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Whole 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/28105640/the-genotype-phenotype-landscape-of-familial-amyotrophic-lateral-sclerosis-in-australia
#5
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/28104354/profound-loss-of-esophageal-tissue-differentiation-in-eosinophilic-esophagitis
#6
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
#7
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/28100915/whole-exome-sequencing-study-reveals-common-copy-number-variants-in-protocadherin-genes-associated-with-childhood-obesity-in-koreans
#8
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/28099461/whole-exome-sequencing-of-growing-and-non-growing-cutaneous-neurofibromas-from-a-single-patient-with-neurofibromatosis-type-1
#9
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/28099038/an-exome-sequencing-study-to-assess-the-role-of-rare-genetic-variation-in-pulmonary-fibrosis
#10
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
#11
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/28096458/more-severe-disease-and-slower-recovery-in-younger-patients-with-anti-3-hydroxy-3-methylglutaryl-coenzyme-a-reductase-associated-autoimmune-myopathy
#12
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
https://www.readbyqxmd.com/read/28095098/reduced-penetrance-in-a-large-caucasian-pedigree-with-stickler-syndrome
#13
Stuart W Tompson, Charles Johnson, Diana Abbott, Benjamin Bakall, Vincent Soler, Tammy L Yanovitch, Kristina N Whisenhunt, Thomas Klemm, Steve Rozen, Edwin M Stone, Max Johnson, Terri L Young
BACKGROUND: In a four-generation Caucasian family variably diagnosed with autosomal dominant (AD) Stickler or Wagner disease, commercial gene screening failed to identify a mutation in COL2A1 or VCAN. We utilized linkage mapping and exome sequencing to identify the causal variant. MATERIALS AND METHODS: Genomic DNA samples collected from 40 family members were analyzed. A whole-genome linkage scan was performed using Illumina HumanLinkage-24 BeadChip followed by two-point and multipoint linkage analyses using FASTLINK and MERLIN...
January 17, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28093659/clinical-and-molecular-relevance-of-mutant-allele-tumor-heterogeneity-in-breast-cancer
#14
Ding Ma, Yi-Zhou Jiang, Xi-Yu Liu, Yi-Rong Liu, Zhi-Ming Shao
PURPOSE: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. We used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and explored its correlation with clinical parameters and multi-omics data. METHODS: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. We calculated the MATH values from whole-exome sequencing data and further investigated their correlation with clinical characteristics, somatic mutations, somatic copy number alterations (SCNAs), and gene enrichment...
January 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28090092/the-clonal-origins-of-leukemic-progression-of-myelodysplasia
#15
T H Kim, M S Tyndel, H J Kim, J-S Ahn, S H Choi, H J Park, Y-K Kim, D-H Yang, J-J Lee, S-H Jung, S Y Kim, Y H Min, J-W Cheong, S K Sohn, J H Moon, M Choi, M Lee, Z Zhang, D Dong Hwan Kim
The genetics behind the progression of myelodysplasia to secondary acute myeloid leukemia (sAML) is poorly understood. In this study, we profiled somatic mutations and their dynamics using next generation sequencing on serial samples from a total of 124 patients, consisting of a 31 patient discovery cohort and 93 patients from two validation cohorts. Whole-exome analysis on the discovery cohort revealed that 29 of 31 patients carry mutations related to at least one of 8 commonly mutated pathways in AML. Mutations in genes related to DNA methylation and splicing machinery were found in T-cell samples, which expand at the initial diagnosis of the myelodysplasia, suggesting their importance as early disease events...
January 16, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28088513/an-immunogram-for-the-cancer-immunity-cycle-towards-personalized-immunotherapy-of-lung-cancer
#16
Takahiro Karasaki, Kazuhiro Nagayama, Hideki Kuwano, Jun-Ichi Nitadori, Masaaki Sato, Masaki Anraku, Akihiro Hosoi, Hirokazu Matsushita, Yasuyuki Morishita, Kosuke Kashiwabara, Masaki Takazawa, Osamu Ohara, Kazuhiro Kakimi, Jun Nakajima
INTRODUCTION: The interaction of immune cells and cancer cells shapes the immunosuppressive tumor microenvironment. For successful cancer immunotherapy, comprehensive knowledge of anti-tumor immunity as a dynamic spacio-temporal process is required for each individual patient. To this end, we developed an immunogram for the cancer-immunity cycle using next-generation sequencing. METHODS: Whole-exome sequencing and RNA-Seq was performed in 20 non-small cell lung cancer patients (12 adenocarcinoma, 7 squamous cell carcinoma, and 1 large cell neuroendocrine carcinoma)...
January 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28087737/a-homozygous-mutation-in-trim36-causes-autosomal-recessive-anencephaly-in-an-indian-family
#17
Nivedita Singh, Vishwanath Kumble Bhat, Ankana Tiwari, Srinivas G Kodaganur, Sagar J Tontanahal, Astha Sarda, K V Malini, Arun Kumar
Anencephaly is characterized by the absence of brain tissues and cranium. During primary neurulation stage of the embryo, the rostral part of the neural pore fails to close, leading to anencephaly. Anencephaly shows a heterogeneous etiology, ranging from environmental to genetic causes. The autosomal recessive inheritance of anencephaly has been reported in several populations. In this study, we employed whole-exome sequencing and identified a homozygous missense mutation c.1522C>A (p.Pro508Thr) in the TRIM36 gene as the cause of autosomal recessive anencephaly (APH) in an Indian family...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087721/joubert-syndrome-neuroimaging-findings-in-110-patients-in-correlation-with-cognitive-function-and-genetic-cause
#18
Andrea Poretti, Joseph Snow, Angela C Summers, Aylin Tekes, Thierry A G M Huisman, Nafi Aygun, Kathryn A Carson, Dan Doherty, Melissa A Parisi, Camilo Toro, Deniz Yildirimli, Meghana Vemulapalli, Jim C Mullikin, Andrew R Cullinane, Thierry Vilboux, William A Gahl, Meral Gunay-Aygun
BACKGROUND: Joubert syndrome is a clinically and genetically heterogeneous ciliopathy. Neuroimaging findings have not been systematically evaluated in a large cohort of patients with Joubert syndrome in correlation with molecular genetic cause and cognitive function. METHODS: Brain MRI of 110 patients with Joubert syndrome was included in this study. A comprehensive evaluation of brain MRI studies for infratentorial and supratentorial morphological abnormalities was performed...
January 13, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28087566/application-of-whole-exome-sequencing-in-the-clinical-diagnosis-and-management-of-inherited-cardiovascular-diseases-in-adults
#19
Sara B Seidelmann, Emily Smith, Lakshman Subrahmanyan, Daniel Dykas, Maen D Abou Ziki, Bani Azari, Fady Hannah-Shmouni, Yuexin Jiang, Joseph G Akar, Mark Marieb, Daniel Jacoby, Allen E Bale, Richard P Lifton, Arya Mani
BACKGROUND: With the advent of high throughput sequencing, the identification of genetic causes of cardiovascular disease (CVD) has become an integral part of medical diagnosis and management and at the forefront of personalized medicine in this field. The use of whole exome sequencing for clinical diagnosis, risk stratification, and management of inherited CVD has not been previously evaluated. METHODS AND RESULTS: We analyzed the results of whole exome sequencing in first 200 adult patients with inherited CVD, who underwent genetic testing at the Yale Program for Cardiovascular Genetics...
February 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28087116/application-of-whole-exome-sequencing-in-elucidating-the-phenotype-and-genotype-spectrum-of-junctional-epidermolysis-bullosa-a-preliminary-experience-of-a-tertiary-care-centre-in-india
#20
Vamsi K Yenamandra, Shamsudheen K Vellarikkal, Manoj Kumar, Madhumita R Chowdhury, Rijith Jayarajan, Ankit Verma, Vinod Scaria, Sridhar Sivasubbu, Subrata B Ray, Amit K Dinda, Madhulika Kabra, Punit Kaur, Vinod K Sharma, Gomathy Sethuraman
BACKGROUND: Junctional epidermolysis bullosa (JEB) is a diverse group of genodermatoses associated with extreme skin fragility. Despite several well-characterized genetic studies, molecular diagnosis of this heterogeneous group is still challenging. Recent advances in the field of genomics have seen the successful implementation of whole exome sequencing (WES) as a fast and efficient diagnostic strategy in several genodermatoses. OBJECTIVE: In view of the scarcity and need of molecular studies for JEB in India, we sought to explore the potential of WES in understanding the mutational spectrum of this rare, in certain subtypes lethal, sub-group of EB...
December 29, 2016: Journal of Dermatological Science
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