanekiyo, Yaroslav Tsybovsky, Eun Sung Yang, Yongping Yang, Priyamvada Acharya, Marie Pancera, Paul V Thomas, Timothy Wanninger, Hadi Yassine, Ulrich Baxa, Nicole Doria-Rose, Cheng Cheng, Barney S Graham, John R Mascola, Peter D Kwong
Antigen multimerization on a nanoparticle can result in improved neutralizing antibody responses. A platform that has been successfully used for displaying antigens from a number of different viruses is ferritin, a self-assembling protein nanoparticle that allows the attachment of multiple copies (twenty-four monomers or eight trimers) of a single antigen. Here we design two-component ferritin variants that allow the attachment of two diverse antigens on a single particle in a defined ratio and geometric pattern...
February 16, 2018: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29449575/actionable-perturbations-of-damage-responses-by-tcl1-atm-and-epigenetic-lesions-form-the-basis-of-t-pll
#5
A Schrader, G Crispatzu, S Oberbeck, P Mayer, S Pützer, J von Jan, E Vasyutina, K Warner, N Weit, N Pflug, T Braun, E I Andersson, B Yadav, A Riabinska, B Maurer, M S Ventura Ferreira, F Beier, J Altmüller, M Lanasa, C D Herling, T Haferlach, S Stilgenbauer, G Hopfinger, M Peifer, T H Brümmendorf, P Nürnberg, K S J Elenitoba-Johnson, S Zha, M Hallek, R Moriggl, H C Reinhardt, M-H Stern, S Mustjoki, S Newrzela, P Frommolt, M Herling
T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. Here we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identify novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor/cytokine signaling, and histone modulation...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29444201/hierarchical-analysis-of-rna-seq-reads-improves-the-accuracy-of-allele-specific-expression
#6
Narayanan Raghupathy, Kwangbom Choi, Matthew J Vincent, Glen L Beane, Keith Sheppard, Steven C Munger, Ron Korstanje, Fernando Pardo-Manual de Villena, Gary A Churchill, Alfonso Valencia
Motivation: Allele-specific expression (ASE) refers to the differential abundance of the allelic copies of a transcript. RNA sequencing (RNA-Seq) can provide quantitative estimates of ASE for genes with transcribed polymorphisms. When short-read sequences are aligned to a diploid transcriptome, readmapping ambiguities confound our ability to directly count reads. Multi-mapping reads aligning equally well to multiple genomic locations, isoforms, or alleles can comprise the majority (>85%) of reads...
February 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29441128/chromosomal-microarray-analysis-in-the-genetic-evaluation-of-279-patients-with-syndromic-obesity
#7
Carla Sustek D'Angelo, Monica Castro Varela, Claudia Irene Emílio de Castro, Paulo Alberto Otto, Ana Beatriz Alvarez Perez, Charles Marques Lourenço, Chong Ae Kim, Debora Romeo Bertola, Fernando Kok, Luis Garcia-Alonso, Celia Priszkulnik Koiffmann
Background: Syndromic obesity is an umbrella term used to describe cases where obesity occurs with additional phenotypes. It often arises as part of a distinct genetic syndrome with Prader-Willi syndrome being a classical example. These rare forms of obesity provide a unique source for identifying obesity-related genetic changes. Chromosomal microarray analysis (CMA) has allowed the characterization of new genetic forms of syndromic obesity, which are due to copy number variants (CNVs); however, CMA in large cohorts requires more study...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29440707/systematic-assessment-of-the-performance-of-whole-genome-amplification-for-snp-cnv-detection-and-%C3%AE-thalassemia-genotyping
#8
Fei He, Wanjun Zhou, Ren Cai, Tizhen Yan, Xiangmin Xu
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods...
February 13, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29440233/comprehensive-characterisation-of-compartment-specific-long-non-coding-rnas-associated-with-pancreatic-ductal-adenocarcinoma
#9
Luis Arnes, Zhaoqi Liu, Jiguang Wang, Hans Carlo Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana C Garofalo, Dina A Balderes, Lori Sussel, Kenneth P Olive, Raul Rabadan
OBJECTIVE: Pancreatic ductal adenocarcinoma (PDA) is a highly metastatic disease with limited therapeutic options. Genome and transcriptome analyses have identified signalling pathways and cancer driver genes with implications in patient stratification and targeted therapy. However, these analyses were performed in bulk samples and focused on coding genes, which represent a small fraction of the genome. DESIGN: We developed a computational framework to reconstruct the non-coding transcriptome from cross-sectional RNA-Seq, integrating somatic copy number alterations (SCNA), common germline variants associated to PDA risk and clinical outcome...
February 10, 2018: Gut
https://www.readbyqxmd.com/read/29434842/comprehensive-characterization-of-cancer-genes-in-hepatocellular-carcinoma-genomes
#10
Zhihao Zhang, Liping Xu, Changyu Sun
The present study was performed to detect moderate or low-frequency mutated cancer driver genes in hepatocellular carcinoma (HCC), using OncodriveFM and Dendrix. Following this, integrated analyses were conducted on these novel cancer driver genes. A total of 112,980 somatic mutations were retrieved from TCGA and classified into 11 categories based on their function. Driver genes and pathways were predicted by OncodriveFM and Dendrix, followed by differential expression, DNA-methylation, copy number variations and survival analyses...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434669/copy-number-variation-and-regions-of-homozygosity-analysis-in-patients-with-m%C3%A3-llerian-aplasia
#11
Durkadin Demir Eksi, Yiping Shen, Munire Erman, Lynn P Chorich, Megan E Sullivan, Meric Bilekdemir, Elanur Yılmaz, Guven Luleci, Hyung-Goo Kim, Ozgul M Alper, Lawrence C Layman
Background: Little is known about the genetic contribution to Müllerian aplasia, better known to patients as Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome. Mutations in two genes (WNT4 and HNF1B) account for a small number of patients, but heterozygous copy number variants (CNVs) have been described. However, the significance of these CNVs in the pathogenesis of MRKH is unknown, but suggests possible autosomal dominant inheritance. We are not aware of CNV studies in consanguineous patients, which could pinpoint genes important in autosomal recessive MRKH...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29433456/exome-sequencing-of-primary-breast-cancers-with-paired-metastatic-lesions-reveals-metastasis-enriched-mutations-in-the-a-kinase-anchoring-protein-family-akaps
#12
Una Kjällquist, Rikard Erlandsson, Nicholas P Tobin, Amjad Alkodsi, Ikram Ullah, Gustav Stålhammar, Eva Karlsson, Thomas Hatschek, Johan Hartman, Sten Linnarsson, Jonas Bergh
BACKGROUND: Tumor heterogeneity in breast cancer tumors is today widely recognized. Most of the available knowledge in genetic variation however, relates to the primary tumor while metastatic lesions are much less studied. Many studies have revealed marked alterations of standard prognostic and predictive factors during tumor progression. Characterization of paired primary- and metastatic tissues should therefore be fundamental in order to understand mechanisms of tumor progression, clonal relationship to tumor evolution as well as the therapeutic aspects of systemic disease...
February 12, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29433427/methcna-a-database-for-integrating-genomic-and-epigenomic-data-in-human-cancer
#13
Gaofeng Deng, Jian Yang, Qing Zhang, Zhi-Xiong Xiao, Haoyang Cai
BACKGROUND: The integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29431110/the-personal-genome-project-canada-findings-from-whole-genome-sequences-of-the-inaugural-56-participants
#14
Miriam S Reuter, Susan Walker, Bhooma Thiruvahindrapuram, Joe Whitney, Iris Cohn, Neal Sondheimer, Ryan K C Yuen, Brett Trost, Tara A Paton, Sergio L Pereira, Jo-Anne Herbrick, Richard F Wintle, Daniele Merico, Jennifer Howe, Jeffrey R MacDonald, Chao Lu, Thomas Nalpathamkalam, Wilson W L Sung, Zhuozhi Wang, Rohan V Patel, Giovanna Pellecchia, John Wei, Lisa J Strug, Sherilyn Bell, Barbara Kellam, Melanie M Mahtani, Anne S Bassett, Yvonne Bombard, Rosanna Weksberg, Cheryl Shuman, Ronald D Cohn, Dimitri J Stavropoulos, Sarah Bowdin, Matthew R Hildebrandt, Wei Wei, Asli Romm, Peter Pasceri, James Ellis, Peter Ray, M Stephen Meyn, Nasim Monfared, S Mohsen Hosseini, Ann M Joseph-George, Fred W Keeley, Ryan A Cook, Marc Fiume, Hin C Lee, Christian R Marshall, Jill Davies, Allison Hazell, Janet A Buchanan, Michael J Szego, Stephen W Scherer
BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant...
February 5, 2018: CMAJ: Canadian Medical Association Journal, Journal de L'Association Medicale Canadienne
https://www.readbyqxmd.com/read/29428286/the-use-of-chromosomal-microarray-analysis-in-prenatal-diagnosis
#15
REVIEW
Melissa Stosic, Brynn Levy, Ronald Wapner
Chromosomal microarray analysis (CMA) identifies microdeletions and duplications undetected on karyotype analysis. Copy number variants (CNVs) occur in 1% to 1.7% of all pregnancies, with clinical implications. All women undergoing invasive testing for routine indications should be offered microarray. Clinically significant CNVs are seen in approximately 6% of pregnancies with ultrasound anomalies, making CMAs the current standard of cytogenomic analysis. Clinicians should be familiar with different technologies and laboratory reporting practices...
March 2018: Obstetrics and Gynecology Clinics of North America
https://www.readbyqxmd.com/read/29428281/cell-free-dna-screening-for-aneuploidy-and-microdeletion-syndromes
#16
REVIEW
Brian L Shaffer, Mary E Norton
Cell-free DNA (cfDNA) screening for the common aneuploidies is an accurate noninvasive screen for the common autosomal and sex chromosome aneuploidies. However, cfDNA screening should not be considered a diagnostic test, and the positive predictive value should be used in counseling women with a positive test regarding the option for diagnostic testing. Compared with traditional screening, cfDNA may not detect as many chromosomal abnormalities of importance. Furthermore, due to the low prevalence of recurrent copy number variants, the clinical utility in screening for microdeletions and duplications is uncertain and is not recommended for the general obstetric population...
March 2018: Obstetrics and Gynecology Clinics of North America
https://www.readbyqxmd.com/read/29415173/integrative-pipeline-for-profiling-dna-copy-number-and-inferring-tumor-phylogeny
#17
Eugene Urrutia, Hao Chen, Zilu Zhou, Nancy R Zhang, Yuchao Jiang
Summary: Copy number variation is an important and abundant source of variation in the human genome, which has been associated with a number of diseases, especially cancer. Massively parallel next-generation sequencing allows copy number profiling with fine resolution. Such efforts, however, have met with mixed successes, with setbacks arising partly from the lack of reliable analytical methods to meet the diverse and unique challenges arising from the myriad experimental designs and study goals in genetic studies...
February 5, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29415044/a-computational-approach-to-distinguish-somatic-vs-germline-origin-of-genomic-alterations-from-deep-sequencing-of-cancer-specimens-without-a-matched-normal
#18
James X Sun, Yuting He, Eric Sanford, Meagan Montesion, Garrett M Frampton, Stéphane Vignot, Jean-Charles Soria, Jeffrey S Ross, Vincent A Miller, Phil J Stephens, Doron Lipson, Roman Yelensky
A key constraint in genomic testing in oncology is that matched normal specimens are not commonly obtained in clinical practice. Thus, while well-characterized genomic alterations do not require normal tissue for interpretation, a significant number of alterations will be unknown in whether they are germline or somatic, in the absence of a matched normal control. We introduce SGZ (somatic-germline-zygosity), a computational method for predicting somatic vs. germline origin and homozygous vs. heterozygous or sub-clonal state of variants identified from deep massively parallel sequencing (MPS) of cancer specimens...
February 7, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29410473/offering-pregnant-women-different-levels-of-genetic-information-from-prenatal-chromosome-microarray-a-prospective-study
#19
Jane L Halliday, Cecile Muller, Taryn Charles, Fiona Norris, Joanne Kennedy, Sharon Lewis, Bettina Meiser, Susan Donath, Zornitza Stark, George McGillivray, Melody Menezes, Sian K Smith, Della Forster, Susan Walker, Mark Pertile, David J Amor
This study aimed to examine the choice pregnant women make about the amount of fetal genetic information they want from chromosome microarray. Women having invasive prenatal testing in the absence of fetal structural abnormality were recruited in Victoria, Australia. A decision aid for women described 'targeted' analysis as reporting only copy number variants implicated in a highly penetrant and well-described phenotype and 'extended' as additionally reporting variants of uncertain or unknown significance. Participant's choice and demographics were collected by survey before chorionic villus sampling or amniocentesis; psychological data were also collected then and again about 10 days after receiving results...
February 6, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29407415/waardenburg-syndrome-novel-mutations-in-a-large-brazilian-sample
#20
Magnolia Astrid Pretell Bocángel, Uirá Souto Melo, Leandro Ucela Alves, Eliete Pardono, Naila Cristina Vilaça Lourenço, Humberto Vicente Cezar Marcolino, Paulo Alberto Otto, Regina Célia Mingroni-Netto
This paper deals with the molecular investigation of Waardenburg syndrome (WS) in a sample of 49 clinically diagnosed probands (most from southeastern Brazil), 24 of them having the type 1 (WS1) variant (10 familial and 14 isolated cases) and 25 being affected by the type 2 (WS2) variant (five familial and 20 isolated cases). Sequential Sanger sequencing of all coding exons of PAX3, MITF, EDN3, EDNRB, SOX10 and SNAI2 genes, followed by CNV detection by MLPA of PAX3, MITF and SOX10 genes in selected cases revealed many novel pathogenic variants...
January 30, 2018: European Journal of Medical Genetics
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