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Whole exome sequencing

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https://www.readbyqxmd.com/read/29235529/identification-of-mylk3-mutations-in-familial-dilated-cardiomyopathy
#1
Takashige Tobita, Seitaro Nomura, Hiroyuki Morita, Toshiyuki Ko, Takanori Fujita, Haruhiro Toko, Kenta Uto, Nobuhisa Hagiwara, Hiroyuki Aburatani, Issei Komuro
Dilated cardiomyopathy (DCM) is a primary cause of heart failure, life-threatening arrhythmias, and cardiac death. Pathogenic mutations have been identified at the loci of more than 50 genes in approximately 50% of DCM cases, while the etiologies of the remainder have yet to be determined. In this study, we applied whole exome sequencing in combination with segregation analysis to one pedigree with familial DCM, and identified a read-through mutation (c.2459 A > C; p.*820Sext*19) in the myosin light chain kinase 3 gene (MYLK3)...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233928/integrated-molecular-characterization-of-the-lethal-pediatric-cancer-pancreatoblastoma
#2
Tomoya Isobe, Masafumi Seki, Kenichi Yoshida, Masahiro Sekiguchi, Yusuke Shiozawa, Yuichi Shiraishi, Shunsuke Kimura, Misa Yoshida, Yoshikage Inoue, Akira Yokoyama, Nobuyuki Kakiuchi, Hiromichi Suzuki, Keisuke Kataoka, Yusuke Sato, Tomoko Kawai, Kenichi Chiba, Hiroko Tanaka, Teppei Shimamura, Motohiro Kato, Akihiro Iguchi, Asahito Hama, Tomoaki Taguchi, Masaharu Akiyama, Junya Fujimura, Akiko Inoue, Tsuyoshi Ito, Takao Deguchi, Chikako Kiyotani, Tomoko Iehara, Hajime Hosoi, Akira Oka, Masashi Sanada, Yukichi Tanaka, Kenichiro Hata, Satoru Miyano, Seishi Ogawa, Junko Takita
Pancreatoblastoma (PBL) is a rare pediatric pancreatic malignancy for which the molecular pathogenesis is not understood. In this study, we report the findings of an integrated multi-omics study of whole exome and RNA sequencing as well as genome-wide copy number and methylation analyses of 10 PBL cases. The PBL genome was characterized by a high frequency of aberrant activation of the Wnt signaling pathway, either via somatic mutations of CTNNB1 (90%) and copy-neutral loss of heterozygosity (CN-LOH) of APC (10%)...
December 12, 2017: Cancer Research
https://www.readbyqxmd.com/read/29233531/genomic-landscape-of-ovarian-clear-cell-carcinoma-via-whole-exome-sequencing
#3
Se Ik Kim, Ji Won Lee, Maria Lee, Hee Seung Kim, Hyun Hoon Chung, Jae-Weon Kim, Noh Hyun Park, Yong-Sang Song, Jeong-Sun Seo
OBJECTIVE: To analyze whole exome sequencing (WES) data on ovarian clear cell carcinoma (OCCC) in Korean patients via the technique of next generation sequencing (NGS). Genomic profiles were compared between endometriosis-associated OCCC (EMS-OCCC) and Non-EMS-OCCC. METHODS: We used serum samples and cancer tissues, stored at the Seoul National University Hospital Human Biobank, that were initially collected from women diagnosed with OCCC between 2012 and 2016. In total, 15 patients were enrolled: 5 with pathologically confirmed EMS-OCCC and 10 with Non-EMS-OCCC...
December 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29233175/exome-sequencing-of-multiple-sclerosis-patients-and-their-unaffected-first-degree-relatives
#4
Sheila Garcia-Rosa, Maria Galli de Amorim, Renan Valieris, Vanessa Daccach Marques, Julio Cesar Cetrulo Lorenzi, Vania Balardin Toller, Guilherme Sciascia do Olival, Wilson Araújo da Silva Júnior, Israel Tojal da Silva, Amilton Antunes Barreira, Diana Noronha Nunes, Emmanuel Dias-Neto
OBJECTIVES: The understanding of complex multifactorial diseases requires the availability of a variety of data for a large-number of affected individuals. In this data note here we provide whole exome sequencing data from a set of non-familiar multiple-sclerosis (MS) patients as well as their unaffected first-degree relatives. This data might help the identification of genomic alterations, including single nucleotide polymorphisms, de novo variations and structural genomic variations, such as copy-number alterations that may impact this disease...
December 12, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29232904/an-expanded-multi-organ-disease-phenotype-associated-with-mutations-in-yars
#5
Anna Tracewska-Siemiątkowska, Lonneke Haer-Wigman, Danielle G M Bosch, Deborah Nickerson, Michael J Bamshad, Maartje van de Vorst, Nanna Dahl Rendtorff, Claes Möller, Ulrika Kjellström, Sten Andréasson, Frans P M Cremers, Lisbeth Tranebjærg
Whole exome sequence analysis was performed in a Swedish mother-father-affected proband trio with a phenotype characterized by progressive retinal degeneration with congenital nystagmus, profound congenital hearing impairment, primary amenorrhea, agenesis of the corpus callosum, and liver disease. A homozygous variant c.806T > C, p.(F269S) in the tyrosyl-tRNA synthetase gene (YARS) was the only identified candidate variant consistent with autosomal recessive inheritance. Mutations in YARS have previously been associated with both autosomal dominant Charcot-Marie-Tooth syndrome and a recently reported autosomal recessive multiorgan disease...
December 11, 2017: Genes
https://www.readbyqxmd.com/read/29230941/a-child-with-myhre-syndrome-presenting-with-corectopia-and-tetralogy-of-fallot
#6
Marianna Alagia, Gerarda Cappuccio, Michele Pinelli, Annalaura Torella, Raffaella Brunetti-Pierri, Francesca Simonelli, Giuseppe Limongelli, Guido Oppido, Vincenzo Nigro, Nicola Brunetti-Pierri
Myhre syndrome is a rare autosomal dominant disorder caused by a narrow spectrum of missense mutations in the SMAD4 gene. Typical features of this disorder are distinctive facial appearance, deafness, intellectual disability, cardiovascular abnormalities, short stature, short hands and feet, compact build, joint stiffness, and skeletal anomalies. The clinical features generally appear during childhood and become more evident in older patients. Therefore, the diagnosis of this syndrome in the first years of life is challenging...
December 12, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29230811/whole-exome-sequencing-of-oral-mucosal-melanoma-reveals-mutational-profile-and-therapeutic-targets
#7
Jiong Lyu, Zhijian Song, Jianhua Chen, Matthew J Shepard, Hao Song, Guoxin Ren, Zhiqiang Li, Wei Guo, Zhengping Zhuang, Yongyong Shi
Oral mucosal melanoma (OMM) is rare and aggressive subtype of melanoma with little known about its pathogenesis carcinogenesis. We therefore performed whole-exome sequencing (WES) on 19 matched OMM tumor/normal pairs in order to gain insight on potential genetic drivers of tumor formation. For the first time we describe the comprehensive mutational profile of OMM. Our data suggests that the genetic background of OMM differs from those of other melanoma subtypes. We identified recurrent mutations involving KIT, POLE,PTPRD, PTCHD2 and DMXL2...
December 12, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29230160/whole-exome-sequencing-identifies-a-de-novo-ahdc1-mutation-in-a-colombian-patient-with-xia-gibbs-syndrome
#8
Mary García-Acero, Johanna Acosta
Xia-Gibbs syndrome is an autosomal dominant multisystem developmental disorder characterized by global developmental delay, hypotonia, obstructive sleep apnea, seizures, retrocerebellar cysts, delayed myelination, micrognathia, and mild dysmorphic features. Using whole-exome sequencing, we identified a de novo AHDC1 frameshift mutation c.2030_2030delG (p.G677Afs*52) in a Colombian patient, which was absent in both parents. Furthermore, we summarized the phenotypes of patients reported in the literature.
November 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/29230157/novel-stil-compound-heterozygous-mutations-cause-severe-fetal-microcephaly-and-centriolar-lengthening
#9
Francesca Cristofoli, Bart De Keersmaecker, Luc De Catte, Joris R Vermeesch, Hilde Van Esch
STIL (SCL/TAL1 interrupting locus) is a core component of the centriole duplication process. STIL mutations have been associated with both autosomal recessive primary microcephaly (MCPH) and holoprosencephaly. In this report, we describe a family with multiple miscarriages and 2 terminations of pregnancy due to marked fetal microcephaly, delayed cortical gyrification, and dysgenesis of the corpus callosum. Whole exome sequencing allowed us to identify novel compound heterozygous mutations in STIL. The mutations lie, respectively, in the CPAP/CENPJ and the hsSAS6 interacting domains of STIL...
November 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/29230040/congenital-embryonal-rhabdomyosarcoma-caused-by-heterozygous-concomitant-ptch1-and-ptch2-germline-mutations
#10
Julia Taeubner, Triantafyllia Brozou, Nan Qin, Jasmin Bartl, Sebastian Ginzel, Joerg Schaper, Joerg Felsberg, Simone Fulda, Christian Vokuhl, Arndt Borkhardt, Michaela Kuhlen
The sonic hedgehog (SHH) signaling pathway has been shown to play important roles in embryogenesis, cell proliferation as well as in cell differentiation. It is aberrantly activated in various common cancers in adults, but also in pediatric neoplasms, such as rhabdomyosarcoma (RMS) and atypical teratoid/rhabdoid tumors (AT/RTs). Dysregulation and germline mutation in PATCHED1 (PTCH1), a receptor for SHH, is responsible for the Gorlin Syndrome, a familial cancer predisposing syndrome including RMS. Here, we report a newborn diagnosed with congenital embryonal RMS...
December 11, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29228253/rare-potentially-pathogenic-variants-in-znf469-are-not-enriched-in-keratoconus-in-a-large-australian-cohort-of-european-descent
#11
Sionne E M Lucas, Tiger Zhou, Nicholas B Blackburn, Richard A Mills, Jonathan Ellis, Paul Leo, Emmanuelle Souzeau, Bronwyn Ridge, Jac C Charlesworth, Matthew A Brown, Richard Lindsay, Jamie E Craig, Kathryn P Burdon
Purpose: The Zinc Finger Protein 469 (ZNF469) gene has been proposed as a candidate gene for keratoconus due to the association of an upstream polymorphism (rs9938149) with the disease in two independent studies, and the role of the gene in the autosomal recessive disease Brittle Cornea Syndrome. Coding variants in ZNF469 have been assessed for association with keratoconus in several small studies, with conflicting results. We assessed rare, potentially pathogenic variants in ZNF469 for enrichment in keratoconus patients in a cohort larger than all previous studies combined...
December 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29227308/medical-bioinformatics-in-melanoma
#12
Phil F Cheng
PURPOSE OF REVIEW: Bioinformatic insights from next-generation sequencing has been integral in understanding melanoma biology, resistance to treatment and provided new avenues for melanoma treatment. Whole-genome sequencing, whole-exome sequencing and RNA sequencing has redefined the molecular classification of melanoma, revealed distinct genetic aberrations that define clinical subtypes of melanoma and uncovered the diverse heterogeneity that resides in an individual tumor. RECENT FINDINGS: In this review, we will summarize the recent whole-genome study that catalogs the genomic landscape across many melanoma subtypes, the single-cell RNA sequencing studies that interrogates tumor heterogeneity and the personalized vaccine approaches to melanoma treatment...
December 8, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29226631/novel-compound-heterozygous-mutations-in-gpt2-linked-to-microcephaly-and-intellectual-developmental-disability-with-or-without-spastic-paraplegia
#13
Hande Kaymakcalan, Yanki Yarman, Nukte Goc, Fatih Toy, Cihan Meral, A Gulhan Ercan-Sencicek, Murat Gunel
We here describe novel compound heterozygous missense variants, NM_133443:c.[400C>T] and NM_133443:[1435G>A], in the glutamic-pyruvic transaminase 2 (GPT2) gene in a large consanguineous family with two affected siblings diagnosed with microcephaly intellectual disability and developmental delay (IDD). In addition to these clinical phenotypes, the male sibling has spastic paraplegia, and the female sibling has epilepsy. Their four extended family members have IDD and microcephaly. Both of these variants, c...
December 11, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29226520/a-novel-homozygous-slc25a1-mutation-with-impaired-mitochondrial-complex-v-possible-phenotypic-expansion
#14
Idan Cohen, Orna Staretz-Chacham, Ohad Wormser, Yonatan Perez, Ann Saada, Rotem Kadir, Ohad S Birk
SLC25A1 mutations are associated with combined D,L-2-hydroxyglutaric aciduria (DL- 2HGA; OMIM #615182), characterized by muscular hypotonia, severe neurodevelopmental dysfunction and intractable seizures. SLC25A1 encodes the mitochondrial citrate carrier (CIC), which mediates efflux of the mitochondrial tricarboxylic acid (TCA) cycle intermediates citrate and isocitrate in exchange for cytosolic malate. Only a single family with an SLC25A1 mutation has been described in which mitochondrial respiratory chain dysfunction was documented, specifically in complex IV...
December 11, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29226118/identification-of-a-novel-heterozygous-de-novo-7-bp-frameshift-deletion-in-pbx1-by-whole-exome-sequencing-causing-a-multi-organ-syndrome-including-bilateral-dysplastic-kidneys-and-hypoplastic-clavicles
#15
Korbinian Maria Riedhammer, Corinna Siegel, Bader Alhaddad, Carmen Montoya, Reka Kovacs-Nagy, Matias Wagner, Thomas Meitinger, Julia Hoefele
Introduction: Congenital anomalies of the kidney and urinary tract (CAKUT) represent the primary cause of chronic kidney disease in children. Many genes have been attributed to the genesis of this disorder. Recently, haploinsufficiency of PBX1 caused by microdeletions has been shown to result in bilateral renal hypoplasia and other organ malformations. Materials and methods: Here, we report on a 14-year-old male patient with congenital bilateral dysplastic kidneys, cryptorchidism, hypoplastic clavicles, developmental delay, impaired intelligence, and minor dysmorphic features...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/29225788/whole-exome-sequencing-for-detecting-inborn-errors-of-immunity-overview-and-perspectives
#16
REVIEW
Barbara Bosch, Yuval Itan, Isabelle Meyts
The study of inborn errors of immunity is based on a comprehensive clinical description of the patient's phenotype and the elucidation of the underlying molecular mechanisms and their genetic etiology. Deciphering the pathogenesis is key to genetic counseling and the development of targeted therapy. This review shows the power of whole-exome sequencing in detecting inborn errors of immunity along five central steps taken in whole-exome sequencing analysis. In parallel, we highlight the challenges for the clinical and scientific use of the method and how these hurdles are currently being addressed...
2017: F1000Research
https://www.readbyqxmd.com/read/29225264/a-homozygous-lama2-mutation-of-c-818g-a-caused-partial-merosin-deficiency-in-a-japanese-patient
#17
Akatsuki Kubota, Hiroyuki Ishiura, Jun Mitsui, Kaori Sakuishi, Atsushi Iwata, Tomotaka Yamamoto, Ichizo Nishino, Shoji Tsuji, Jun Shimizu
A complete loss of merosin, which is encoded by LAMA2, causes congenital muscular dystrophy with leukoencephalopathy. Partial merosin deficiency can be caused not only by primarily LAMA2 mutations, but also secondarily by dystroglycanopathy. Although it can be molecularly diagnosed based on a genetic analysis, this method is labor-intensive because of its huge genome size. A 26-year-old male patient presented with mild muscular weakness, joint contractures, and epilepsy. Double immunofluorescence staining of a muscle biopsy specimen showed mislocalization of merosin, and a genetic analysis revealed a homozygous c...
December 8, 2017: Internal Medicine
https://www.readbyqxmd.com/read/29223623/gene-indexed-mutations-in-maize-zea-mays
#18
Xiaoduo Lu, Jisheng Liu, Wen Ren, Qun Yang, Zhenguang Chai, Rumei Chen, Lei Wang, Jun Zhao, Zhihong Lang, Haiyang Wang, Yunliu Fan, Jiuran Zhao, Chunyi Zhang
The availability of the B73 inbred reference genome sets the stage for high- throughput functional characterisation of maize genes on a whole-genome scale. Among the 39,324 protein-coding genes predicted, the vast majority has been untapped due to the lack of suitable high throughput reverse genetic resources. We have generated a gene-indexed maize mutant collection through ethyl methanesulfonate (EMS) mutagenesis and detected the mutations by combining exome capture and next-generation sequencing. A total of 1,086 mutated M1 plants were sequenced and 195,268 CG>TA-type point mutations, including stop gain/loss, missplice, start gain/loss, and various non-synonymous protein mutations as well as 4,610 InDel mutations, were identified...
December 6, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29222305/biology-of-cns-lymphoma-and-the-potential-of-novel-agents
#19
REVIEW
James L Rubenstein
Primary and secondary CNS lymphomas are aggressive brain tumors that pose an immense challenge to define in terms of molecular pathogenesis, as well as to effectively treat. During the past 10 years improvements in survival have been achieved with the implementation of anti-CD20 immunotherapy and optimization of dose-intensive consolidation strategies. The applications of whole-exome sequencing, comparative genomic hybridization, transcriptional profiling, and examination of the tumor microenvironment, particularly in the context of clinical investigation, provide insights that create a roadmap for the development and implementation of novel targeted agents for this disease...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29222063/evolutionary-dynamism-in-bryophytes-phylogenomic-inferences-confirm-rapid-radiation-in-the-moss-family-funariaceae
#20
Rafael Medina, Matthew Johnson, Yang Liu, Nicholas Wilding, Terry A Hedderson, Norman Wickett, Bernard Goffinet
Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture...
December 5, 2017: Molecular Phylogenetics and Evolution
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