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https://www.readbyqxmd.com/read/29240998/orthogonality-and-burdens-of-heterologous-and-gate-gene-circuits-in-e-coli
#1
Qijun Liu, Jörg Schumacher, Xinyi Wan, Chunbo Lou, Baojun Wang
Synthetic biology approaches commonly introduce heterologous gene networks into a host to predictably program cells, with the expectation of the synthetic network being orthogonal to the host background. However, introduced circuits may interfere with the host's physiology, either indirectly by posing a metabolic burden and/or through unintended direct interactions between parts of the circuit with those of the host, affecting functionality. Here we used RNA-Seq transcriptome analysis to quantify the interactions between a representative heterologous AND gate circuit and the host Escherichia coli under various conditions including circuit designs and plasmid copy numbers...
December 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29236091/noncoding-copy-number-variations-are-associated-with-congenital-limb-malformation
#2
Ricarda Flöttmann, Bjørt K Kragesteen, Sinje Geuer, Magdalena Socha, Lila Allou, Anna Sowińska-Seidler, Laure Bosquillon de Jarcy, Johannes Wagner, Aleksander Jamsheer, Barbara Oehl-Jaschkowitz, Lars Wittler, Deepthi de Silva, Ingo Kurth, Idit Maya, Fernando Santos-Simarro, Wiebke Hülsemann, Eva Klopocki, Roger Mountford, Alan Fryer, Guntram Borck, Denise Horn, Pablo Lapunzina, Meredith Wilson, Bénédicte Mascrez, Denis Duboule, Stefan Mundlos, Malte Spielmann
PurposeCopy-number variants (CNVs) are generally interpreted by linking the effects of gene dosage with phenotypes. The clinical interpretation of noncoding CNVs remains challenging. We investigated the percentage of disease-associated CNVs in patients with congenital limb malformations that affect noncoding cis-regulatory sequences versus genes sensitive to gene dosage effects.MethodsWe applied high-resolution copy-number analysis to 340 unrelated individuals with isolated limb malformation. To investigate novel candidate CNVs, we re-engineered human CNVs in mice using clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing...
October 12, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29234170/a-missense-point-mutation-in-col10a1-identified-with-whole-genome-deep-sequencing-in-a-7-generation-pakistan-dwarf-family
#3
Chao Zhang, Jiaojiao Liu, Furhan Iqbal, Yan Lu, Saima Mustafa, Firdous Bukhari, Haiyi Lou, Ruiqing Fu, Zhendong Wu, Xiong Yang, Ihtisham Bukhari, Muhammad Aslam, Shuhua Xu
Disease-associated variants in the human genome are continually being identified using DNA sequencing technologies that are especially effective for Mendelian disorders. Here we sequenced whole genome to high coverage (>30×) of 6 members of a 7-generation family with dwarfism from a consanguineous tribe in Pakistan to determine the causal variant(s). We identified a missense variant rs111033552 (c.2011T>C [p.Ser671Pro]) located in COL10A1 (encodes the alpha chain of type X collagen) as the most likely contributor to the dwarfism...
January 2018: Heredity
https://www.readbyqxmd.com/read/29233531/genomic-landscape-of-ovarian-clear-cell-carcinoma-via-whole-exome-sequencing
#4
Se Ik Kim, Ji Won Lee, Maria Lee, Hee Seung Kim, Hyun Hoon Chung, Jae-Weon Kim, Noh Hyun Park, Yong-Sang Song, Jeong-Sun Seo
OBJECTIVE: To analyze whole exome sequencing (WES) data on ovarian clear cell carcinoma (OCCC) in Korean patients via the technique of next generation sequencing (NGS). Genomic profiles were compared between endometriosis-associated OCCC (EMS-OCCC) and Non-EMS-OCCC. METHODS: We used serum samples and cancer tissues, stored at the Seoul National University Hospital Human Biobank, that were initially collected from women diagnosed with OCCC between 2012 and 2016. In total, 15 patients were enrolled: 5 with pathologically confirmed EMS-OCCC and 10 with Non-EMS-OCCC...
December 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29233499/the-role-of-the-carboxyl-ester-lipase-cel-gene-in-pancreatic-disease
#5
REVIEW
Bente B Johansson, Karianne Fjeld, Khadija El Jellas, Anny Gravdal, Monica Dalva, Erling Tjora, Helge Ræder, Rohit N Kulkarni, Stefan Johansson, Pål R Njølstad, Anders Molven
The enzyme carboxyl ester lipase (CEL), also known as bile salt-dependent or -stimulated lipase (BSDL, BSSL), hydrolyzes dietary fat, cholesteryl esters and fat-soluble vitamins in the duodenum. CEL is mainly expressed in pancreatic acinar cells and lactating mammary glands. The human CEL gene resides on chromosome 9q34.3 and contains a variable number of tandem repeats (VNTR) region that encodes a mucin-like protein tail. Although the number of normal repeats does not appear to significantly influence the risk for pancreatic disease, single-base pair deletions in the first VNTR repeat cause a syndrome of endocrine and exocrine dysfunction denoted MODY8...
December 5, 2017: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
https://www.readbyqxmd.com/read/29233175/exome-sequencing-of-multiple-sclerosis-patients-and-their-unaffected-first-degree-relatives
#6
Sheila Garcia-Rosa, Maria Galli de Amorim, Renan Valieris, Vanessa Daccach Marques, Julio Cesar Cetrulo Lorenzi, Vania Balardin Toller, Guilherme Sciascia do Olival, Wilson Araújo da Silva Júnior, Israel Tojal da Silva, Amilton Antunes Barreira, Diana Noronha Nunes, Emmanuel Dias-Neto
OBJECTIVES: The understanding of complex multifactorial diseases requires the availability of a variety of data for a large-number of affected individuals. In this data note here we provide whole exome sequencing data from a set of non-familiar multiple-sclerosis (MS) patients as well as their unaffected first-degree relatives. This data might help the identification of genomic alterations, including single nucleotide polymorphisms, de novo variations and structural genomic variations, such as copy-number alterations that may impact this disease...
December 12, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29230583/mutation-screening-of-chinese-treacher-collins-syndrome-patients-identified-novel-tcof1-mutations
#7
Ying Chen, Luo Guo, Chen-Long Li, Jing Shan, Hai-Song Xu, Jie-Ying Li, Shan Sun, Shao-Juan Hao, Lei Jin, Gang Chai, Tian-Yu Zhang
Treacher Collins syndrome (TCS) (OMIM 154500) is a rare congenital craniofacial disorder with an autosomal dominant manner of inheritance in most cases. To date, three pathogenic genes (TCOF1, POLR1D and POLR1C) have been identified. In this study, we conducted mutational analysis on Chinese TCS patients to reveal a mutational spectrum of known causative genes and show phenotype-genotype data to provide more information for gene counselling and future studies on the pathogenesis of TCS. Twenty-two TCS patients were recruited from two tertiary referral centres, and Sanger sequencing for the coding exons and exon-intron boundaries of TCOF1, POLR1D and POLR1C was performed...
December 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29230163/genetic-counselling-pitfall-co-occurrence-of-an-11-8-mb-xp22-duplication-and-an-xp21-2-duplication-disrupting-il1rapl1
#8
Nicolas Chatron, Lucie Thibault, James Lespinasse, Audrey Labalme, Caroline Schluth-Bolard, Marianne Till, Patrick Edery, Renaud Touraine, Vincent des Portes, Gaetan Lesca, Damien Sanlaville
We report a 3-generation family in which 2 Xp copy number variations (CNVs) co-segregate. The proband presented with syndromic intellectual disability. The CNV had been revealed by conventional karyotyping, identifying a large Xp22 duplication causing an Xp functional disomy. Family studies found that this duplication was inherited from the proband's mother and was also present in one of his sisters. This sister had conventional karyotyping performed during pregnancy with a normal result. Postnatally, her child, the proband's nephew, presented with autism spectrum disorders...
November 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/29229672/detecting-differential-copy-number-variation-between-groups-of-samples
#9
Craig B Lowe, Nicelio Sanchez-Luege, Timothy R Howes, Shannon D Brady, Rhea R Richardson, Felicity C Jones, Michael A Bell, David M Kingsley
We present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use a finite-state transducer where the emitted read depth is conditioned on the mappability and GC-content of all reads that occur at a given base position. In this model, the read depth within a region is a mixture of binomials, which in simulations matches the read depth more closely than the often-used negative binomial distribution. The method analyzes all samples simultaneously, preserving uncertainty as to the breakpoints and magnitude of CNVs present in an individual when it identifies CNVs differentially present between the two groups...
December 11, 2017: Genome Research
https://www.readbyqxmd.com/read/29228597/diversity-index-as-a-novel-prognostic-factor-in-breast-cancer
#10
Yul Ri Chung, Hyun Jeong Kim, Young A Kim, Mee Soo Chang, Ki-Tae Hwang, So Yeon Park
Intratumoral genetic heterogeneity leads to tumor progression and therapeutic resistance. However, due to the difficulty associated with its assessment, the use of this heterogeneity as a prognostic or predictive marker remains limited. To investigate the significance of the Shannon diversity index of gene copy number variation as a tool for measuring genetic heterogeneity in breast cancer, we performed fluorescence in situ hybridization of c-MYC in two sets of invasive breast cancer samples and correlated the Shannon index of c-MYC copy number variation with clinicopathologic features and patient survival...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29226566/probing-the-importance-of-clonality-single-cell-subcloning-of-clonally-derived-cho-cell-lines-yields-widely-diverse-clones-differing-in-growth-productivity-and-product-quality
#11
Peggy Ko, Shahram Misaghi, Zhilan Hu, Dejin Zhan, Joni Tsukuda, Mandy Yim, Mark Sanford, David Shaw, Masaru Shiratori, Brad Snedecor, Michael Laird, Amy Shen
In the past few decades, a large variety of therapeutic antibodies and proteins have been expressed in Chinese hamster ovary (CHO) cells. This mammalian expression system is robust, scalable, relatively inexpensive, and importantly allows for post-translational modifications that are important for some therapeutic proteins. Historically, CHO cell lines were derived from colonies of cells grown in semi-solid or liquid plates using either serum-containing or serum-free media. Current advancements in cell sorting and imaging technologies have allowed for isolating and imaging single cell progenitors at the seeding step, significantly increasing the probability of isolating clonally-derived cell lines...
December 11, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/29226118/identification-of-a-novel-heterozygous-de-novo-7-bp-frameshift-deletion-in-pbx1-by-whole-exome-sequencing-causing-a-multi-organ-syndrome-including-bilateral-dysplastic-kidneys-and-hypoplastic-clavicles
#12
Korbinian Maria Riedhammer, Corinna Siegel, Bader Alhaddad, Carmen Montoya, Reka Kovacs-Nagy, Matias Wagner, Thomas Meitinger, Julia Hoefele
Introduction: Congenital anomalies of the kidney and urinary tract (CAKUT) represent the primary cause of chronic kidney disease in children. Many genes have been attributed to the genesis of this disorder. Recently, haploinsufficiency of PBX1 caused by microdeletions has been shown to result in bilateral renal hypoplasia and other organ malformations. Materials and methods: Here, we report on a 14-year-old male patient with congenital bilateral dysplastic kidneys, cryptorchidism, hypoplastic clavicles, developmental delay, impaired intelligence, and minor dysmorphic features...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/29224780/a-living-biobank-of-breast-cancer-organoids-captures-disease-heterogeneity
#13
Norman Sachs, Joep de Ligt, Oded Kopper, Ewa Gogola, Gergana Bounova, Fleur Weeber, Anjali Vanita Balgobind, Karin Wind, Ana Gracanin, Harry Begthel, Jeroen Korving, Ruben van Boxtel, Alexandra Alves Duarte, Daphne Lelieveld, Arne van Hoeck, Robert Frans Ernst, Francis Blokzijl, Isaac Johannes Nijman, Marlous Hoogstraat, Marieke van de Ven, David Anthony Egan, Vittoria Zinzalla, Jurgen Moll, Sylvia Fernandez Boj, Emile Eugene Voest, Lodewyk Wessels, Paul Joannes van Diest, Sven Rottenberg, Robert Gerhardus Jacob Vries, Edwin Cuppen, Hans Clevers
Breast cancer (BC) comprises multiple distinct subtypes that differ genetically, pathologically, and clinically. Here, we describe a robust protocol for long-term culturing of human mammary epithelial organoids. Using this protocol, >100 primary and metastatic BC organoid lines were generated, broadly recapitulating the diversity of the disease. BC organoid morphologies typically matched the histopathology, hormone receptor status, and HER2 status of the original tumor. DNA copy number variations as well as sequence changes were consistent within tumor-organoid pairs and largely retained even after extended passaging...
December 5, 2017: Cell
https://www.readbyqxmd.com/read/29220491/cnvcaller-highly-efficient-and-widely-applicable-software-for-detecting-copy-number-variations-in-large-populations
#14
Xihong Wang, Zhuqing Zheng, Yudong Cai, Ting Chen, Chao Li, Weiwei Fu, Yu Jiang
Background: The increasing amount of sequencing data available for a wide variety of species can be theoretically used for detecting copy number variations (CNVs) at the population level. However, the growing sample sizes and the divergent complexity of non-human genomes challenge the efficiency and robustness of current human-oriented CNV detection methods. Results: Here, we present CNVcaller, a read-depth method for discovering CNVs in population sequencing data...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29219038/duplication-and-variation-in-the-major-histocompatibility-complex-genes-in-blakiston-s-fish-owl-bubo-blakistoni
#15
Keita Omote, Tetsuo I Kohyama, Chizuko Nishida, Keisuke Saito, Satoshi Fujimoto, Ryuichi Masuda
The major histocompatibility complex (MHC) includes many genes that are essential for the adaptive immune system, and variation in the antigen binding site (ABS) is related to resistance against pathogens. In the present study, quantitative real-time PCR indicated a larger number of MHC gene copies in the endangered population of Blakiston's fish owl (Bubo blakistoni) than in five other owl species, and massively parallel pyrosequencing detected more MHC class IIβ per individual alleles in B. blakistoni than in the other species...
December 2017: Zoological Science
https://www.readbyqxmd.com/read/29218910/pan-cancer-analysis-of-expressed-somatic-nucleotide-variants-in-long-intergenic-non-coding-rna
#16
Travers Ching, Lana X Garmire
Long intergenic non-coding RNAs have been shown to play important roles in cancer. However, because lincRNAs are a relatively new class of RNAs compared to protein-coding mRNAs, the mutational landscape of lincRNAs has not been as extensively studied. Here we characterize expressed somatic nucleotide variants within lincRNAs using 12 cancer RNA-Seq datasets in TCGA. We build machine-learning models to discriminate somatic variants from germline variants within lincRNA regions (AUC 0.987). We build another model to differentiate lincRNA somatic mutations from background regions (AUC 0...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29215049/str-profiling-and-copy-number-variation-analysis-on-single-preserved-cells-using-current-whole-genome-amplification-methods
#17
Ann-Sophie Vander Plaetsen, Lieselot Deleye, Senne Cornelis, Laurentijn Tilleman, Filip Van Nieuwerburgh, Dieter Deforce
The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29213072/characterization-of-large-copy-number-variation-in-mexican-type-2-diabetes-subjects
#18
Iván de Jesús Ascencio-Montiel, Dalila Pinto, Esteban J Parra, Adán Valladares-Salgado, Miguel Cruz, Stephen W Scherer
The effect of Copy Number Variants (CNVs) on Type 2 Diabetes (T2D) remains little explored. The present study characterized large rare CNVs in 686 T2D and 194 non-T2D subjects of Mexican ancestry genotyped using the Affymetrix Genome-Wide Human SNP array 5.0. Rare CNVs with ≥ 100 kb length were identified using a stringent strategy based on merging CNVs calls generated using Birdsuit, iPattern and PennCNV algorithms. We applied three different strategies to evaluate the distribution of CNVs in the T2D and non-T2D samples: 1) Burden analysis, 2) Identification of CNVs in loci previously associated to T2D, and 3) Identification of CNVs observed only in the T2D group...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29212915/altered-synaptic-transmission-and-maturation-of-hippocampal-ca1-neurons-in-a-mouse-model-of-human-chr16p11-2-microdeletion
#19
Hung-Chi Lu, Alea A Mills, Di Tian
The pathophysiology of neurodevelopmental disorders is often expressed early in infancy and toddlerhood. Mouse models of syndromic disorders have provided insight regarding mechanisms of action, but most studies have focused on characterization in juveniles and adults. Insight into developmental trajectories, particularly related to circuit and synaptic function, likely will yield important information regarding disorder pathogenesis that leads to symptom progression. Chromosome 16p11.2 microdeletion is one of the most common copy number variations associated with a spectrum of neurodevelopmental disorders...
December 6, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/29209947/copy-number-variation-arising-from-gene-conversion-on-the-human-y-chromosome
#20
Wentao Shi, Andrea Massaia, Sandra Louzada, Ruby Banerjee, Pille Hallast, Yuan Chen, Anders Bergström, Yong Gu, Steven Leonard, Michael A Quail, Qasim Ayub, Fengtang Yang, Chris Tyler-Smith, Yali Xue
We describe the variation in copy number of a ~ 10 kb region overlapping the long intergenic noncoding RNA (lincRNA) gene, TTTY22, within the IR3 inverted repeat on the short arm of the human Y chromosome, leading to individuals with 0-3 copies of this region in the general population. Variation of this CNV is common, with 266 individuals having 0 copies, 943 (including the reference sequence) having 1, 23 having 2 copies, and two having 3 copies, and was validated by breakpoint PCR, fibre-FISH, and 10× Genomics Chromium linked-read sequencing in subsets of 1234 individuals from the 1000 Genomes Project...
December 5, 2017: Human Genetics
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