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https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#1
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641109/rare-copy-number-variants-in-nrxn1-and-cntn6-increase-risk-for-tourette-syndrome
#2
Alden Y Huang, Dongmei Yu, Lea K Davis, Jae Hoon Sul, Fotis Tsetsos, Vasily Ramensky, Ivette Zelaya, Eliana Marisa Ramos, Lisa Osiecki, Jason A Chen, Lauren M McGrath, Cornelia Illmann, Paul Sandor, Cathy L Barr, Marco Grados, Harvey S Singer, Markus M Nöthen, Johannes Hebebrand, Robert A King, Yves Dion, Guy Rouleau, Cathy L Budman, Christel Depienne, Yulia Worbe, Andreas Hartmann, Kirsten R Müller-Vahl, Manfred Stuhrmann, Harald Aschauer, Mara Stamenkovic, Monika Schloegelhofer, Anastasios Konstantinidis, Gholson J Lyon, William M McMahon, Csaba Barta, Zsanett Tarnok, Peter Nagy, James R Batterson, Renata Rizzo, Danielle C Cath, Tomasz Wolanczyk, Cheston Berlin, Irene A Malaty, Michael S Okun, Douglas W Woods, Elliott Rees, Carlos N Pato, Michele T Pato, James A Knowles, Danielle Posthuma, David L Pauls, Nancy J Cox, Benjamin M Neale, Nelson B Freimer, Peristera Paschou, Carol A Mathews, Jeremiah M Scharf, Giovanni Coppola
Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (< 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (> 1 Mb), singleton events (OR = 2...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28639280/mutational-profiles-of-brenner-tumors-show-distinctive-features-uncoupling-urothelial-carcinomas-and-ovarian-carcinoma-with-transitional-cell-histology
#3
Nicole Pfarr, Silvia Darb-Esfahani, Jonas Leichsenring, Eliane Taube, Melanie Boxberg, Ioana Braicu, Moritz Jesinghaus, Roland Penzel, Volker Endris, Aurelia Noske, Wilko Weichert, Peter Schirmacher, Carsten Denkert, Albrecht Stenzinger
Brenner tumors (BT) are rare ovarian tumors encompassing benign, borderline and malignant variants. While the histopathology of BTs and their clinical course is well described, little is known about the underlying genetic defects. We employed targeted next generation sequencing to analyze the mutational landscape in a cohort of 23 BT cases (17 benign, 2 borderline, 4 malignant) and 3 ovarian carcinomas with transitional cell histology (TCC). Copy number variations (CNV) were validated by fluorescence in-situ hybridization (FISH) and quantitative PCR-based copy number assays...
June 22, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28639189/enhancing-neuronogenesis-and-counteracting-neuropathogenic-gene-haploinsufficiencies-by-rna-gene-activation
#4
Antonello Mallamaci
Small activating RNAs (saRNAs), targeting endogenous genes and stimulating their transcription, are a promising tool for implementing a variety of neurotherapeutic strategies. Among these there is the stimulation of select histogenetic subroutines for purposes of cell-based brain repair, as well as the therapeutic treatment of gene expression deficits underlying severe neurological disorders.We employed RNA activation (RNAa) to transactivate the Emx2 transcription factor gene in embryonic cortico-cerebral precursor cells...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28638988/same-day-genomic-and-epigenomic-diagnosis-of-brain-tumors-using-real-time-nanopore-sequencing
#5
Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P Kloosterman, Shai Rosenberg, Mailys Daniau, Charlotte Schmitt, Julien Masliah-Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean-Yves Delattre, Ahmed Idbaih
Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making...
June 21, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28631888/the-importance-of-phase-analysis-in-multiexon-copy-number-variation-detected-by-acgh-in-autosomal-recessive-disorder-loci
#6
Madelyn A Gillentine, Christian P Schaaf, Ankita Patel
Cohen Syndrome (CS) is a rare autosomal recessive disorder caused by homozygous or compound heterozygous pathogenic variants in VPS13B, also known as COH1. Over 100 pathogenic variants in VSP13B, primarily truncations, and copy number variants, have been found in patients with CS. Here, we present an 11-month-old girl with CS caused by two multi-exonic small deletions in VSP13B in trans. Array comparative genomic hybridization has revolutionized the field of genome copy number analysis down to the exonic level, however it has its limitations...
June 20, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28630456/rare-disruptive-variants-in-the-disc1-interactome-and-regulome-association-with-cognitive-ability-and-schizophrenia
#7
S Teng, P A Thomson, S McCarthy, M Kramer, S Muller, J Lihm, S Morris, D C Soares, W Hennah, S Harris, L M Camargo, V Malkov, A M McIntosh, J K Millar, D H Blackwood, K L Evans, I J Deary, D J Porteous, W R McCombie
Schizophrenia (SCZ), bipolar disorder (BD) and recurrent major depressive disorder (rMDD) are common psychiatric illnesses. All have been associated with lower cognitive ability, and show evidence of genetic overlap and substantial evidence of pleiotropy with cognitive function and neuroticism. Disrupted in schizophrenia 1 (DISC1) protein directly interacts with a large set of proteins (DISC1 Interactome) that are involved in brain development and signaling. Modulation of DISC1 expression alters the expression of a circumscribed set of genes (DISC1 Regulome) that are also implicated in brain biology and disorder...
June 20, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28629877/the-effect-of-a-genetic-variant-on-quantitative-real-time-pcr-in-a-case-of-disseminated-adenovirus-infection
#8
Thomas J Gniadek, Michael T Forman, Isabella Martin, Ravit Arav-Boger, Alexandra Valsamakis
A patient developed disseminated adenovirus infection following bone marrow transplant. TaqMan real-time PCR showed reduced maximum fluorescence in the amplification curve from all plasma samples. Sequencing revealed three single nucleotide mismatches between the TaqMan probe and probe binding region. Real-time PCR with probe matching the isolate sequence showed normal amplification and a higher copy number result.
June 1, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#9
Stephanie U Greer, Lincoln D Nadauld, Billy T Lau, Jiamin Chen, Christina Wood-Bouwens, James M Ford, Calvin J Kuo, Hanlee P Ji
BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing. METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater...
June 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28626423/ubiquitin-proteasome-collagen-cup-pathway-in-preterm-premature-rupture-of-fetal-membranes
#10
Xinliang Zhao, Xiaoyan Dong, Xiucui Luo, Jing Pan, Weina Ju, Meijiao Zhang, Peirong Wang, Mei Zhong, Yanhong Yu, W Ted Brown, Nanbert Zhong
Spontaneous preterm birth (sPTB) occurs before 37 gestational weeks, with preterm premature rupture of the membranes (PPROM) and spontaneous preterm labor (sPTL) as the predominant adverse outcomes. Previously, we identified altered expression of long non-coding RNAs (lncRNAs) and message RNAs (mRNAs) related to the ubiquitin proteasome system (UPS) in human placentas following pregnancy loss and PTB. We therefore hypothesized that similar mechanisms might underlie PPROM. In the current study, nine pairs of ubiquitin-proteasome-collagen (CUP) pathway-related mRNAs and associated lncRNAs were found to be differentially expressed in PPROM and sPTL...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28618053/association-of-aberrant-right-subclavian-artery-with-abnormal-karyotype-and-microarray-results
#11
Ran Svirsky, Adi Reches, Dana Brabbing-Goldstein, Anat Bar Shira, Yuval Yaron
OBJECTIVES: to evaluate the incidence of chromosomal aberration (both microscopic and sub-microscopic) in fetuses with an aberrant right subclavian artery (ARSA) detected by ultrasonographic anomaly scan. METHODS: The study included 62 pregnant women whose fetuses were diagnosed with ARSA who were referred for genetic counseling. Of these, 55 patients underwent amniocentesis and 7 declined invasive testing. All 55 amniocentesis samples were tested by standard G-banding and chromosomal microarray (CMA), except for 2 samples for which only karyotype and FISH for 22q11...
June 15, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28613040/chromosomal-microarray-in-clinical-diagnosis-a-study-of-337-patients-with-congenital-anomalies-and-developmental-delays-or-intellectual-disability
#12
Ivona Sansović, Ana-Maria Ivankov, Adriana Bobinec, Mijana Kero, Ingeborg Barišić
AIM: To determine the diagnostic yield and criteria that could help to classify and interpret the copy number variations (CNVs) detected by chromosomal microarray (CMA) technique in patients with congenital and developmental abnormalities including dysmorphia, developmental delay (DD) or intellectual disability (ID), autism spectrum disorders (ASD) and congenital anomalies (CA). METHOD: CMA analysis was performed in 337 patients with DD/ID with or without dysmorphism, ASD, and/or CA...
June 14, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28612834/sex-chromosome-aneuploidies-and-copy-number-variants-a-further-explanation-for-neurodevelopmental-prognosis-variability
#13
Jessica Le Gall, Mathilde Nizon, Olivier Pichon, Joris Andrieux, Séverine Audebert-Bellanger, Sabine Baron, Claire Beneteau, Frédéric Bilan, Odile Boute, Tiffany Busa, Valérie Cormier-Daire, Claude Ferec, Mélanie Fradin, Brigitte Gilbert-Dussardier, Sylvie Jaillard, Aia Jønch, Dominique Martin-Coignard, Sandra Mercier, Sébastien Moutton, Caroline Rooryck, Elise Schaefer, Marie Vincent, Damien Sanlaville, Cédric Le Caignec, Sébastien Jacquemont, Albert David, Bertrand Isidor
Sex chromosome aneuploidies (SCA) is a group of conditions in which individuals have an abnormal number of sex chromosomes. SCA, such as Klinefelter's syndrome, XYY syndrome, and Triple X syndrome are associated with a large range of neurological outcome. Another genetic event such as another cytogenetic abnormality may explain a part of this variable expressivity. In this study, we have recruited fourteen patients with intellectual disability or developmental delay carrying SCA associated with a copy-number variant (CNV)...
June 14, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28611458/performance-of-four-modern-whole-genome-amplification-methods-for-copy-number-variant-detection-in-single-cells
#14
Lieselot Deleye, Laurentijn Tilleman, Ann-Sophie Vander Plaetsen, Senne Cornelis, Dieter Deforce, Filip Van Nieuwerburgh
Whole genome amplification (WGA) has become an invaluable tool to perform copy number variation (CNV) detection in single, or a limited number of cells. Unfortunately, current WGA methods introduce representation bias that limits the detection of small CNVs. New WGA methods have been introduced that might have the potential to reduce this bias. We compared the performance of PicoPLEX DNA-Seq (Picoseq), DOPlify, REPLI-g and Ampli-1 WGA for aneuploidy screening and copy number analysis using shallow whole genome massively parallel sequencing (MPS), starting from single or a limited number of cells...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28608362/chromosomal-microarray-as-a-primary-diagnostic-genomic-tool-for-pregnancies-defined-as-being-at-increased-risk-within-a-population-based-combined-first-trimester-screening-program
#15
Ida Vogel, Olav Bjørn Petersen, Rikke Christensen, Jon Hyett, Stina Lou, Else Marie Vestergaard
OBJECTIVE: To evaluate the impact of using high-resolution chromosomal microarray (CMA) as the standard diagnostic approach to examine for genomic imbalances in pregnancies with increased risk (≥1 in 300) defined through combined first trimester screening (cFTS). METHODS: A cohort of 575 consecutive pregnancies that had cFTS risk ≥1:300 through a publicly funded population based screening program in the Central and Northern Regions of Denmark between September 2015 and September 2016...
June 13, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28607503/reproductive-fitness-and-genetic-risk-of-psychiatric-disorders-in-the-general-population
#16
Niamh Mullins, Andrés Ingason, Heather Porter, Jack Euesden, Alexandra Gillett, Sigurgeir Ólafsson, Daniel F Gudbjartsson, Cathryn M Lewis, Engilbert Sigurdsson, Evald Saemundsen, Ólafur Ó Gudmundsson, Michael L Frigge, Augustine Kong, Agnar Helgason, G Bragi Walters, Omar Gustafsson, Hreinn Stefansson, Kari Stefansson
The persistence of common, heritable psychiatric disorders that reduce reproductive fitness is an evolutionary paradox. Here, we investigate the selection pressures on sequence variants that predispose to schizophrenia, autism, bipolar disorder, major depression and attention deficit hyperactivity disorder (ADHD) using genomic data from 150,656 Icelanders, excluding those diagnosed with these psychiatric diseases. Polygenic risk of autism and ADHD is associated with number of children. Higher polygenic risk of autism is associated with fewer children and older age at first child whereas higher polygenic risk of ADHD is associated with having more children...
June 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28605529/the-genomic-impact-of-gene-retrocopies-what-have-we-learned-from-comparative-genomics-population-genomics-and-transcriptomic-analyses
#17
Claudio Casola, Esther Betrán
Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene's transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28605459/copy-number-variants-are-enriched-in-individuals-with-early-onset-obesity-and-highlight-novel-pathogenic-pathways
#18
Maria Pettersson, Heli Viljakainen, Petra Loid, Taina Mustila, Minna Pekkinen, Miriam Armenio, Johanna C Andersson-Assarsson, Outi Mäkitie, Anna Lindstrand
Context: Only a handful of genetic causes for childhood obesity have been identified to date. Copy number variants (CNVs) are known to contribute to obesity, both syndromic (15q11.2 deletions, Prader-Willi syndrome) and non-syndromic (16p11.2 deletions) obesity. Objective: To study the contribution of CNVs to early-onset obesity and evaluate the expression of candidate genes in subcutaneous adipose tissue. Design and Setting: A case-control study in a tertiary academic center...
June 12, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28604968/-prenatal-diagnosis-of-a-fetus-with-5p15-33-microdeletion
#19
Xueping Shen, Pingya He, Rong Fang, Juan Yao, Wenwen Li
OBJECTIVE: To screen for genomic copy number variants (CNVs) in a fetus with one sibling affected with Prader-Willi syndrome using single nucleotide polymorphism (SNP) array. METHODS: The fetus and its parents were subjected to chromosomal karyotyping and SNP array analysis. RESULTS: A 5p15.33 microdeletions was identified in the fetus and its phenotypically normal mother with a size of 344 kb (113 576 to 457 213). The father was normal for both testing...
June 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28600675/a-novel-capillary-nano-immunoassay-for-assessing-androgen-receptor-splice-variant-7-in-plasma-correlation-with-cd133-antigen-expression-in-circulating-tumor-cells-a-pilot-study-in-prostate-cancer-patients
#20
J L García, R Lozano, I Misiewicz-Krzeminska, J Fernández-Mateos, P Krzeminski, S Alfonso, R A Marcos, R García, F Gómez-Veiga, Á Virseda, M Herrero, D Olmos, J J Cruz-Hernández
PURPOSE: Androgen receptor (AR) splice variant 7 (AR-V7) has been related with both a higher risk of prostate cancer (PC) progression and differential responsiveness to hormonal agents versus chemotherapy. The objective of this study was to investigate the feasibility of a novel capillary nano-immunoassay in assessing AR-V7 in plasma from PC patients. METHODS: Patients with either localized or advanced PC were included in the study. Assessment of AR-V7 in plasma was performed through a capillary nano-immunoassay platform...
June 9, 2017: Clinical & Translational Oncology
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