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https://www.readbyqxmd.com/read/28817954/dissecting-amyloid-beta-deposition-using-distinct-strains-of-the-neurotropic-parasite-toxoplasma-gondii-as-a-novel-tool
#1
Carla M Cabral, Kathryn E McGovern, Wes R MacDonald, Jenna Franco, Anita A Koshy
Genetic and pathologic data suggest that amyloid beta (Aβ), produced by processing of the amyloid precursor protein, is a major initiator of Alzheimer's disease (AD). To gain new insights into Aβ modulation, we sought to harness the power of the coevolution between the neurotropic parasite Toxoplasma gondii and the mammalian brain. Two prior studies attributed Toxoplasma-associated protection against Aβ to increases in anti-inflammatory cytokines (TGF-β and IL-10) and infiltrating phagocytic monocytes. These studies only used one Toxoplasma strain making it difficult to determine if the noted changes were associated with Aβ protection or simply infection...
July 2017: ASN Neuro
https://www.readbyqxmd.com/read/28817111/prospective-cohort-study-for-identification-of-underlying-genetic-causes-in-neonatal-encephalopathy-using-whole-exome-sequencing
#2
Theodora U J Bruun, Caro-Lyne DesRoches, Diane Wilson, Vann Chau, Tadashi Nakagawa, Masahiro Yamasaki, Shinya Hasegawa, Toshiyuki Fukao, Christian Marshall, Saadet Mercimek-Andrews
PurposeNeonatal encephalopathy, which is characterized by a decreased level of consciousness, occurs in 1-7/1,000 live-term births. In more than half of term newborns, there is no identifiable etiological factor. To identify underlying genetic defects, we applied whole-exome sequencing (WES) in term newborns with neonatal encephalopathy as a prospective cohort study.MethodsTerm newborns with neonatal encephalopathy and no history of perinatal asphyxia were included. WES was performed using patient and both parents' DNA...
August 17, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28816949/whole-exome-sequencing-identifies-a-kcnj12-mutation-as-a-cause-of-familial-dilated-cardiomyopathy
#3
Hai-Xin Yuan, Kai Yan, Dong-Yan Hou, Zhi-Yong Zhang, Hua Wang, Xin Wang, Juan Zhang, Xiao-Rong Xu, Yan-Hong Liang, Wen-Shu Zhao, Lin Xu, Lin Zhang
Dilated cardiomyopathy (DCM) is characterized by left ventricular dilation, and is associated with systolic dysfunction and increased action potential duration. Approximately 50% of DCM cases are caused by inherited gene mutations with genetic and phenotypic heterogeneity. Next generation sequencing may be useful in screening unknown mutations in such cases.A family was identified with DCM, in which the affected family members developed heart failure, arrhythmia, and sudden death. Probands and 4 affected family members underwent whole exome sequencing (WES), bioinformatics methods, and gene annotation to identify potentially causative variants...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28807864/reducing-diagnostic-turnaround-times-of-exome-sequencing-for-families-requiring-timely-diagnoses
#4
Aurélie Bourchany, Christel Thauvin-Robinet, Daphné Lehalle, Ange-Line Bruel, Alice Masurel-Paulet, Nolwenn Jean, Sophie Nambot, Marjorie Willems, Laetitia Lambert, Salima El Chehadeh-Djebbar, Elise Schaefer, Aurélia Jaquette, Judith St-Onge, Charlotte Poe, Thibaud Jouan, Martin Chevarin, Patrick Callier, Anne-Laure Mosca-Boidron, Nicole Laurent, Mathilde Lefebvre, Frédéric Huet, Nada Houcinat, Sébastien Moutton, Christophe Philippe, Frédéric Tran-Mau-Them, Antonio Vitobello, Paul Kuentz, Yannis Duffourd, Jean-Baptiste Rivière, Julien Thevenon, Laurence Faivre
BACKGROUND AND OBJECTIVE: Whole-exome sequencing (WES) has now entered medical practice with powerful applications in the diagnosis of rare Mendelian disorders. Although the usefulness and cost-effectiveness of WES have been widely demonstrated, it is essential to reduce the diagnostic turnaround time to make WES a first-line procedure. Since 2011, the automation of laboratory procedures and advances in sequencing chemistry have made it possible to carry out diagnostic whole genome sequencing from the blood sample to molecular diagnosis of suspected genetic disorders within 50 h...
August 11, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28805105/economic-burden-of-multiple-myeloma-among-patients-in-successive-lines-of-therapy-in-the-united-states
#5
Joanna P MacEwan, Katharine Batt, Wes Yin, Desi Peneva, Steve Sison, Seanna Vine, Clara Chen
This study characterized the costs of multiple myeloma (MM) during first-line (1L), second-line (2L) and third-line (3L) treatment from the US payer perspective. Patients with ≥2 outpatient or ≥1 inpatient claims with a primary MM diagnosis and 12 months continuous enrollment post index were identified in a retrospective claims database between 1 July 2006 and 30 June 2013. A cost per-patient per-month (PPPM) metric was used to calculate total all-cause and anti-MM pharmacy costs in 1L, 2L, and 3L treatment...
August 13, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28801648/an-effective-combination-of-whole-exome-sequencing-and-runs-of-homozygosity-for-the-diagnosis-of-primary-ciliary-dyskinesia-in-consanguineous-families
#6
Ting Guo, Zhi-Ping Tan, Hua-Mei Chen, Dong-Yuan Zheng, Lv Liu, Xin-Gang Huang, Ping Chen, Hong Luo, Yi-Feng Yang
Primary ciliary dyskinesia (PCD) is clinically characterized by neonatal respiratory distress, chronic sinusitis, bronchiectasis and infertility, and situs inversus in 50% of the patients. PCD is a result of mutations in genes encoding proteins involved in ciliary function, and is primarily inherited in an autosomal recessive fashion. Diagnosis of PCD is often a challenging task due to its high clinical and genetic heterogeneities. In the present study, we attempted to use whole-exome sequencing (WES) combined with runs of homozygosity (ROH) approaches to identify the genetic defects in four Chinese consanguineous families with clinical PCD...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28792971/optimized-detection-of-insertions-deletions-indels-in-whole-exome-sequencing-data
#7
Bo-Young Kim, Jung Hoon Park, Hye-Yeong Jo, Soo Kyung Koo, Mi-Hyun Park
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging...
2017: PloS One
https://www.readbyqxmd.com/read/28783747/comprehensive-investigation-of-cask-mutations-and-other-genetic-etiologies-in-41-patients-with-intellectual-disability-and-microcephaly-with-pontine-and-cerebellar-hypoplasia-micpch
#8
Shin Hayashi, Daniela Tiaki Uehara, Kousuke Tanimoto, Seiji Mizuno, Yasutsugu Chinen, Shinobu Fukumura, Jun-Ichi Takanashi, Hitoshi Osaka, Nobuhiko Okamoto, Johji Inazawa
The CASK gene (Xp11.4) is highly expressed in the mammalian nervous system and plays several roles in neural development and synaptic function. Loss-of-function mutations of CASK are associated with intellectual disability and microcephaly with pontine and cerebellar hypoplasia (MICPCH), especially in females. Here, we present a comprehensive investigation of 41 MICPCH patients, analyzed by mutational search of CASK and screening of candidate genes using an SNP array, targeted resequencing and whole-exome sequencing (WES)...
2017: PloS One
https://www.readbyqxmd.com/read/28782633/plasma-cell-deficiency-in-humans-with-heterozygous-mutations-in-sec61a1
#9
Desirée Schubert, Marie-Christine Klein, Sarah Hassdenteufel, Andrés Caballero-Oteyza, Linlin Yang, Michele Proietti, Alla Bulashevska, Janine Kemming, Johannes Kühn, Sandra Winzer, Stephan Rusch, Manfred Fliegauf, Alejandro A Schäffer, Stefan Pfeffer, Roger Geiger, Adolfo Cavalié, Hongzhi Cao, Fang Yang, Yong Li, Marta Rizzi, Hermann Eibel, Robin Kobbe, Amy L Marks, Brian P Peppers, Robert W Hostoffer, Jennifer M Puck, Richard Zimmermann, Bodo Grimbacher
BACKGROUND: Primary antibody deficiencies (PAD) are the most frequent primary immunodeficiencies in humans. The genetic causes for PADs are largely unknown. Sec61 translocon alpha 1 subunit (SEC61A1) is the major subunit of the Sec61 complex, which is the main polypeptide-conducting channel in the endoplasmic reticulum (ER) membrane. SEC61A1 is a target gene of XBP1s and strongly induced during plasma cell differentiation. OBJECTIVE: Characterization of a novel genetic defect and its pathological mechanism in eleven patients from two unrelated families with PAD...
August 3, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28777004/whole-exome-sequencing-identify-the-6q12-q16-linkage-region-and-a-candidate-gene-ttk-for-pulmonary-nontuberculous-mycobacterial-disease
#10
Fei Chen, Eva P Szymanski, Kenneth N Olivier, Xinyue Liu, Hervé Tettelin, Steven M Holland, Priya Duggal
RATIONALE: Pulmonary nontuberculous mycobacterial (PNTM) disease often affects white postmenopausal women, with a tall and lean body habitus and higher rates of scoliosis, pectus excavatum, mitral valve prolapse, and mutations in the CFTR gene. These clinical features and the familial clustering of the disease suggest an underlying genetic mechanism. OBJECTIVES: To map the genes associated with PNTM, whole-exome sequencing (WES) was conducted in 12 PNTM families and 57 sporadic cases recruited at the NIH Clinical Center during 2001-2013...
August 4, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28768552/a-mild-form-of-adenylosuccinate-lyase-deficiency-in-absence-of-typical-brain-mri-features-diagnosed-by-whole-exome-sequencing
#11
Marina Macchiaiolo, Sabina Barresi, Francesco Cecconi, Ginevra Zanni, Marcello Niceta, Emanuele Bellacchio, Giacomo Lazzarino, Angela Maria Amorini, Enrico Silvio Bertini, Salvatore Rizza, Benedetta Contardi, Marco Tartaglia, Andrea Bartuli
BACKGROUND: Adenylosuccinate lyase (ADSL) deficiency is a defect of purine metabolism affecting purinosome assembly and reducing metabolite fluxes through purine de novo synthesis and purine nucleotide recycling pathways. The disorder shows a wide spectrum of symptoms from slowly to rapidly progressing forms. The most severe form is characterized by neonatal encephalopathy, absence of spontaneous movement, respiratory failure, intractable seizures, and early death within the first weeks of life...
August 2, 2017: Italian Journal of Pediatrics
https://www.readbyqxmd.com/read/28768491/succinate-dehydrogenase-deficiency-in-a-pdgfra-mutated-gist
#12
Martin G Belinsky, Kathy Q Cai, Yan Zhou, Biao Luo, Jianming Pei, Lori Rink, Margaret von Mehren
BACKGROUND: Most gastrointestinal stromal tumors (GISTs) harbor mutually exclusive gain of function mutations in the receptor tyrosine kinase (RTK) KIT (70-80%) or in the related receptor PDGFRA (~10%). These GISTs generally respond well to therapy with the RTK inhibitor imatinib mesylate (IM), although initial response is genotype-dependent. An alternate mechanism leading to GIST oncogenesis is deficiency in the succinate dehydrogenase (SDH) enzyme complex resulting from genetic or epigenetic inactivation of one of the four SDH subunit genes (SDHA, SDHB, SDHC, SDHD, collectively referred to as SDHX)...
August 2, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28767663/contribution-of-exome-sequencing-for-genetic-diagnostic-in-arrhythmogenic-right-ventricular-cardiomyopathy-dysplasia
#13
Joel Fedida, Veronique Fressart, Philippe Charron, Elodie Surget, Tiphaine Hery, Pascale Richard, Erwan Donal, Boris Keren, Guillaume Duthoit, Françoise Hidden-Lucet, Eric Villard, Estelle Gandjbakhch
BACKGROUND: Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia (ARVC/D) is an inherited cardiomyopathy mainly caused by heterozygous desmosomal gene mutations, the major gene being PKP2. The genetic cause remains unknown in ~50% of probands with routine desmosomal gene screening. The aim of this study was to assess the diagnostic accuracy of whole exome sequencing (WES) in ARVC/D with negative genetic testing. METHODS: WES was performed in 22 patients, all without a mutation identified in desmosomal genes...
2017: PloS One
https://www.readbyqxmd.com/read/28767323/candidate-genes-for-nonsyndromic-cleft-palate-detected-by-exome-sequencing
#14
A K Hoebel, D Drichel, M van de Vorst, A C Böhmer, S Sivalingam, N Ishorst, J Klamt, L Gölz, M Alblas, A Maaser, K Keppler, A M Zink, M J Dixon, J Dixon, A Hemprich, T Kruse, I Graf, A Dunsche, G Schmidt, N Daratsianos, S Nowak, K A Aldhorae, M M Nöthen, M Knapp, H Thiele, C Gilissen, H Reutter, A Hoischen, E Mangold, K U Ludwig
Nonsyndromic cleft palate only (nsCPO) is a facial malformation that has a livebirth prevalence of 1 in 2,500. Research suggests that the etiology of nsCPO is multifactorial, with a clear genetic component. To date, genome-wide association studies have identified only 1 conclusive common variant for nsCPO, that is, a missense variant in the gene grainyhead-like-3 ( GRHL3). Thus, the underlying genetic causes of nsCPO remain largely unknown. The present study aimed at identifying rare variants that might contribute to nsCPO risk, via whole-exome sequencing (WES), in multiply affected Central European nsCPO pedigrees...
August 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28765789/deep-sequencing-reveals-variations-in-somatic-cell-mosaic-mutations-between-monozygotic-twins-with-discordant-psychiatric-disease
#15
Yoshiro Morimoto, Shinji Ono, Akira Imamura, Yuji Okazaki, Akira Kinoshita, Hiroyuki Mishima, Hideyuki Nakane, Hiroki Ozawa, Koh-Ichiro Yoshiura, Naohiro Kurotaki
Monozygotic (MZ) twins have been thought to be genetically identical. However, recent studies have shown discordant variants between them. We performed whole-exome sequencing (WES) in five MZ twin pairs with discordant neurodevelopmental disorders and one healthy control MZ twin to detect discordant variants. We identified three discordant variants confirmed by deep sequencing after analysis by personalized next-generation sequencing (NGS). Three mutations in FBXO38 (chr5:147774428;T>G), SMOC2 (chr6:169051385;A>G) and TDRP (chr8:442616;A>G), were detected with low allele frequency of mutant alleles on deep sequencing, suggesting that these loci are mosaic due to somatic mutations in a developmental stage...
2017: Human Genome Variation
https://www.readbyqxmd.com/read/28759686/diagnostic-impact-and-cost-effectiveness-of-whole-exome-sequencing-for-ambulant-children-with-suspected-monogenic-conditions
#16
Tiong Yang Tan, Oliver James Dillon, Zornitza Stark, Deborah Schofield, Khurshid Alam, Rupendra Shrestha, Belinda Chong, Dean Phelan, Gemma R Brett, Emma Creed, Anna Jarmolowicz, Patrick Yap, Maie Walsh, Lilian Downie, David J Amor, Ravi Savarirayan, George McGillivray, Alison Yeung, Heidi Peters, Susan J Robertson, Aaron J Robinson, Ivan Macciocca, Simon Sadedin, Katrina Bell, Alicia Oshlack, Peter Georgeson, Natalie Thorne, Clara Gaff, Susan M White
Importance: Optimal use of whole-exome sequencing (WES) in the pediatric setting requires an understanding of who should be considered for testing and when it should be performed to maximize clinical utility and cost-effectiveness. Objectives: To investigate the impact of WES in sequencing-naive children suspected of having a monogenic disorder and evaluate its cost-effectiveness if WES had been available at different time points in their diagnostic trajectory. Design, Setting, and Participants: This prospective study was part of the Melbourne Genomics Health Alliance demonstration project...
July 31, 2017: JAMA Pediatrics
https://www.readbyqxmd.com/read/28751446/gene-copy-number-estimation-from-targeted-next-generation-sequencing-of-prostate-cancer-biopsies-analytic-validation-and-clinical-qualification
#17
George Seed, Wei Yuan, Joaquin Mateo, Suzanne Carreira, Claudia Bertan, Maryou Lambros, Gunther Boysen, Roberta Ferraldeschi, Susana Miranda, Ines Figueiredo, Ruth Riisnaes, Mateus Crespo, Daniel Nava Rodrigues, Eric Talevich, Dan R Robinson, Lakshmi P Kunju, Yi-Mi Wu, Robert Lonigro, Shahneen Sandhu, Arul Chinnayan, Johann S de Bono
Abstract <p>Purpose</p> <p>Precise detection of copy number aberrations (CNAs) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next generation sequencing (NGS) is inexpensive, high throughput and easily feasible, allowing single nucleotide variant calls, but CNA estimation from this remains challenging..</p> <p>Experimental Design</p> <p>We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration resistant prostate cancer biopsies, and used capture based whole exome sequencing (WES), array comparative genomic hybridization (aCGH), and fluorescent in situ hybridization (FISH) to explore the viability of this approach...
July 27, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28749586/patient-decisions-to-receive-secondary-pharmacogenomic-findings-and-development-of-a-multidisciplinary-practice-model-to-integrate-results-into-patient-care
#18
J Kevin Hicks, Amy Shealy, Allison Schreiber, Marissa Coleridge, Ryan Noss, Marvin Natowicz, Rocio Moran, Timothy Moss, Angelika Erwin, Charis Eng
Whole exome sequencing (WES) has the potential of identifying secondary findings that are predictive of poor pharmacotherapy outcomes. The purpose of this study was to investigate patients' wishes regarding the reporting of secondary pharmacogenomic findings. WES results (n = 106 patients) were retrospectively reviewed to determine the number of patients electing to receive secondary pharmacogenomic results. Phenotypes were assigned based on Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines...
July 27, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/28749476/the-wide-genetic-landscape-of-clinical-frontotemporal-dementia-systematic-combined-sequencing-of-121-consecutive-subjects
#19
Cornelis Blauwendraat, Carlo Wilke, Javier Simón-Sánchez, Iris E Jansen, Anika Reifschneider, Anja Capell, Christian Haass, Melissa Castillo-Lizardo, Saskia Biskup, Walter Maetzler, Patrizia Rizzu, Peter Heutink, Matthis Synofzik
PurposeTo define the genetic spectrum and relative gene frequencies underlying clinical frontotemporal dementia (FTD).MethodsWe investigated the frequencies and mutations in neurodegenerative disease genes in 121 consecutive FTD subjects using an unbiased, combined sequencing approach, complemented by cerebrospinal fluid Aβ1-42 and serum progranulin measurements. Subjects were screened for C9orf72 repeat expansions, GRN and MAPT mutations, and, if negative, mutations in other neurodegenerative disease genes, by whole-exome sequencing (WES) (n = 108), including WES-based copy-number variant (CNV) analysis...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28748635/copy-number-changes-identified-using-whole-exome-sequencing-in-nonsyndromic-cleft-lip-and-palate-in-a-honduran-population
#20
Yi Cai, Karynne E Patterson, Frederic Reinier, Sarah E Keesecker, Elizabeth Blue, Michael Bamshad, Joseph Haddad
BACKGROUND: The majority of cleft lip with or without cleft palate cases appear as an isolated, nonsyndromic entity (NSCLP). With the advent of next generation sequencing, whole exome sequencing (WES) has been used to identify single nucleotide variants and insertion/deletions which cause or increase the risk of NSCLP. However, to our knowledge, there are no published studies using WES in NSCLP to investigate copy number changes (CNCs), which are a major component of human genetic variation...
July 27, 2017: Birth defects research
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