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Copy-number variant

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https://www.readbyqxmd.com/read/29236091/noncoding-copy-number-variations-are-associated-with-congenital-limb-malformation
#1
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
#2
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/29233499/the-role-of-the-carboxyl-ester-lipase-cel-gene-in-pancreatic-disease
#3
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/29230583/mutation-screening-of-chinese-treacher-collins-syndrome-patients-identified-novel-tcof1-mutations
#4
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/29229672/detecting-differential-copy-number-variation-between-groups-of-samples
#5
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/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
#6
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/29225144/copy-number-variants-in-people-with-autism-spectrum-disorders-and-co-morbid-psychosis
#7
Felicity V Larson, John R Arrand, Digby Tantam, Peter B Jones, Anthony J Holland
The genetic association between autism spectrum disorder (ASD) and psychotic disorders such as schizophrenia is complicated and mirrors the clinical overlap between these conditions to some degree. However, no studies to date have examined the genetics of individuals dually diagnosed with both ASD and psychosis. In this study, we present findings of copy number variants (CNVs) from a study of 116 well-characterised individuals with this dual diagnosis. DNA was extracted and arrayed using the Affymetrix CytoScan HD 2...
December 7, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29224162/methylation-specific-multiplex-ligation-dependent-probe-amplification-ms-mlpa
#8
Cathy B Moelans, Lilit Atanesyan, Suvi P Savola, Paul J van Diest
This chapter describes a method for the rapid assessment of promoter hypermethylation levels or methylation of imprinted regions in human genomic DNA extracted from various sources using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Multiplex ligation-dependent probe amplification (MLPA) is a powerful and easy-to-perform PCR-based technique that can identify gains, amplifications, losses, deletions, methylation and mutations of up to 55 targets in a single reaction, while requiring only minute quantities of DNA (about 50 ng) extracted from blood, fresh frozen or formalin-fixed paraffin-embedded materials...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223763/dyrk1a-haploinsufficiency-in-mice-causes-autistic-like-features-and-febrile-seizures
#9
Matthieu Raveau, Atsushi Shimohata, Kenji Amano, Hiroyuki Miyamoto, Kazuhiro Yamakawa
Mutations and copy number variants affecting DYRK1A gene encoding the dual-specificity tyrosine phosphorylation-regulated kinase 1A are among the most frequent genetic causes of neurodevelopmental disorders including autism spectrum disorder (ASD) associated with microcephaly, febrile seizures and severe speech acquisition delay. Here we developed a mouse model harboring a frame-shift mutation in Dyrk1a resulting in a protein truncation and elimination of its kinase activity site. Dyrk1a+/- mice showed significant impairments in cognition and cognitive flexibility, communicative ultrasonic vocalizations, and social contacts...
December 6, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/29218910/pan-cancer-analysis-of-expressed-somatic-nucleotide-variants-in-long-intergenic-non-coding-rna
#10
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/29216221/copy-number-variants-in-ebstein-anomaly
#11
Andreas Giannakou, Robert J Sicko, Wei Zhang, Paul Romitti, Marilyn L Browne, Michele Caggana, Lawrence C Brody, Laura Jelliffe-Pawlowski, Gary M Shaw, Denise M Kay, James L Mills
BACKGROUND: Ebstein anomaly (EA) is a rare congenital defect characterized by apical displacement of the septal tricuspid leaflets and atrialization of the right ventricle. The etiology of EA is unclear; however, recurrence in families and the association of EA with genetic syndromes and copy number variants (CNVs) suggest a genetic component. OBJECTIVE: We performed a population-based study to search for recurrent and novel CNVs in a previously unreported set of EA cases...
2017: PloS One
https://www.readbyqxmd.com/read/29215645/cherchez-la-femme-maternal-incidental-findings-can-explain-discordant-prenatal-cell-free-dna-sequencing-results
#12
REVIEW
Diana W Bianchi
Circulating DNA fragments in a pregnant woman's plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215049/str-profiling-and-copy-number-variation-analysis-on-single-preserved-cells-using-current-whole-genome-amplification-methods
#13
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
#14
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/29212016/cellular-phenotypes-in-human-ipsc-derived-neurons-from-a-genetic-model-of-autism-spectrum-disorder
#15
Aditi Deshpande, Smita Yadav, Dang Q Dao, Zhi-Yong Wu, Kenton C Hokanson, Michelle K Cahill, Arun P Wiita, Yuh-Nung Jan, Erik M Ullian, Lauren A Weiss
A deletion or duplication in the 16p11.2 region is associated with neurodevelopmental disorders, including autism spectrum disorder and schizophrenia. In addition to clinical characteristics, carriers of the 16p11.2 copy-number variant (CNV) manifest opposing neuroanatomical phenotypes-e.g., macrocephaly in deletion carriers (16pdel) and microcephaly in duplication carriers (16pdup). Using fibroblasts obtained from 16pdel and 16pdup carriers, we generated induced pluripotent stem cells (iPSCs) and differentiated them into neurons to identify causal cellular mechanisms underlying neurobiological phenotypes...
December 5, 2017: Cell Reports
https://www.readbyqxmd.com/read/29210335/predictive-role-of-nudt15-variants-on-thiopurine-induced-myelotoxicity-in-asian-inflammatory-bowel-disease-patients
#16
Natalia Sutiman, Sylvia Chen, Khoon Lin Ling, Sai Wei Chuah, Wai Fook Leong, Vinayak Nadiger, Madeline Tjai, Chris San Choon Kong, Brian John Schwender, Webber Chan, Hang Hock Shim, Wee Chian Lim, Chiea Chuen Khor, Yin Bun Cheung, Balram Chowbay
BACKGROUND: Genetic variants of TPMT and NUDT15 have been reported to predict the inter-patient variability in response and toxicity profiles of patients receiving thiopurine therapy. However, the clinical utility of TPMT genotyping in guiding thiopurine doses has been questionable, in part due to underlying differences in the prevalence of TPMT variants in both Caucasian and Asian populations. Several NUDT15 variants have been associated with thiopurine-induced leukopenia, particularly in Asian cohorts...
December 6, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/29209947/copy-number-variation-arising-from-gene-conversion-on-the-human-y-chromosome
#17
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
https://www.readbyqxmd.com/read/29206995/concordance-of-circulating-tumor-dna-and-matched-metastatic-tissue-biopsy-in-prostate-cancer
#18
Alexander W Wyatt, Matti Annala, Rahul Aggarwal, Kevin Beja, Felix Feng, Jack Youngren, Adam Foye, Paul Lloyd, Matti Nykter, Tomasz M Beer, Joshi J Alumkal, George V Thomas, Robert E Reiter, Matthew B Rettig, Christopher P Evans, Allen C Gao, Kim N Chi, Eric J Small, Martin E Gleave
Background: Real-time knowledge of the somatic genome can influence management of patients with metastatic castration-resistant prostate cancer (mCRPC). While routine metastatic tissue biopsy is challenging in mCRPC, plasma circulating tumor DNA (ctDNA) has emerged as a minimally invasive tool to sample the tumor genome. However, no systematic comparisons of matched "liquid" and "solid" biopsies have been performed that would enable ctDNA profiling to replace the need for direct tissue sampling...
December 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29197855/detection-of-genome-wide-copy-number-variants-in-myeloid-malignancies-using-next-generation-sequencing
#19
Wei Shen, Christian N Paxton, Philippe Szankasi, Maria Longhurst, Jonathan A Schumacher, Kimberly A Frizzell, Shelly M Sorrells, Adam L Clayton, Rakhi P Jattani, Jay L Patel, Reha Toydemir, Todd W Kelley, Xinjie Xu
AIMS: Genetic abnormalities, including copy number variants (CNV), copy number neutral loss of heterozygosity (CN-LOH) and gene mutations, underlie the pathogenesis of myeloid malignancies and serve as important diagnostic, prognostic and/or therapeutic markers. Currently, multiple testing strategies are required for comprehensive genetic testing in myeloid malignancies. The aim of this proof-of-principle study was to investigate the feasibility of combining detection of genome-wide large CNVs, CN-LOH and targeted gene mutations into a single assay using next-generation sequencing (NGS)...
December 2, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29196752/combined-genetic-approaches-yield-a-48-diagnostic-rate-in-a-large-cohort-of-french-hearing-impaired-patients
#20
D Baux, C Vaché, C Blanchet, M Willems, C Baudoin, M Moclyn, V Faugère, R Touraine, B Isidor, D Dupin-Deguine, M Nizon, M Vincent, S Mercier, C Calais, G García-García, Z Azher, L Lambert, Y Perdomo-Trujillo, F Giuliano, M Claustres, M Koenig, M Mondain, A F Roux
Hearing loss is the most common sensory disorder and because of its high genetic heterogeneity, implementation of Massively Parallel Sequencing (MPS) in diagnostic laboratories is greatly improving the possibilities of offering optimal care to patients. We present the results of a two-year period of molecular diagnosis that included 207 French families referred for non-syndromic hearing loss. Our multi-step strategy involved (i) DFNB1 locus analysis, (ii) MPS of 74 genes, and (iii) additional approaches including Copy Number Variations, in silico analyses, minigene studies coupled when appropriate with complete gene sequencing, and a specific assay for STRC...
December 1, 2017: Scientific Reports
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