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https://www.readbyqxmd.com/read/27913932/almost-2-of-spanish-breast-cancer-families-are-associated-to-germline-pathogenic-mutations-in-the-atm-gene
#1
A Tavera-Tapia, L Pérez-Cabornero, J A Macías, M I Ceballos, G Roncador, M de la Hoya, A Barroso, V Felipe-Ponce, R Serrano-Blanch, C Hinojo, M D Miramar-Gallart, M Urioste, T Caldés, S Santillan-Garzón, J Benitez, A Osorio
PURPOSE: There is still a considerable percentage of hereditary breast and ovarian cancer (HBOC) cases not explained by BRCA1 and BRCA2 genes. In this report, next-generation sequencing (NGS) techniques were applied to identify novel variants and/or genes involved in HBOC susceptibility. METHODS: Using whole exome sequencing, we identified a novel germline mutation in the moderate-risk gene ATM (c.5441delT; p.Leu1814Trpfs*14) in a family negative for mutations in BRCA1/2 (BRCAX)...
December 2, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/27913610/whole-exome-sequencing-of-thymic-neuroendocrine-tumor-with-ectopic-acth-syndrome
#2
Yanli Li, Ying Peng, Xiuli Jiang, Yulong Cheng, Weiwei Zhou, Tingwei Su, Jing Xie, Xu Zhong, Dalong Song, Luming Wu, Liwen Fan, Min Li, Jie Hong, Weiqing Wang, Guang Ning, Yanan Cao
OBJECTIVE: Thymic neuroendocrine tumor is the second-most prevalent cause of ectopic adrenocorticotropic hormone (ACTH) syndrome (EAS), which is a rare disease characterized by ectopic ACTH oversecretion from nonpituitary tumors. However, the genetic abnormalities of thymic neuroendocrine tumors with EAS remain largely unknown. We aim to elucidate the genetic abnormalities and identify the somatic mutations of potential tumor-related genes of thymic neuroendocrine tumors with EAS by whole exome sequencing...
February 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/27913435/idh2-mutations-define-a-unique-subtype-of-breast-cancer-with-altered-nuclear-polarity
#3
Sarah Chiang, Britta Weigelt, Huei-Chi Wen, Fresia Pareja, Ashwini Raghavendra, Luciano G Martelotto, Kathleen A Burke, Thais Basili, Anqi Li, Felipe C Geyer, Salvatore Piscuoglio, Charlotte K Y Ng, Achim A Jungbluth, Jörg Balss, Stefan Pusch, Gabrielle M Baker, Kimberly S Cole, Andreas von Deimling, Julie M Batten, Jonathan D Marotti, Hwei-Choo Soh, Benjamin L McCalip, Jonathan Serrano, Raymond S Lim, Kalliopi P Siziopikou, Song Lu, Xiaolong Liu, Tarek Hammour, Edi Brogi, Matija Snuderl, A John Iafrate, Jorge S Reis-Filho, Stuart J Schnitt
Solid papillary carcinoma with reverse polarity (SPCRP) is a rare breast cancer subtype with an obscure etiology. In this study, we sought to describe its unique histopathologic features and to identify the genetic alterations that underpin SPCRP using massively parallel whole-exome and targeted sequencing. The morphologic and immunohistochemical features of SPCRP support the invasive nature of this subtype. Ten of 13 (77%) SPCRPs harbored hotspot mutations at R172 of the isocitrate dehydrogenase IDH2, of which 8 of 10 displayed concurrent pathogenic mutations affecting PIK3CA or PIK3R1 One of the IDH2 wild-type SPCRPs harbored a TET2 Q548* truncating mutation coupled with a PIK3CA H1047R hotspot mutation...
October 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27912749/whole-exome-sequencing-identifies-a-novel-missense-fbn2-mutation-co-segregating-in-a-four-generation-chinese-family-with-congenital-contractural-arachnodactyly
#4
Xingping Guo, Chunying Song, Yaping Shi, Hongxia Li, Weijing Meng, Qinzhao Yuan, Jinjie Xue, Jun Xie, Yunxia Liang, Yanan Yuan, Baofeng Yu, Huaixiu Wang, Yun Chen, Lixin Qi, Xinmin Li
BACKGROUND: Congenital contractural arachnodactyly (CCA) is an autosomal dominant rare genetic disease, estimated to be less than 1 in 10,000 worldwide. People with this condition often have permanently bent joints (contractures), like bent fingers and toes (camptodactyly). CASE PRESENTATION: In this study, we investigated the genetic aetiology of CCA in a four-generation Chinese family. The blood samples were collected from 22 living members of the family in the Yangquan County, Shanxi Province, China...
December 3, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27912315/genetics-of-infectious-and-inflammatory-diseases-overlapping-discoveries-from-association-and-exome-sequencing-studies
#5
David Langlais, Nassima Fodil, Philippe Gros
Genome technologies have defined a complex genetic architecture in major infectious, inflammatory, and autoimmune disorders. High density marker arrays and Immunochips have powered genome-wide association studies (GWAS) that have mapped nearly 450 genetic risk loci in 22 major inflammatory diseases, including a core of common genes that play a central role in pathological inflammation. Whole-exome and whole-genome sequencing have identified more than 265 genes in which mutations cause primary immunodeficiencies and rare forms of severe inflammatory bowel disease...
December 1, 2016: Annual Review of Immunology
https://www.readbyqxmd.com/read/27912044/mutations-in-prosc-disrupt-cellular-pyridoxal-phosphate-homeostasis-and-cause-vitamin-b6-dependent-epilepsy
#6
Niklas Darin, Emma Reid, Laurence Prunetti, Lena Samuelsson, Ralf A Husain, Matthew Wilson, Basma El Yacoubi, Emma Footitt, W K Chong, Louise C Wilson, Helen Prunty, Simon Pope, Simon Heales, Karine Lascelles, Mike Champion, Evangeline Wassmer, Pierangelo Veggiotti, Valérie de Crécy-Lagard, Philippa B Mills, Peter T Clayton
Pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, functions as a cofactor in humans for more than 140 enzymes, many of which are involved in neurotransmitter synthesis and degradation. A deficiency of PLP can present, therefore, as seizures and other symptoms that are treatable with PLP and/or pyridoxine. Deficiency of PLP in the brain can be caused by inborn errors affecting B6 vitamer metabolism or by inactivation of PLP, which can occur when compounds accumulate as a result of inborn errors of other pathways or when small molecules are ingested...
December 1, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27910721/care-delivery-considerations-for-widespread-and-equitable-implementation-of-inherited-cancer-predisposition-testing
#7
Deborah Cragun, Anita Y Kinney, Tuya Pal
DNA sequencing advances through next-generation sequencing (NGS) and several practice changing events, have led to shifting paradigms for inherited cancer predisposition testing. These changes necessitated a means by which to maximize health benefits without unnecessarily inflating healthcare costs and exacerbating health disparities. Areas covered: NGS-based tests encompass multi-gene panel tests, whole exome sequencing, and whole genome sequencing, all of which test for multiple genes simultaneously, compared to prior sequencing practices through which testing was performed sequentially for one or two genes...
December 2, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27910131/whole-exome-association-of-rare-deletions-in-multiplex-oral-cleft-families
#8
Jack Fu, Terri H Beaty, Alan F Scott, Jacqueline Hetmanski, Margaret M Parker, Joan E Bailey Wilson, Mary L Marazita, Elisabeth Mangold, Hasan Albacha-Hejazi, Jeffrey C Murray, Alexandre Bureau, Jacob Carey, Stephen Cristiano, Ingo Ruczinski, Robert B Scharpf
By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood...
December 1, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27908673/darwin-comes-to-clinic
#9
Arthur L Beaudet
What might be the benefits of whole-genome rather than whole-exome sequencing (WES) for identifying the genetic causes of human disabilities? A recent paper by Doan et al. focuses attention on mutations in human accelerated regions (HARs), a subset of genomic regulatory elements showing accelerated evolution between chimpanzees and humans.
November 28, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27908631/confirmation-of-the-gnb4-gene-as-causal-for-charcot-marie-tooth-disease-by-a-novel-de-novo-mutation-in-a-czech-patient
#10
Laššuthová Petra, Šafka Brožková Dana, Neupauerová Jana, Krůtová Marcela, Mazanec Radim, Seeman Pavel
The association of GNB4 with Charcot-Marie-Tooth (CMT) has recently been described in a publication by Soong et al. (Soong, et al., 2013). Here we present a patient with CMT in whom whole exome sequencing identified the mutation p.Lys57Glu in the GNB4 gene (NM_021629.3:c.169A>G). The patient, now 41 years old, is a sporadic case in the family. At the age of 35 he presented with severe disability (CMT neuropathy score 29), profound muscle atrophies, pes cavus and scoliosis. Previously, the patient was tested for PMP22 duplications/deletions and later also with 64 CMT gene panel, with no causal variant found...
September 22, 2016: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/27907889/denovo-db-a-compendium-of-human-de-novo-variants
#11
Tychele N Turner, Qian Yi, Niklas Krumm, John Huddleston, Kendra Hoekzema, Holly A F Stessman, Anna-Lisa Doebley, Raphael A Bernier, Deborah A Nickerson, Evan E Eichler
Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (http://denovo-db...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27905446/genomic-evolution-and-chemoresistance-in-germ-cell-tumours
#12
Amaro Taylor-Weiner, Travis Zack, Elizabeth O'Donnell, Jennifer L Guerriero, Brandon Bernard, Anita Reddy, G Celine Han, Saud AlDubayan, Ali Amin-Mansour, Steven E Schumacher, Kevin Litchfield, Clare Turnbull, Stacey Gabriel, Rameen Beroukhim, Gad Getz, Scott L Carter, Michelle S Hirsch, Anthony Letai, Christopher Sweeney, Eliezer M Van Allen
Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27905264/biotin-thiamine-responsive-basal-ganglia-disease-catastrophic-consequences-of-delay-in-diagnosis-and-treatment
#13
Hussein Algahtani, Saeed Ghamdi, Bader Shirah, Bader Alharbi, Raghad Algahtani, Abdulrahman Bazaid
BACKGROUND: Biotin-thiamine-responsive basal ganglia disease (BTBGD) is an autosomal recessive neurometabolic disorder caused by mutations in the SLC19A3 gene. The disease is characterized by subacute encephalopathy with confusion, dysphagia, dysarthria, and seizures. METHODS: We diagnosed a family affected by BTBGD and studied them including prognosis of cases when diagnosed and treated early in the disease process. We also review the literature comprehensively and summarize all published data about this disorder...
December 1, 2016: Neurological Research
https://www.readbyqxmd.com/read/27905109/a-lethal-neonatal-phenotype-of-mitochondrial-short-chain-enoyl-coa-hydratase-1-deficiency
#14
F Al Mutairi, H E Shamseldin, M Alfadhel, R J Rodenburg, F S Alkuraya
Short-chain enoyl-CoA hydratase (SCEH) is a mitochondrial enzyme involved in the oxidation of fatty acids and the catabolic pathway of valine and, to a lesser extent, isoleucine. Deficiency of this enzyme was recently shown to cause an early childhood Leigh syndrome phenotype. The few reported patients were compound heterozygotes for two missense or missense with truncating variants in ECHS1 that encodes SCEH. We describe two siblings with severe refractory lactic acidosis and death within the first 2 days of life...
October 13, 2016: Clinical Genetics
https://www.readbyqxmd.com/read/27904835/a-novel-dominant-d109a-cryab-mutation-in-a-family-with-myofibrillar-myopathy-affects-%C3%AE-b-crystallin-structure
#15
Jakub P Fichna, Anna Potulska-Chromik, Przemysław Miszta, Maria Jolanta Redowicz, Anna M Kaminska, Cezary Zekanowski, Sławomir Filipek
Myofibrillar myopathy (MFM) is a group of inherited muscular disorders characterized by myofibrils dissolution and abnormal accumulation of degradation products. So far causative mutations have been identified in nine genes encoding Z-disk proteins, including αB-crystallin (CRYAB), a small heat shock protein (also called HSPB5). Here, we report a case study of a 63-year-old Polish female with a progressive lower limb weakness and muscle biopsy suggesting a myofibrillar myopathy, and extra-muscular multisystemic involvement, including cataract and cardiomiopathy...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/27903883/function-driven-discovery-of-disease-genes-in-zebrafish-using-an-integrated-genomics-big-data-resource
#16
Hongseok Shim, Ji Hyun Kim, Chan Yeong Kim, Sohyun Hwang, Hyojin Kim, Sunmo Yang, Ji Eun Lee, Insuk Lee
Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www...
November 16, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903293/personalized-medicine-approach-confirms-a-milder-case-of-abat-deficiency
#17
A Besse, A K Petersen, J V Hunter, V Appadurai, S R Lalani, P E Bonnen
ABAT deficiency (OMIM 613163) is a rare inborn error of metabolism caused by recessive variants in the gene 4-aminobutyric acid transaminase (ABAT), which is responsible for both the catalysis of GABA and maintenance of nucleoside pools in the mitochondria. To date, only a few patients have been reported worldwide. Their clinical presentation has been remarkably consistent with primary features of severe psychomotor retardation, encephalopathy, hypotonia, and infantile-onset refractory epilepsy. We report a new case of ABAT deficiency that marks an important departure from previous clinical findings...
December 1, 2016: Molecular Brain
https://www.readbyqxmd.com/read/27902597/whole-exome-sequencing-of-independent-lung-adenocarcinoma-lung-squamous-cell-carcinoma-and-malignant-peritoneal-mesothelioma-a-case-report
#18
Irene Vanni, Simona Coco, Silvia Bonfiglio, Davide Cittaro, Carlo Genova, Federica Biello, Marco Mora, Valeria Rossella, Maria Giovanna Dal Bello, Anna Truini, Barbara Banelli, Dejan Lazarevic, Angela Alama, Erika Rijavec, Giulia Barletta, Francesco Grossi
The presence of multiple primary tumors (MPT) in a single patient has been identified with an increasing frequency. A critical issue is to establish if the second tumor represents an independent primary cancer or a metastasis. Therefore, the assessment of MPT clonal origin might help understand the disease behavior and improve the management/prognosis of the patient.Herein, we report a 73-year-old male smoker who developed 2 primary lung cancers (adenocarcinoma and squamous cell carcinoma) and a malignant peritoneal mesothelioma (PM)...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27902461/whole-exome-sequencing-in-75-high-risk-families-with-validation-and-replication-in-independent-case-control-studies-identifies-tango2-or5h14-and-chad-as-new-prostate-cancer-susceptibility-genes
#19
Danielle M Karyadi, Milan S Geybels, Eric Karlins, Brennan Decker, Laura McIntosh, Amy Hutchinson, Suzanne Kolb, Shannon K McDonnell, Belynda Hicks, Sumit Middha, Liesel M FitzGerald, Melissa S DeRycke, Meredith Yeager, Daniel J Schaid, Stephen J Chanock, Stephen N Thibodeau, Sonja I Berndt, Janet L Stanford, Elaine A Ostrander
Prostate cancer (PCa) susceptibility is defined by a continuum from rare, high-penetrance to common, low-penetrance alleles. Research to date has concentrated on identification of variants at the ends of that continuum. Taking an alternate approach, we focused on the important but elusive class of low-frequency, moderately penetrant variants by performing disease model-based variant filtering of whole exome sequence data from 75 hereditary PCa families. Analysis of 341 candidate risk variants identified nine variants significantly associated with increased PCa risk in a population-based, case-control study of 2,495 men...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27901492/genomic-and-transcriptomic-characterization-of-skull-base-chordoma
#20
Jason K Sa, In-Hee Lee, Sang Duk Hong, Doo-Sik Kong, Do-Hyun Nam
Skull base chordoma is a primary rare malignant bone-origin tumor showing relatively slow growth pattern and locally destructive lesions, which can only be characterized by histologic components. There is no available prognostic or therapeutic biomarker to predict clinical outcome or treatment response and the molecular mechanisms underlying chordoma development still remain unexplored. Therefore, we sought out to identify novel somatic variations that are associated with chordoma progression and potentially employed as therapeutic targets...
November 25, 2016: Oncotarget
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