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Exome sequencing

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https://www.readbyqxmd.com/read/28107443/identification-of-the-pla2g6-c-1579g-a-missense-mutation-in-papillon-dog-neuroaxonal-dystrophy-using-whole-exome-sequencing-analysis
#1
Masaya Tsuboi, Manabu Watanabe, Kazumi Nibe, Natsuko Yoshimi, Akihisa Kato, Masahiro Sakaguchi, Osamu Yamato, Miyuu Tanaka, Mitsuru Kuwamura, Kazuya Kushida, Takashi Ishikura, Tomoyuki Harada, James Kenn Chambers, Sumio Sugano, Kazuyuki Uchida, Hiroyuki Nakayama
Whole exome sequencing (WES) has become a common tool for identifying genetic causes of human inherited disorders, and it has also recently been applied to canine genome research. We conducted WES analysis of neuroaxonal dystrophy (NAD), a neurodegenerative disease that sporadically occurs worldwide in Papillon dogs. The disease is considered an autosomal recessive monogenic disease, which is histopathologically characterized by severe axonal swelling, known as "spheroids," throughout the nervous system. By sequencing all eleven DNA samples from one NAD-affected Papillon dog and her parents, two unrelated NAD-affected Papillon dogs, and six unaffected control Papillon dogs, we identified 10 candidate mutations...
2017: PloS One
https://www.readbyqxmd.com/read/28106895/identification-of-a-novel-nrl-mutation-in-a-chinese-family-with-retinitis-pigmentosa-by-whole-exome-sequencing
#2
Y Qin, F Liu, S Yu, L Yang, M Gao, Z Tang, A Y Guo, M Zhang, P Li, M Liu
No abstract text is available yet for this article.
January 20, 2017: Eye
https://www.readbyqxmd.com/read/28106782/from-clinical-standards-to-translating-next-generation-sequencing-research-into-patient-care-improvement-for-hepatobiliary-and-pancreatic-cancers
#3
REVIEW
Ioannis D Kyrochristos, Georgios K Glantzounis, Demosthenes E Ziogas, Ioannis Gizas, Dimitrios Schizas, Efstathios G Lykoudis, Evangelos Felekouras, Anastasios Machairas, Christos Katsios, Theodoros Liakakos, William C Cho, Dimitrios H Roukos
Hepatobiliary and pancreatic (HBP) cancers are associated with high cancer-related death rates. Surgery aiming for complete tumor resection (R0) remains the cornerstone of the treatment for HBP cancers. The current progress in the adjuvant treatment is quite slow, with gemcitabine chemotherapy available only for pancreatic ductal adenocarcinoma (PDA). In the advanced and metastatic setting, only two targeted drugs have been approved by the Food & Drug Administration (FDA), which are sorafenib for hepatocellular carcinoma and erlotinib for PDA...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106563/comprehensive-screening-for-disease-risk-variants-in-early-onset-alzheimer-s-disease-genes-in-african-americans-identifies-novel-psen-variants
#4
Aurelie N'Songo, Minerva M Carrasquillo, Xue Wang, Thuy Nguyen, Yan Asmann, Steven G Younkin, Mariet Allen, Ranjan Duara, Maria T Greig Custo, Neill Graff-Radford, Nilüfer Ertekin-Taner
We conducted a comprehensive screening of rare coding variants in an African American cohort to identify novel pathogenic mutations within the early-onset Alzheimer's disease (EOAD) genes (APP, PSEN1, and PSEN2) in this understudied population. Whole-exome sequencing of 238 African American subjects identified 6 rare missense variants within the EOAD genes, which were observed in AD cases but never among controls. These variants were analyzed in an independent cohort of 300 African American subjects in which PSEN2:NM_000447:exon5:c...
January 19, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28106320/classification-of-genes-standardized-clinical-validity-assessment-of-gene-disease-associations-aids-diagnostic-exome-analysis-and-reclassifications
#5
Erica D Smith, Kelly Radtke, Mari Rossi, Deepali N Shinde, Sourat Darabi, Dima El-Khechen, Zöe Powis, Katherine Helbig, Kendra Waller, Dorothy K Grange, Sha Tang, Kelly D Farwell Hagman
Ascertaining a diagnosis through exome sequencing can provide potential benefits to patients, insurance companies, and the healthcare system. Yet as diagnostic sequencing is increasingly employed, vast amounts of human genetic data are produced that need careful curation. We discuss methods for accurately assessing the clinical validity of gene-disease relationships to interpret new research findings in a clinical context and increase the diagnostic rate. The specifics of a gene-disease scoring system adapted for use in a clinical laboratory are described...
January 20, 2017: Human Mutation
https://www.readbyqxmd.com/read/28105640/the-genotype-phenotype-landscape-of-familial-amyotrophic-lateral-sclerosis-in-australia
#6
Emily P McCann, Kelly L Williams, Jennifer A Fifita, Ingrid S Tarr, Jody O'Connor, Dominic B Rowe, Garth A Nicholson, Ian P Blair
Amyotrophic lateral sclerosis (ALS) is a clinically and genetically heterogeneous fatal neurodegenerative disease. Around 10% of ALS cases are hereditary. ALS gene discoveries have provided most of our understanding of disease pathogenesis. We aimed to describe the genetic landscape of ALS in Australia by assessing 1013 Australian ALS patients for known ALS mutations by direct sequencing, whole exome sequencing or repeat primed PCR. Age of disease onset and disease duration were used for genotype-phenotype correlations...
January 20, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28104717/clinical-targeted-exome-based-sequencing-in-combination-with-genome-wide-copy-number-profiling-precision-medicine-analysis-of-203-pediatric-brain-tumors
#7
Shakti H Ramkissoon, Pratiti Bandopadhayay, Jaeho Hwang, Lori A Ramkissoon, Noah F Greenwald, Steven E Schumacher, Ryan O'Rourke, Nathan Pinches, Patricia Ho, Hayley Malkin, Claire Sinai, Mariella Filbin, Ashley Plant, Wenya Linda Bi, Michael S Chang, Edward Yang, Karen D Wright, Peter E Manley, Matthew Ducar, Sanda Alexandrescu, Hart Lidov, Ivana Delalle, Liliana C Goumnerova, Alanna J Church, Katherine A Janeway, Marian H Harris, Laura E MacConaill, Rebecca D Folkerth, Neal I Lindeman, Charles D Stiles, Mark W Kieran, Azra H Ligon, Sandro Santagata, Adrian M Dubuc, Susan N Chi, Rameen Beroukhim, Keith L Ligon
BACKGROUND: Clinical genomics platforms are needed to identify targetable alterations, but implementation of these technologies and best practices in routine clinical pediatric oncology practice are not yet well established. METHODS: Profile is an institution-wide prospective clinical research initiative that uses targeted sequencing to identify targetable alterations in tumors. OncoPanel, a multiplexed targeted exome-sequencing platform that includes 300 cancer-causing genes, was used to assess single nucleotide variants and rearrangements/indels...
January 19, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28104354/profound-loss-of-esophageal-tissue-differentiation-in-eosinophilic-esophagitis
#8
M Rochman, J Travers, C E Miracle, M C Bedard, T Wen, N P Azouz, J M Caldwell, K Kc, J D Sherrill, B P Davis, J K Rymer, K M Kaufman, M E Rothenberg
BACKGROUND: A key question in the allergy field is to understand how tissue specific disease is manifested. Eosinophilic esophagitis (EoE) is an emerging tissue specific allergic disease whose pathogenesis remains unclear. OBJECTIVE: Herein, we tested the hypothesis that a defect in tissue specific esophageal genes is an integral part of EoE pathogenesis. METHODS: We interrogated the pattern of expression of esophagus-specific signature genes derived from the Human Protein Atlas in the EoE transcriptome and in EPC2 esophageal epithelial cells...
January 16, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28102861/clinical-utility-of-next-generation-sequencing-for-inherited-bone-marrow-failure-syndromes
#9
Hideki Muramatsu, Yusuke Okuno, Kenichi Yoshida, Yuichi Shiraishi, Sayoko Doisaki, Atsushi Narita, Hirotoshi Sakaguchi, Nozomu Kawashima, Xinan Wang, Yinyan Xu, Kenichi Chiba, Hiroko Tanaka, Asahito Hama, Masashi Sanada, Yoshiyuki Takahashi, Hitoshi Kanno, Hiroki Yamaguchi, Shouichi Ohga, Atsushi Manabe, Hideo Harigae, Shinji Kunishima, Eiichi Ishii, Masao Kobayashi, Kenichi Koike, Kenichiro Watanabe, Etsuro Ito, Minoru Takata, Miharu Yabe, Seishi Ogawa, Satoru Miyano, Seiji Kojima
PURPOSE: Precise genetic diagnosis of inherited bone marrow failure syndromes (IBMFS), a heterogeneous group of genetic disorders, is challenging but essential for precise clinical decision making. METHODS: We analyzed 121 IBMFS patients using a targeted sequencing covering 184 associated genes and 250 IBMFS patients using whole-exome sequencing (WES). RESULTS: We achieved successful genetic diagnoses for 53 of 121 patients (44%) using targeted sequencing and for 68 of 250 patients (27%) using WES...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28102150/ultra-rare-genetic-variation-in-common-epilepsies-a-case-control-sequencing-study
#10
(no author information available yet)
BACKGROUND: Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies. METHODS: We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy...
February 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28100915/whole-exome-sequencing-study-reveals-common-copy-number-variants-in-protocadherin-genes-associated-with-childhood-obesity-in-koreans
#11
S Moon, M Y Hwang, H B Jang, S Han, Y J Kim, J-Y Hwang, H-J Lee, S I Park, J Song, B-J Kim
Recently, the prevalence of childhood obesity has significantly increased in industrialized countries, including Korea, and now controlling obesity is becoming an economic burden. However, knowledge of the risk factors associated with obesity is still limited. In this study, we aimed to discover additional obesity-associated loci in children. To achieve this, we conducted an exome-wide association analysis of copy number variation (CNV) using whole-exome sequencing (WES) data from a total of 102 cases and 86 controls...
January 19, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28100473/delineating-the-phenotypic-spectrum-of-bainbridge-ropers-syndrome-12-new-patients-with-de-novo-heterozygous-loss-of-function-mutations-in-asxl3-and-review-of-published-literature
#12
M Balasubramanian, J Willoughby, A E Fry, A Weber, H V Firth, C Deshpande, J N Berg, K Chandler, K A Metcalfe, W Lam, D Pilz, S Tomkins
BACKGROUND: Bainbridge-Ropers syndrome (BRPS) is a recently described developmental disorder caused by de novo truncating mutations in the additional sex combs like 3 (ASXL3) gene. To date, there have been fewer than 10 reported patients. OBJECTIVES: Here, we delineate the BRPS phenotype further by describing a series of 12 previously unreported patients identified by the Deciphering Developmental Disorders study. METHODS: Trio-based exome sequencing was performed on all 12 patients included in this study, which found a de novo truncating mutation in ASXL3...
January 18, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28099595/exome-sequence-analysis-of-kaposiform-hemangioendothelioma-identification-of-putative-driver-mutations
#13
Sho Egashira, Masatoshi Jinnin, Miho Harada, Shinichi Masuguchi, Satoshi Fukushima, Hironobu Ihn
BACKGROUND: Kaposiform hemangioendothelioma is a rare, intermediate, malignant tumor. The tumor's etiology remains unknown and there are no specific treatments. OBJECTIVE: In this study, we performed exome sequencing using DNA from a Kaposiform hemangioendothelioma patient, and found putative candidates for the responsible mutations. METHOD: The genomic DNA for exome sequencing was obtained from the tumor tissue and matched normal tissue from the same individual...
November 2016: Anais Brasileiros de Dermatologia
https://www.readbyqxmd.com/read/28099461/whole-exome-sequencing-of-growing-and-non-growing-cutaneous-neurofibromas-from-a-single-patient-with-neurofibromatosis-type-1
#14
Daniel L Faden, Saurabh Asthana, Tarik Tihan, Joseph DeRisi, Michel Kliot
The growth behaviors of cutaneous neurofibromas in patients with Neurofibromatosis type 1 are highly variable. The role of the germline NF1 mutation, somatic NF1 mutation and mutations at modifying loci, are poorly understood. We performed whole exome sequencing of three growing and three non-growing neurofibromas from a single individual to assess the role of acquired somatic mutations in neurofibroma growth behavior. 1-11 mutations were identified in each sample, including two deleterious NF1 mutations. No trends were present between the types of somatic mutations identified and growth behavior...
2017: PloS One
https://www.readbyqxmd.com/read/28099363/different-ret-gene-mutation-induced-multiple-endocrine-neoplasia-type-2a-in-3-chinese-families
#15
Qiuli Liu, Dali Tong, Wenqiang Yuan, Gaolei Liu, Gang Yuan, Weihua Lan, Dianzheng Zhang, Jun Zhang, Zaoming Huang, Yao Zhang, Jun Jiang
BACKGROUD: Multiple endocrine neoplasia type 2A (MEN2A) is a condition with inherited autosomal dominant mutations in RET (rearranged during transfection) gene that predisposes the carrier to extremely high risk of medullary thyroid cancer (MTC) and other MEN2A-associated tumors such as parathyroid cancer and/or pheochromocytoma. Little is reported about MEN2A syndrome in the Chinese population. METHODS: All members of the 3 families along with specific probands of MEN2A were analyzed for their clinical, laboratory, and genetic characteristics...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28099038/an-exome-sequencing-study-to-assess-the-role-of-rare-genetic-variation-in-pulmonary-fibrosis
#16
Slavé Petrovski, Jamie L Todd, Michael T Durheim, Quanli Wang, Jason W Chien, Fran L Kelly, Courtney Frankel, Caroline M Mebane, Zhong Ren, Joshua Bridgers, Thomas J Urban, Colin D Malone, Ashley Finlen Copeland, Christie Brinkley, Andrew S Allen, Thomas O'Riordan, John G McHutchison, Scott M Palmer, David B Goldstein
RATIONALE: Idiopathic pulmonary fibrosis (IPF) is an increasingly recognized, often fatal lung disease of unknown etiology. OBJECTIVES: The aim of this study was to use whole-exome sequencing to improve our understanding of the genetic architecture of pulmonary fibrosis. METHODS: We performed a case-control exome-wide collapsing analysis including 262 unrelated individuals with pulmonary fibrosis; clinically classified as IPF according to ATS/ERS/JRS/ALAT guidelines (81...
January 18, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28098136/exome-and-genome-sequencing-of-nasopharynx-cancer-identifies-nf-%C3%AE%C2%BAb-pathway-activating-mutations
#17
Yvonne Y Li, Grace T Y Chung, Vivian W Y Lui, Ka-Fai To, Brigette B Y Ma, Chit Chow, John K S Woo, Kevin Y Yip, Jeongsun Seo, Edwin P Hui, Michael K F Mak, Maria Rusan, Nicole G Chau, Yvonne Y Y Or, Marcus H N Law, Peggy P Y Law, Zoey W Y Liu, Hoi-Lam Ngan, Pok-Man Hau, Krista R Verhoeft, Peony H Y Poon, Seong-Keun Yoo, Jong-Yeon Shin, Sau-Dan Lee, Samantha W M Lun, Lin Jia, Anthony W H Chan, Jason Y K Chan, Paul B S Lai, Choi-Yi Fung, Suet-Ting Hung, Lin Wang, Ann Margaret V Chang, Simion I Chiosea, Matthew L Hedberg, Sai-Wah Tsao, Andrew C van Hasselt, Anthony T C Chan, Jennifer R Grandis, Peter S Hammerman, Kwok-Wai Lo
Nasopharyngeal carcinoma (NPC) is an aggressive head and neck cancer characterized by Epstein-Barr virus (EBV) infection and dense lymphocyte infiltration. The scarcity of NPC genomic data hinders the understanding of NPC biology, disease progression and rational therapy design. Here we performed whole-exome sequencing (WES) on 111 micro-dissected EBV-positive NPCs, with 15 cases subjected to further whole-genome sequencing (WGS), to determine its mutational landscape. We identified enrichment for genomic aberrations of multiple negative regulators of the NF-κB pathway, including CYLD, TRAF3, NFKBIA and NLRC5, in a total of 41% of cases...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097321/diagnostic-yield-and-novel-candidate-genes-by-exome-sequencing-in-152-consanguineous-families-with-neurodevelopmental-disorders
#18
Miriam S Reuter, Hasan Tawamie, Rebecca Buchert, Ola Hosny Gebril, Tawfiq Froukh, Christian Thiel, Steffen Uebe, Arif B Ekici, Mandy Krumbiegel, Christiane Zweier, Juliane Hoyer, Karolin Eberlein, Judith Bauer, Ute Scheller, Tim M Strom, Sabine Hoffjan, Ehab R Abdelraouf, Nagwa A Meguid, Ahmad Abboud, Mohammed Ayman Al Khateeb, Mahmoud Fakher, Saber Hamdan, Amina Ismael, Safia Muhammad, Ebtessam Abdallah, Heinrich Sticht, Dagmar Wieczorek, André Reis, Rami Abou Jamra
Importance: Autosomal recessive inherited neurodevelopmental disorders are highly heterogeneous, and many, possibly most, of the disease genes are still unknown. Objectives: To promote the identification of disease genes through confirmation of previously described genes and presentation of novel candidates and provide an overview of the diagnostic yield of exome sequencing in consanguineous families. Design, Setting, and Participants: Autozygosity mapping in families and exome sequencing of index patients were performed in 152 consanguineous families (the parents descended from a same ancestor) with at least 1 offspring with intellectual disability (ID)...
January 11, 2017: JAMA Psychiatry
https://www.readbyqxmd.com/read/28097046/molecular-classification-of-tissue-from-a-transformed-non-hogkin-s-lymphoma-case-with-unexpected-long-time-remission
#19
Julie Støve Bødker, Marianne Tang Severinsen, Tarec Christoffer El-Galaly, Rasmus Froberg Brøndum, Maria Bach Laursen, Steffen Falgreen, Mette Nyegaard, Alexander Schmitz, Lasse Hjort Jakobsen, Anna Amanda Schönherz, Hanne Due, Linn Reinholdt, Martin Bøgsted, Karen Dybkær, Hans Erik Johnsen
BACKGROUND: The concept of precision medicine in cancer includes individual molecular studies to predict clinical outcomes. In the present N = 1 case we retrospectively have analysed lymphoma tissue by exome sequencing and global gene expression in a patient with unexpected long-term remission following relaps. The goals were to phenotype the diagnostic and relapsed lymphoma tissue and evaluate its pattern. Furthermore, to identify mutations available for targeted therapy and expression of genes to predict specific drug effects by resistance gene signatures (REGS) for R-CHOP as described at http://www...
2017: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/28096458/more-severe-disease-and-slower-recovery-in-younger-patients-with-anti-3-hydroxy-3-methylglutaryl-coenzyme-a-reductase-associated-autoimmune-myopathy
#20
Eleni Tiniakou, Iago Pinal-Fernandez, Thomas E Lloyd, Jemima Albayda, Julie Paik, Jessie L Werner, Cassie A Parks, Livia Casciola-Rosen, Lisa Christopher-Stine, Andrew L Mammen
OBJECTIVE: To study disease severity and response to therapy in a large cohort of patients with anti-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR)-associated myositis. METHODS: Muscle strength, creatine kinase levels and treatments were assessed in anti-HMGCR-positive patients at each clinical visit. Univariate and multivariate analyses were used to analyse the influence of clinical characteristics on strength and the change in strength over time. Whole exome sequencing was performed in a subset of patients...
January 17, 2017: Rheumatology
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