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Copy-number variant

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https://www.readbyqxmd.com/read/28822785/next-generation-sequencing-based-detection-of-germline-copy-number-variations-in-brca1-brca2-validation-of-a-one-step-diagnostic-work-flow
#1
Ane Y Schmidt, Thomas V O Hansen, Lise B Ahlborn, Lars Jønson, Christina W Yde, Finn C Nielsen
Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small indels as well as larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS), it has become feasible to provide CNV information as well as sequence data using a single platform. We report the use of NGS gene panel sequencing on the Illumina MiSeq platform and JSI SeqPilot SeqNext software to call germline CNVs in BRCA1 and BRCA2...
August 16, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28818680/clinical-validation-of-copy-number-variant-detection-from-targeted-next-generation-sequencing-panels
#2
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin, David Rodenhiser, Joan Knoll, Peter J Ainsworth, Bekim Sadikovic
Next-generation sequencing (NGS) technology has rapidly replaced Sanger sequencing in the assessment of sequence variations in clinical genetics laboratories. One major limitation of current NGS approaches is the ability to detect copy number variations (CNVs) greater than approximately 50bp. Since these represent a major mutational burden in many genetic disorders, parallel CNV assessment using alternate supplemental methods, along with the NGS analysis, is normally required resulting in increased labor, costs, and turnaround times...
August 14, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28817303/chrna7-deletions-are-enriched-in-risperidone-treated-children-and-adolescents
#3
Madelyn A Gillentine, Janson J White, Christopher M Grochowski, James R Lupski, Christian P Schaaf, Chadi A Calarge
OBJECTIVE: Aggression is among the most common indications for referral to child and adolescent mental health services and is often challenging to treat. Understanding the biological underpinnings of aggression could help optimize treatment efficacy. Neuronal nicotinic acetylcholine receptors (nAChRs), specifically the α7 nAChR, encoded by the gene CHRNA7, have been implicated in aggressive behaviors in animal models as well as humans. Copy number variants (CNVs) of CHRNA7 are found in individuals with neuropsychiatric disorders, often with comorbid aggression...
August 17, 2017: Journal of Child and Adolescent Psychopharmacology
https://www.readbyqxmd.com/read/28811336/catastrophic-unbalanced-genome-rearrangements-cause-somatic-loss-of-berry-color-in-grapevine
#4
Pablo Carbonell-Bejerano, Carolina Royo, Rafael Torres-Pérez, Jérôme Grimplet, Lucie Fernandez, Jose M Franco-Zorrilla, Diego Lijavetzky, Elisa Baroja, Juana Martínez, Enrique García-Escudero, Javier Ibáñez, José M Martínez-Zapater
Grape color somatic variants that can be used to develop new grapevine cultivars occasionally appear associated to deletion events of uncertain origin. To understand the mutational mechanisms generating somatic structural variation in grapevine, we compared the Tempranillo Blanco (TB) white berry somatic variant to its black berry ancestor, Tempranillo Tinto. Whole-genome sequencing (WGS) uncovered a catastrophic genome rearrangement in TB that caused the hemizygous deletion of 313 genes, including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28808695/resolving-multicopy-duplications-de-novo-using-polyploid-phasing
#5
Mark J Chaisson, Sudipto Mukherjee, Sreeram Kannan, Evan E Eichler
While the rise of single-molecule sequencing systems has enabled an unprecedented rise in the ability to assemble complex regions of the genome, long segmental duplications in the genome still remain a challenging frontier in assembly. Segmental duplications are at the same time both gene rich and prone to large structural rearrangements, making the resolution of their sequences important in medical and evolutionary studies. Duplicated sequences that are collapsed in mammalian de novo assemblies are rarely identical; after a sequence is duplicated, it begins to acquire paralog specific variants...
May 2017: Research in Computational Molecular Biology: ... Annual International Conference, RECOMB ...: Proceedings
https://www.readbyqxmd.com/read/28807343/anisometric-cell-lipoma-insight-from-a-case-series-and-review-of-the-literature-on-adipocytic-neoplasms-in-survivors-of-retinoblastoma-suggest-a-role-for-rb1-loss-and-possible-relationship-to-fat-predominant-fat-only-spindle-cell-lipoma
#6
Abbas Agaimy
The term "anisometric cell lipoma" (ACL) has been proposed recently by Evans for a lipoma variant characterized by striking variation in size and shape of adipocytes but little or no cytological atypia. One patient with multiple ACL had a history of retinoblastoma. The current study analyzed six patients with ACL (4 males and two females aged 34 to 87years; median, 58); all seen in consultation. Five patients presented with solitary and one with multiple subcutaneous masses measuring 5 to 9cm (median, 7.5cm)...
August 2017: Annals of Diagnostic Pathology
https://www.readbyqxmd.com/read/28806978/transcriptome-sequencing-in-pediatric-acute-lymphoblastic-leukemia-identifies-fusion-genes-associated-with-distinct-dna-methylation-profiles
#7
Yanara Marincevic-Zuniga, Johan Dahlberg, Sara Nilsson, Amanda Raine, Sara Nystedt, Carl Mårten Lindqvist, Eva C Berglund, Jonas Abrahamsson, Lucia Cavelier, Erik Forestier, Mats Heyman, Gudmar Lönnerholm, Jessica Nordlund, Ann-Christine Syvänen
BACKGROUND: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes...
August 14, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28801450/genomic-analysis-of-hairy-cell-leukemia-identifies-novel-recurrent-genetic-alterations
#8
Benjamin H Durham, Bartlomiej Getta, Sascha Dietrich, Justin Taylor, Helen Won, James M Bogenberger, Sasinya Scott, Eunhee Kim, Young Rock Chung, Stephen S Chung, Jennifer Hüllein, Tatjana Walther, Lu Wang, Sydney X Lu, Christopher C Oakes, Raoul Tibes, Torsten Haferlach, Barry S Taylor, Martin S Tallman, Michael F Berger, Jae H Park, Thorsten Zenz, Omar Abdel-Wahab
Classical hairy cell leukemia (cHCL) is characterized by a near 100% frequency of the BRAFV600E mutation while ~30% of variant HCL (vHCL) have MAP2K1 mutations. However, recurrent genetic alterations cooperating with BRAFV600E or MAP2K1 mutations in HCL, as well as those in MAP2K1- wildtype vHCL, are not well defined. We therefore performed deep targeted mutational and copy number analysis of cHCL (n=53) and vHCL (n=8). The most common genetic alteration in cHCL outside of BRAFV600E was heterozygous loss of chromosome 7q, the minimally deleted region of which targeted wildtype BRAF, subdividing cHCL into those hemizygous versus heterozygous for the BRAFV600E mutation...
August 11, 2017: Blood
https://www.readbyqxmd.com/read/28799406/a-polymorphic-ggc-repeat-in-the-npas2-gene-and-its-association-with-melanoma
#9
Alessandra Franzoni, Elitza Markova-Car, Sanja Dević-Pavlić, Davor Jurišić, Cinzia Puppin, Catia Mio, Marila De Luca, Giulia Petruz, Giuseppe Damante, Sandra Kraljević Pavelić
Circadian clock regulation in mammals is controlled by feedback loops of a set of circadian genes. One of these circadian genes, NPAS2, encodes for a member of the bHLH-PAS class of transcription factors and is expressed in the forebrain and in some peripheral organs such as liver and skin. Other biological processes are also regulated by circadian genes. For example, NPAS2 is involved in cell proliferation, DNA damage repair and malignant transformation. Aberrant expression of clock genes has been previously observed in melanoma which led to our effort to sequence the NPAS2 promoter region in this cancer type...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28796977/a-novel-de-novo-20q13-11q13-12-microdeletion-in-a-boy-with-neurodevelopmental-disorders-case-report
#10
Joanna Bernaciak, Barbara Wiśniowiecka-Kowalnik, Jennifer Castañeda, Anna Kutkowska-Kaźmierczak, Beata Nowakowska
Copy-number variants (CNVs) are an important cause of human neurodevelopmental disorders. We present the first case of a 424 kb de novo 20q13.11q13.12 microdeletion in a patient with attention deficit disorder, tics and autistic behaviors, such as emotional and behavioral problems, and movement stereotypes. This region includes three genes expressed in the brain: SFRS6, PTPRT and L3MBTL. Our results suggest that loss of the chromosomal region 20q13.11q13.12 is causative for the clinical findings observed in the patient...
2017: Developmental Period Medicine
https://www.readbyqxmd.com/read/28795510/cngb3-mutation-spectrum-including-copy-number-variations-in-485-achromatopsia-patients
#11
Anja Kathrin Mayer, Caroline Van Cauwenbergh, Christine Rother, Britta Baumann, Peggy Reuter, Elfride De Baere, Bernd Wissinger, Susanne Kohl
Achromatopsia is a rare autosomal recessive cone disorder characterized by color vision defects, photophobia, nystagmus and severely reduced visual acuity. The disease is caused by mutations in genes encoding crucial components of the cone phototransduction cascade (CNGA3, CNGB3, GNAT2, PDE6C, and PDE6H) or in ATF6, involved in the unfolded protein response. CNGB3 encoding the beta subunit of the cyclic nucleotide-gated ion channel in cone photoreceptors is the major achromatopsia gene. Here, we present a comprehensive spectrum of CNGB3 mutations and their prevalence in a cohort of 1,074 independent families clinically diagnosed with achromatopsia...
August 10, 2017: Human Mutation
https://www.readbyqxmd.com/read/28793856/mining-sequence-variations-in-representative-polyploid-sugarcane-germplasm-accessions
#12
Xiping Yang, Jian Song, Qian You, Dev R Paudel, Jisen Zhang, Jianping Wang
BACKGROUND: Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions...
August 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28790112/burden-and-profile-of-somatic-mutation-in-duodenal-adenomas-from-patients-with-familial-adenomatous-and-mutyh-associated-polyposis
#13
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/28780565/clinical-genetic-testing-using-a-custom-designed-steroid-resistant-nephrotic-syndrome-gene-panel-analysis-and-recommendations
#14
Ethan S Sen, Philip Dean, Laura Yarram-Smith, Agnieszka Bierzynska, Geoff Woodward, Chris Buxton, Gemma Dennis, Gavin I Welsh, Maggie Williams, Moin A Saleem
BACKGROUND: There are many single-gene causes of steroid-resistant nephrotic syndrome (SRNS) and the list continues to grow rapidly. Prompt comprehensive diagnostic testing is key to realising the clinical benefits of a genetic diagnosis. This report describes a bespoke-designed, targeted next-generation sequencing (NGS) diagnostic gene panel assay to detect variants in 37 genes including the ability to identify copy number variants (CNVs). METHODS: This study reports results of 302 patients referred for SRNS diagnostic gene panel analysis...
August 5, 2017: Journal of Medical Genetics
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
#15
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/28777852/-application-of-chromosome-microarray-analysis-in-489-children-with-developmental-delay-intellectual-disability
#16
Rongyue Wang, Tingying Lei, Fang Fu, Ru Li, Xiangyi Jing, Xin Yang, Min Pan, Dongzhi Li, Can Liao
OBJECTIVE: To assess the value of chromosome microarray analysis (CMA) for identifying the etiology of developmental delay/intellectual disability (DD/ID). METHODS: A total of 489 children referred for DD/ID with or without other abnormalities were recruited. All patients showed a normal karyotype. DNA was extracted and hybridized with Affymetrix CytoScan 750K array by following the manufacturer's protocol. The data was analyzed with CHAS v2.0 software. RESULTS: The children were classified as with isolated DD/ID (n=358), DD/ID with epilepsy (n=49), and DD/ID with other structural anomalies (n=82)...
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/28776210/the-hnrnp-q-like-gene-is-retroinserted-into-the-b-chromosomes-of-the-cichlid-fish-astatotilapia-latifasciata
#17
Bianca O Carmello, Rafael L B Coan, Adauto L Cardoso, Erica Ramos, Bruno E A Fantinatti, Diego F Marques, Rogério A Oliveira, Guilherme T Valente, Cesar Martins
B chromosomes are dispensable elements observed in many eukaryotic species, including the African cichlid Astatotilapia latifasciata, which might have one or two B chromosomes. Although there have been many studies focused on the biology of these chromosomes, questions about the evolution, maintenance, and potential effects of these chromosomes remain. Here, we identified a variant form of the hnRNP Q-like gene inserted into the B chromosome of A. latifasciata that is characterized by a high copy number and intron-less structure...
August 3, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28771489/additional-value-of-screening-for-minor-genes-and-copy-number-variants-in-hypertrophic-cardiomyopathy
#18
Irene Mademont-Soler, Jesus Mates, Raquel Yotti, Maria Angeles Espinosa, Alexandra Pérez-Serra, Ana Isabel Fernandez-Avila, Monica Coll, Irene Méndez, Anna Iglesias, Bernat Del Olmo, Helena Riuró, Sofía Cuenca, Catarina Allegue, Oscar Campuzano, Ferran Picó, Carles Ferrer-Costa, Patricia Álvarez, Sergio Castillo, Pablo Garcia-Pavia, Esther Gonzalez-Lopez, Laura Padron-Barthe, Aranzazu Díaz de Bustamante, María Teresa Darnaude, José Ignacio González-Hevia, Josep Brugada, Francisco Fernandez-Aviles, Ramon Brugada
INTRODUCTION: Hypertrophic cardiomyopathy (HCM) is the most prevalent inherited heart disease. Next-generation sequencing (NGS) is the preferred genetic test, but the diagnostic value of screening for minor and candidate genes, and the role of copy number variants (CNVs) deserves further evaluation. METHODS: Three hundred and eighty-seven consecutive unrelated patients with HCM were screened for genetic variants in the 5 most frequent genes (MYBPC3, MYH7, TNNT2, TNNI3 and TPM1) using Sanger sequencing (N = 84) or NGS (N = 303)...
2017: PloS One
https://www.readbyqxmd.com/read/28770103/subclonal-analysis-in-a-lobular-breast-cancer-with-classical-and-solid-growth-pattern-mimicking-a-solid-papillary-carcinoma
#19
Matthias Christgen, Stephan Bartels, Jana Lisa van Luttikhuizen, Maximilian Schieck, Stefanie Pertschy, Sudip Kundu, Ulrich Lehmann, Bjoern Sander, Enrico Pelz, Florian Länger, Brigitte Schlegelberger, Doris Steinemann, Hans Kreipe
Recently, a new variant of invasive lobular breast cancer (ILBC) with solid-papillary-like growth pattern has been described. We present a case of ILBC with solid-papillary-like growth pattern in the main tumour mass and classical invasive lobular growth pattern in adjacent satellite foci. The two tumour components were subjected to comprehensive molecular analyses. Both components were ER/PR-positive, HER2-negative, and showed a complete loss of E-cadherin and beta-catenin protein expression, as determined by immunohistochemistry...
July 2017: Journal of Pathology. Clinical Research
https://www.readbyqxmd.com/read/28768736/congenital-diaphragmatic-hernias-from-genes-to-mechanisms-to-therapies
#20
REVIEW
Gabrielle Kardon, Kate G Ackerman, David J McCulley, Yufeng Shen, Julia Wynn, Linshan Shang, Eric Bogenschutz, Xin Sun, Wendy K Chung
Congenital diaphragmatic hernias (CDHs) and structural anomalies of the diaphragm are a common class of congenital birth defects that are associated with significant morbidity and mortality due to associated pulmonary hypoplasia, pulmonary hypertension and heart failure. In ∼30% of CDH patients, genomic analyses have identified a range of genetic defects, including chromosomal anomalies, copy number variants and sequence variants. The affected genes identified in CDH patients include transcription factors, such as GATA4, ZFPM2, NR2F2 and WT1, and signaling pathway components, including members of the retinoic acid pathway...
August 1, 2017: Disease Models & Mechanisms
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