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https://www.readbyqxmd.com/read/27909141/developing-a-risk-scoring-model-for-ankylosing-spondylitis-based-on-a-combination-of-hla-b27-single-nucleotide-polymorphism-and-copy-number-variant-markers
#1
Seung-Hyun Jung, Sung-Min Cho, Seon-Hee Yim, So-Hee Kim, Hyeon-Chun Park, Mi-La Cho, Seung-Cheol Shim, Tae-Hwan Kim, Sung-Hwan Park, Yeun-Jun Chung
OBJECTIVE: To develop a genotype-based ankylosing spondylitis (AS) risk prediction model that is more sensitive and specific than HLA-B27 typing. METHODS: To develop the AS genetic risk scoring (AS-GRS) model, 648 individuals (285 cases and 363 controls) were examined for 5 copy number variants (CNV), 7 single-nucleotide polymorphisms (SNP), and an HLA-B27 marker by TaqMan assays. The AS-GRS model was developed using logistic regression and validated with a larger independent set (576 cases and 680 controls)...
December 2016: Journal of Rheumatology
https://www.readbyqxmd.com/read/27905110/distinct-molecular-landscapes-between-endometrioid-and-non-endometrioid-uterine-carcinomas
#2
Nathaniel L Jones, Joanne Xiu, Sudeshna Chatterjee-Paer, Alexandre Buckley de Meritens, William M Burke, Ana I Tergas, Jason D Wright, June Y Hou
Endometrial carcinoma (EC) is traditionally characterized as endometrioid and non-endometrioid based on histo-pathologic phenotypes. Molecular-based classifications have been proposed, but are not widely implemented. Herein we examine molecular profiles between EC histologic subtypes. 3133 ECs were submitted between March 2011 and July 2014: 1634 Type I and 1226 Type II. In situ hybridization and immunohistochemistry were used to assess copy number and protein expression of selected genes. Sequenced variants in 47 genes were analyzed using the Illumina TruSeq Amplicon Cancer Panel...
December 1, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27903293/personalized-medicine-approach-confirms-a-milder-case-of-abat-deficiency
#3
A Besse, A K Petersen, J V Hunter, V Appadurai, S R Lalani, P E Bonnen
ABAT deficiency (OMIM 613163) is a rare inborn error of metabolism caused by recessive variants in the gene 4-aminobutyric acid transaminase (ABAT), which is responsible for both the catalysis of GABA and maintenance of nucleoside pools in the mitochondria. To date, only a few patients have been reported worldwide. Their clinical presentation has been remarkably consistent with primary features of severe psychomotor retardation, encephalopathy, hypotonia, and infantile-onset refractory epilepsy. We report a new case of ABAT deficiency that marks an important departure from previous clinical findings...
December 1, 2016: Molecular Brain
https://www.readbyqxmd.com/read/27901321/copy-number-variants-in-a-population-based-investigation-of-klippel-trenaunay-syndrome
#4
Aggeliki Dimopoulos, Robert J Sicko, Denise M Kay, Shannon L Rigler, Ruzong Fan, Paul A Romitti, Marilyn L Browne, Charlotte M Druschel, Michele Caggana, Lawrence C Brody, James L Mills
Klippel-Trenaunay syndrome (KTS) is a rare congenital vascular disorder that is thought to occur sporadically; however, reports of familial occurrence suggest a genetic component. We examined KTS cases to identify novel, potentially causal copy number variants (CNVs). We identified 17 KTS cases from all live-births occurring in New York (1998-2010). Extracted DNA was genotyped using Illumina microarrays and CNVs were called using PennCNV software. CNVs selected for follow-up had ≥10 single nucleotide polymorphisms (SNPs) and minimal overlap with in-house controls or controls from the Database of Genomic Variants...
November 30, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27899578/cosmic-somatic-cancer-genetics-at-high-resolution
#5
Simon A Forbes, David Beare, Harry Boutselakis, Sally Bamford, Nidhi Bindal, John Tate, Charlotte G Cole, Sari Ward, Elisabeth Dawson, Laura Ponting, Raymund Stefancsik, Bhavana Harsha, Chai Yin Kok, Mingming Jia, Harry Jubb, Zbyslaw Sondka, Sam Thompson, Tisham De, Peter J Campbell
COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899115/characterizing-the-impact-of-sustained-sulfadoxine-pyrimethamine-use-upon-the-plasmodium-falciparum-population-in-malawi
#6
Matt Ravenhall, Ernest Diez Benavente, Mwapatsa Mipando, Anja T R Jensen, Colin J Sutherland, Cally Roper, Nuno Sepúlveda, Dominic P Kwiatkowski, Jacqui Montgomery, Kamija S Phiri, Anja Terlouw, Alister Craig, Susana Campino, Harold Ocholla, Taane G Clark
BACKGROUND: Malawi experienced prolonged use of sulfadoxine/pyrimethamine (SP) as the front-line anti-malarial drug, with early replacement of chloroquine and delayed introduction of artemisinin-based combination therapy. Extended use of SP, and its continued application in pregnancy is impacting the genomic variation of the Plasmodium falciparum population. METHODS: Whole genome sequence data of P. falciparum isolates covering 2 years of transmission within Malawi, alongside global datasets, were used...
November 29, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27897270/trueprime-is-a-novel-method-for-whole-genome-amplification-from-single-cells-based-on-tthprimpol
#7
Ángel J Picher, Bettina Budeus, Oliver Wafzig, Carola Krüger, Sara García-Gómez, María I Martínez-Jiménez, Alberto Díaz-Talavera, Daniela Weber, Luis Blanco, Armin Schneider
Sequencing of a single-cell genome requires DNA amplification, a process prone to introducing bias and errors into the amplified genome. Here we introduce a novel multiple displacement amplification (MDA) method based on the unique DNA primase features of Thermus thermophilus (Tth) PrimPol. TthPrimPol displays a potent primase activity preferring dNTPs as substrates unlike conventional primases. A combination of TthPrimPol's unique ability to synthesize DNA primers with the highly processive Phi29 DNA polymerase (Φ29DNApol) enables near-complete whole genome amplification from single cells...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27896429/copy-number-variability-in-parkinson-s-disease-assembling-the-puzzle-through-a-systems-biology-approach
#8
REVIEW
Valentina La Cognata, Giovanna Morello, Velia D'Agata, Sebastiano Cavallaro
Parkinson's disease (PD), the second most common progressive neurodegenerative disorder of aging, was long believed to be a non-genetic sporadic origin syndrome. The proof that several genetic loci are responsible for rare Mendelian forms has represented a revolutionary breakthrough, enabling to reveal molecular mechanisms underlying this debilitating still incurable condition. While single nucleotide polymorphisms (SNPs) and small indels constitute the most commonly investigated DNA variations accounting for only a limited number of PD cases, larger genomic molecular rearrangements have emerged as significant PD-causing mutations, including submicroscopic Copy Number Variations (CNVs)...
November 28, 2016: Human Genetics
https://www.readbyqxmd.com/read/27895020/a-naturally-occurring-snp-in-plasmid-pb1000-produces-a-reversible-increase-in-antibiotic-resistance
#9
Alfonso Santos-Lopez, Cristina Bernabe-Balas, Manuel Ares-Arroyo, Rafael Ortega-Huedo, Andreas Hoefer, Alvaro San Millan, Bruno Gonzalez-Zorn
ColE1 plasmids are small mobilizable replicons that play an important role in the spread of antibiotic resistance in Pasteurellaceae. In this study we describe how a natural single nucleotide polymorphism (SNP) near the origin of replication of the ColE1-type plasmid pB1000 found in a Pasteurella multocida clinical isolate, generates two independent plasmid variants able to coexist in the same cell simultaneously. Using Haemophilus influenzae Rd strain as a model system, we combined antibiotic susceptibility tests, quantitative PCRs, competition assays and experimental evolution to characterize the consequences of the coexistence of the pB1000 plasmid variants...
November 28, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27893202/role-of-gstm1-copy-number-variant-in-the-prognosis-of-thai-colorectal-cancer-patients-treated-with-5-fu-based-chemotherapy
#10
Tanett Pongtheerat, Pensri Saelee
Background: Glutathione S-transferase M1 (GSTM1) is involved in the detoxification of carcinogenic agents. DNA copy number variants of GSTM1 may be associated with cancer progression and may result in reduced survival time of various cancers. Determination of DNA copy number variants was here used to assess the association between GSTM1 copy number variant and pathological status and survival time of colorectal-cancer patients treated with 5-fluorouracil-based chemotherapy. Methods: One hundred thirteen Thai colorectal-cancer patients were investigated for GSTM1 copy number variant by real-time PCR...
January 10, 2016: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/27891178/enrichment-of-small-pathogenic-deletions-at-chromosome-9p24-3-and-9q34-3-involving-dock8-kank1-ehmt1-genes-identified-by-using-high-resolution-oligonucleotide-single-nucleotide-polymorphism-array-analysis
#11
Jia-Chi Wang, Loretta W Mahon, Leslie P Ross, Arturo Anguiano, Renius Owen, Fatih Z Boyar
BACKGROUND: High-resolution oligo-SNP array allowed the identification of extremely small pathogenic deletions at numerous clinically relevant regions. In our clinical practice, we found that small pathogenic deletions were frequently encountered at chromosome 9p and 9q terminal regions. RESULTS: A review of 531 cases with reportable copy number changes on chromosome 9 revealed142 pathogenic copy number variants (CNVs): 104 losses, 31 gains, 7 complex chromosomal rearrangements...
2016: Molecular Cytogenetics
https://www.readbyqxmd.com/read/27888582/nucleotide-substitutions-in-cd101-the-human-homolog-of-a-diabetes-susceptibility-gene-in-non-obese-diabetic-mouse-in-patients-with-type-1-diabetes
#12
Misako Okuno, Yoshihito Kasahara, Masafumi Onodera, Noriyuki Takubo, Michiko Okajima, Shigeru Suga, Nobuyuki Watanabe, Junichi Suzuki, Tadayuki Ayabe, Tatsuhiko Urakami, Tomoyuki Kawamura, Nobuyuki Kikuchi, Ichiro Yokota, Toru Kikuchi, Shin Amemiya, Kazuhiko Nakabayashi, Keiko Hayashi, Kenichiro Hata, Yoichi Matsubara, Tsutomu Ogata, Maki Fukami, Shigetaka Sugihara
AIMS/INTRODUCTION: Although genome-wide association studies have identified more than 50 susceptibility genes for type 1 diabetes, low-frequency risk variants could remain unrecognized. The present study aimed to identify novel type 1 diabetes susceptibility genes by newly established methods. MATERIALS AND METHODS: We carried out whole-exome sequencing and genome-wide copy-number analysis for a Japanese family consisting of two patients with type 1 diabetes and three unaffected relatives...
October 19, 2016: Journal of Diabetes Investigation
https://www.readbyqxmd.com/read/27888432/candidate-predisposing-germline-copy-number-variants-in-early-onset-colorectal-cancer-patients
#13
A J Brea-Fernandez, C Fernandez-Rozadilla, M Alvarez-Barona, D Azuara, M M Ginesta, J Clofent, L de Castro, D Gonzalez, M Andreu, X Bessa, X Llor, R Xicola, R Jover, A Castells, S Castellvi-Bel, G Capella, A Carracedo, C Ruiz-Ponte
PURPOSE: A great proportion of the heritability of colorectal cancer (CRC) still remains unexplained, and rare variants, as well as copy number changes, have been proposed as potential candidates to explain the so-called 'missing heritability'. We aimed to identify rare high-to-moderately penetrant copy number variants (CNVs) in patients suspected of having hereditary CRC due to an early onset. METHODS/PATIENTS: We have selected for genome-wide copy number analysis, 27 MMR-proficient early onset CRC patients (<50 years) without identifiable germline mutations in Mendelian genes related to this phenotype...
November 25, 2016: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/27883173/clinical-application-of-snp-array-analysis-in-first-trimester-pregnancy-loss-a-prospective-study
#14
Yan Wang, Qing Cheng, Lulu Meng, Chunyu Luo, Huanran Hu, Jingjing Zhang, Jian Cheng, Tianhui Xu, Tao Jiang, Dong Liang, Ping Hu, Zhengfeng Xu
Chromosomal microarray analysis (CMA) has been used routinely in pediatric and prenatal genetic diagnosis in clinical practice, but it has rarely been applied to miscarriage analysis. In this study, we conducted a prospective study to evaluate the feasibility of CMA for genetic diagnosis of first-trimester miscarriage specimens. We successfully analyzed 551 fresh miscarriage specimens using SNP array. Among the specimens, 2.9% (16/551) had significant maternal cell contamination and were excluded from the study...
November 24, 2016: Clinical Genetics
https://www.readbyqxmd.com/read/27882129/whole-genome-resequencing-of-100-healthy-individuals-using-dna-pooling
#15
Xiaobin Wang, Weiguo Sui, Weiqing Wu, Xianliang Hou, Minglin Ou, Yueying Xiang, Yong Dai
With the advent of next-generation sequencing technology, the cost of sequencing has significantly decreased. However, sequencing costs remain high for large-scale studies. In the present study, DNA pooling was applied as a cost-effective strategy for sequencing. The sequencing results for 100 healthy individuals obtained via whole-genome resequencing and using DNA pooling are presented in the present study. In order to minimise the likelihood of systematic bias in sampling, paired-end libraries with an insert size of 500 bp were prepared for all samples and then subjected to whole-genome sequencing using four lanes for each library and resulting in at least a 30-fold haploid coverage for each sample...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27881083/loss-of-maternal-annexin-a10-via-a-34-kb-deleted-type-copy-number-variation-is-associated-with-embryonic-mortality-in-japanese-black-cattle
#16
Shinji Sasaki, Takayuki Ibi, Takayuki Akiyama, Moriyuki Fukushima, Yoshikazu Sugimoto
BACKGROUND: Conception is a fundamental trait for successful cattle reproduction. However, conception rates in Japanese Black cattle have been gradually declining over the last two decades. Although conception failures are mainly caused by embryonic mortality, the role of maternal genetic factors in the process remains unknown. Copy number variation (CNV), defined as large-scale genomic structural variants, contributes to several genetic disorders. To identify CNV associated with embryonic mortality in Japanese Black cattle, we evaluated embryonic mortality as a categorical trait with a threshold model and conducted a genome-wide CNV association study for embryonic mortality using 791 animals...
November 24, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27880765/mechanisms-for-complex-chromosomal-insertions
#17
Shen Gu, Przemyslaw Szafranski, Zeynep Coban Akdemir, Bo Yuan, Mitchell L Cooper, Maria A Magriñá, Carlos A Bacino, Seema R Lalani, Amy M Breman, Janice L Smith, Ankita Patel, Rodger H Song, Weimin Bi, Sau Wai Cheung, Claudia M B Carvalho, Paweł Stankiewicz, James R Lupski
Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH)...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27878529/association-between-copy-number-variation-on-metabolic-phenotypes-and-hdl-c-levels-in-patients-with-polycystic-ovary-syndrome
#18
Birgit Knebel, Stefan Lehr, Onno E Janssen, Susanne Hahn, Sylvia Jacob, Ulrike Nitzgen, Dirk Müller-Wieland, Jorg Kotzka
Polygenic diseases with a broad phenotypic spectrum, such as polycystic ovary syndrome (PCOS), present a particular challenge in terms of identifying the underlying genetic mechanisms, nevertheless genetic variants have impact on the individual phenotype. We aimed to determine if next to genetic variations like SNPs further mechanisms might play a role in the pathogenesis of PCOS. We examined the effect of copy-number variations (CNVs) on metabolic phenotypes in PCOS. The intragenic rs1244979, rs2815752 in NEGR1 gene, and rs780094 in GCKR gene were genotyped and CNVs were determined by droplet digital polymerase chain reaction (ddPCR) in PCOS patients (n = 153) and controls without metabolic syndrome (n = 142)...
November 22, 2016: Molecular Biology Reports
https://www.readbyqxmd.com/read/27869829/contribution-of-copy-number-variants-to-schizophrenia-from-a-genome-wide-study-of-41-321-subjects
#19
(no author information available yet)
Copy number variants (CNVs) have been strongly implicated in the genetic etiology of schizophrenia (SCZ). However, genome-wide investigation of the contribution of CNV to risk has been hampered by limited sample sizes. We sought to address this obstacle by applying a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. A global enrichment of CNV burden was observed in cases (odds ratio (OR) = 1.11, P = 5.7 × 10(-15)), which persisted after excluding loci implicated in previous studies (OR = 1...
November 21, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27869554/genome-wide-deletion-screening-with-the-array-cgh-method-in-mouse-offspring-derived-from-irradiated-spermatogonia-indicates-that-mutagenic-responses-are-highly-variable-among-genes
#20
Jun-Ichi Asakawa, Mieko Kodaira, Akiko Miura, Takanori Tsuji, Yoshiko Nakamoto, Masaaki Imanaka, Jun Kitamura, Harry Cullings, Mayumi Nishimura, Yoshiya Shimada, Nori Nakamura
Until the end of the 20th century, mouse germ cell data on induced mutation rates, which were collected using classical genetic methods at preselected specific loci, provided the principal basis for estimates of genetic risks from radiation in humans. The work reported on here is an extension of earlier efforts in this area using molecular methods. It focuses on validating the use of array comparative genomic hybridization (array CGH) methods for identifying radiation-induced copy number variants (CNVs) and specifically for DNA deletions...
November 21, 2016: Radiation Research
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