Read by QxMD icon Read

exom sequencing

Lucie Sedláčková, Petra Laššuthová, Katalin Štěrbová, Jana Haberlová, Emílie Vyhnálková, Jana Neupauerová, David Staněk, Marie Šedivá, Pavel Kršek, Pavel Seeman
INTRODUCTION:  Neurodegenerative diseases of childhood present with progressive decline in cognitive, social, and motor function and are frequently associated with seizures in different stages of the disease. Here we report a patient with severe progressive neurodegeneration with drug-resistant epilepsy of unknown etiology from the age of 2 years. METHODS AND RESULTS:  Using whole exome sequencing, we found heterozygous missense de novo variant c.628G > A (p...
December 5, 2018: Neuropediatrics
Cecilia Chao, Lakshmi Akileswaran, Jessica N Cooke Bailey, Mark Willcox, Russell Van Gelder, Carol Lakkis, Fiona Stapleton, Kathryn Richdale
Purpose: The purpose of this study was to explore differences in genotype, ocular surface microbiome, tear inflammatory markers, and environmental and behavioral exposures in soft contact lens (SCL) wearers with and without a history of corneal infiltrative events (CIEs). Methods: Nine SCL wearers with a recent CIE and nine age-, sex-, and SCL material- and modality-matched controls were enrolled. The Contact Lens Risk Survey, slit-lamp examination data, basal tears, conjunctival microbial cultures, and peripheral blood samples were collected...
December 3, 2018: Investigative Ophthalmology & Visual Science
Jennifer Pugh, Sikandar G Khan, Deborah Tamura, Alisa M Goldstein, Maria Teresa Landi, John J DiGiovanna, Kenneth H Kraemer
Importance: Wide use of genomic sequencing to diagnose disease has raised concern about the extent of genotype-phenotype correlations. Objective: To correlate disease-associated allele frequencies with expected and reported prevalence of clinical disease. Design, Setting, and Participants: Xeroderma pigmentosum (XP), a recessive, cancer-prone, neurocutaneous disorder, was used as a model for this study. From January 1, 2017, to May 4, 2018, the Human Gene Mutation Database and a cohort of patients at the National Institutes of Health were searched and screened to identify reported mutations associated with XP...
December 5, 2018: JAMA Dermatology
Markus T Sainio, Salla Välipakka, Bruno Rinaldi, Helena Lapatto, Anders Paetau, Simo Ojanen, Virginia Brilhante, Manu Jokela, Sanna Huovinen, Mari Auranen, Johanna Palmio, Sylvie Friant, Emil Ylikallio, Bjarne Udd, Henna Tyynismaa
OBJECTIVE: To describe adult-onset limb-girdle-type muscular dystrophy caused by biallelic variants in the PYROXD1 gene, which has been recently linked to early-onset congenital myofibrillar myopathy. METHODS: Whole exome sequencing was performed for adult-onset neuromuscular disease patients with no molecular diagnosis. Patients with PYROXD1 variants underwent clinical characterization, lower limb muscle MRI, muscle biopsy and spirometry. A yeast complementation assay was used to determine the biochemical consequences of the genetic variants...
December 4, 2018: Journal of Neurology
Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
Reconstructing the evolution of tumors is a key aspect towards the identification of appropriate cancer therapies. The task is challenging because tumors evolve as heterogeneous cell populations. Single-cell sequencing holds the promise of resolving the heterogeneity of tumors; however, it has its own challenges including elevated error rates, allelic drop-out, and uneven coverage. Here, we develop a new approach to mutation detection in individual tumor cells by leveraging the evolutionary relationship among cells...
December 4, 2018: Nature Communications
Zhen-Tang Lao, Ling Wen Ding, Omer An, Norimichi Hattori, Qiao-Yang Sun, Kar-Tong Tan, Anand Mayakonda, Wong Gee Chuan, Vikas Madan, De-Chen Lin, Henry Yang, H Phillip Koeffler
Acute leukemia of ambiguous lineage (ALAL) is a rare group of blood cancers that cannot be clearly classified into either myeloid or lymphoid lineage through traditional immunophenotyping (2016 World Health Organization classification). In this study, we performed exome and transcriptome sequencing of 15 diagnosis/relapse samples to identify mutations of this disease. Remarkably, genes involved in DNA repair pathway were frequently mutated and occurred in 80% of the samples. In addition, well known mutations of hematopoietic neoplasms were found in these samples, such as DNMT3A, RUNX1, NOTCH1 and NRAS...
December 4, 2018: Haematologica
Stefano Indraccolo, Giuseppe Lombardi, Matteo Fassan, Lorenza Pasqualini, Silvia Giunco, Raffaella Marcato, Alessandra Gasparini, Cinzia Candiotto, Silvia Nalio, Pasquale Fiduccia, Giuseppe Nicolò Fanelli, Ardi Pambuku, Alessandro Della Puppa, Domenico D'Avella, Laura Bonaldi, Marina P Gardiman, Roberta Bertorelle, Anita De Rossi, Vittorina Zagonel
PURPOSE: In-depth characterization of recurrent glioblastoma (rGBM) might contribute to a better understanding of the mechanisms behind tumor progression and enable rGBM treatment with targeted drugs. EXPERIMENTAL DESIGN: In this study, GBM samples were collected at diagnosis and recurrence from adult patients treated with Stupp protocol. Expression of mismatch repair (MMR) proteins was evaluated by IHC, followed by whole exome sequencing (WES) of tumor samples showing loss of MSH6 reactivity...
December 4, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Hadla Hariri, Mazen Kurban, Christiane Al-Haddad, Akl C Fahed, Sarin Poladian, Athar Kahlil, Oussama Abbas, Mariam Arabi, Fadi Bitar, Georges Nemer
BACKGROUND: Cutaneous malformations are at times associated with some forms of congenital heart defects. Many a times subtle cutaneous phenotypes maybe overlooked as their significance on the lives of individuals is minimal. Lebanon represents an area of high consanguinity, where the rates can go beyond 70% in some districts. For the past 6 years, we have been studying several genodermatoses in Lebanon including those with cardiac malformations. OBJECTIVES: The main aim of this study is to document the genetic basis of a familial case of Axenfeld-Rieger Syndrome (ARS) with a mild cutaneous phenotype represented histologically with degeneration/ absence of hair follicles and incomplete formation of sebaceous and eccrine glands, in addition to the cardiac and ocular phenotypes...
November 10, 2018: Journal of Dermatological Science
Jie Xiong, Wei-Li Zhao
Natural-killer/T cell lymphoma (NKTCL) represents the most common subtype of extranodal lymphoma with aggressive clinical behavior. Prevalent in Asians and South Americans, the pathogenesis of NKTCL remains to be fully elucidated. Using system biology techniques including genomics, transcriptomics, epigenomics, and metabolomics, novel biomarkers and therapeutic targets have been revealed in NKTCL. Whole-exome sequencing studies identify recurrent somatic gene mutations, involving RNA helicases, tumor suppressors, JAK-STAT pathway molecules, and epigenetic modifiers...
December 4, 2018: Journal of Hematology & Oncology
Jean-Alain Martignoles, François Delhommeau, Pierre Hirsch
Recent advances in the field of cancer genome analysis revolutionized the picture we have of acute myeloid leukemia (AML). Pan-genomic studies, using either single nucleotide polymorphism arrays or whole genome/exome next generation sequencing, uncovered alterations in dozens of new genes or pathways, intimately connected with the development of leukemia. From a simple two-hit model in the late nineties, we are now building clonal stories that involve multiple unexpected cellular functions, leading to full-blown AML...
December 3, 2018: International Journal of Molecular Sciences
Xiuhua Bozarth, Jennifer N Dines, Qian Cong, Ghayda M Mirzaa, Kimberly Foss, J Lawrence Merritt, Jenny Thies, Heather C Mefford, Edward Novotny
CACNA1C (NM_000719.6) encodes an L-type calcium voltage-gated calcium channel (Cav 1.2), and pathogenic variants have been associated with two distinct clinical entities: Timothy syndrome and Brugada syndrome. Thus far, CACNA1C has not been reported as a gene associated with epileptic encephalopathy and is less commonly associated with epilepsy. We report three individuals from two families with variants in CACNA1C. Patient 1 presented with neonatal onset epileptic encephalopathy (NOEE) and was found to have a de novo missense variant in CACNA1C (c...
December 4, 2018: American Journal of Medical Genetics. Part A
Ohad Wormser, Libe Gradstein, Einat Kadar, Yuval Yogev, Yonatan Perez, Elena Mashkit, Khalil Elbedour, Max Drabkin, Barak Markus, Rotem Kadir, Daniel Halperin, Soltan Khalaila, Jaime Levy, Tova Lifshitz, Esther Manor, Ohad S Birk
Whole exome sequencing (WES) has become routine in clinical practice, especially in studies of recessive hereditary diseases in inbred consanguineous families, where homozygosity of a founder mutation is assumed. Multiple members of two consanguineous families of a single Bedouin tribe were diagnosed with apparently autosomal recessive/pseudo-dominant retinitis pigmentosa (RP). Affected individuals exhibited severe visual impairment with nyctalopia, marked constriction of visual fields, markedly reduced and delayed responses on electro-retinography (ERG) and eventual loss of central vision...
December 4, 2018: American Journal of Medical Genetics. Part A
Tingying Lei, Fang Fu, Ru Li, Dan Wang, Dan Yang, Fang Wang, Xin Yang, Min Pan, Li Zhen, Jin Han, Dongzhi Li, Can Liao
OBJECTIVE: To explore the genetic etiology of fetuses with congenital anomalies of the kidney and urinary tract (CAKUT) by whole exome sequencing (WES). METHODS: WES was performed on DNA extracted from cord blood samples of 26 fetuses with unexplained CAKUT with/without other structural anomalies. In the first 19 cases, sequencing was performed on fetal DNA only, and the turnaround time was 11-12 weeks. For the remaining 7 cases, the fetus and its parents were sequenced simultaneously, and the turnaround time was 8-9 weeks...
December 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Tingyan He, Dong Cui, Yanyan Huang, Xianze Luo, Jun Yang
OBJECTIVE: To explore the clinical phenotype, genetic variant, treatment and prognosis of a child with mosaic variegated aneuploidy syndrome (MVAS). METHODS: Immunological marker screening, chromosomal karyotyping and whole exome sequencing were carried out. RESULTS: The 1-year-11-month old girl has featured severe growth retardation, feeding difficulty, short stature, microcephaly, facial anomalies, scoliosis, visual impairment, hypotonia, chylothorax, and renal lesions...
December 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Shengfang Qin, Xueyan Wang, Yunxing Li
OBJECTIVE: To explore the pathogenesis of a 46,XY female with sex reversal. METHODS: Peripheral blood lymphocytes of the patient were subjected to G-banding karyotype analysis. Sex chromosomes were analyzed with fluorescence in situ hybridization (FISH). SRY gene was analyzed by Sanger sequencing. The whole exome of the patient was subjected to next generation sequencing. Copy number variations (CNVs) of the NR0B1, SF1, SRY, SOX9 and WNT4 genes were validated by multiplex ligation-dependent probe amplification (MLPA)...
December 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Guillaume P Ramstein, Joseph Evans, Aruna Nandety, Malay C Saha, E Charles Brummer, Shawn M Kaeppler, C Robin Buell, Michael D Casler
Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes...
November 2018: Plant Genome
Nicholas Goel, Charles B Huddleston, Andrew C Fiore
Goel N, Huddleston CB, Fiore AC. A novel mutation of the MYH7 gene in a patient with hypertrophic cardiomyopathy. Turk J Pediatr 2018; 60: 315-318. Hypertrophic cardiomyopathy (HCM) is a genetic disorder characterized by asymmetric cardiac hypertrophy due to inherited mutations in genes that encode sarcomeric proteins. MYH7, which encodes β-myosin heavy chain, is among the most commonly mutated genes in patients affected by HCM. We aimed to identify the specific mutation responsible for HCM in a six-month old Caucasian patient...
2018: Turkish Journal of Pediatrics
Tomoyasu Matsubara, Masaya Oda, Tetsuya Takahashi, Chigusa Watanabe, Yoshiro Tachiyama, Hiroyuki Morino, Hideshi Kawakami, Ryuji Kaji, Hirofumi Maruyama, Shigeo Murayama, Yuishin Izumi
Amyotrophic lateral sclerosis (ALS) primarily affects upper and lower motor neurons. Phosphorylated trans-activation response DNA-binding protein of 43 kDa (TDP-43) inclusion bodies are reportedly a pathological hallmark of sporadic ALS. Here, we present an atypical case of sporadic ALS that progressed very slowly, persisted for 19 years, and clinically appeared to only affect the lower motor neurons; however, upper motor neuron degeneration was detected at autopsy. Furthermore, no inclusion bodies positive for phosphorylated TDP-43, ubiquitin, fused in sarcoma, or superoxide dismutase-1 were detected in the central nervous system...
December 3, 2018: Neuropathology: Official Journal of the Japanese Society of Neuropathology
Chandar Kumar, Shen Song, Lin Jiang, Xiaohong He, Qianjun Zhao, Yabin Pu, Kanwar Kumar Malhi, Asghar Ali Kamboh, Yuehui Ma
The Tibetan cashmere goat is one of the main goat breeds used by people living in the plateau. It exhibits the distinct phenotypic characteristics observed in lowland goats, allowing them to adapt to the challenging conditions at high altitudes. It provides an ideal model for understanding the genetic mechanisms underlying high-altitude adaptation and hypoxia-related diseases. Our previous exome sequencing of five Chinese cashmere breeds revealed a candidate gene, DSG3 (Desmoglein 3 ), responsible for the high-altitude adaptation of the Tibetan goat...
2018: Frontiers in Genetics
Tobias Lange, Su Jung Oh-Hohenhorst, Simon A Joosse, Klaus Pantel, Oliver Hahn, Tobias Gosau, Sergey A Dyshlovoy, Jasmin Wellbrock, Susanne Feldhaus, Hanna Maar, Renate Gehrcke, Martina Kluth, Ronald Simon, Thorsten Schlomm, Hartwig Huland, Udo Schumacher
Here we describe the establishment and characterization of an AR+, PSMA+, ERG+, PTEN-/- , CHD1+/- patient-derived xenograft (PDX) model termed 'C5', which has been developed from a 60 years old patient suffering from castration-resistant prostate cancer (CRPC). The patient underwent radical prostatectomy, showed early tumor marker PSA recurrence and, one year after surgery, abiraterone resistance. Subcutaneous C5 tumors can be serially transplanted between mice and grow within ~90 days to 1.5-2 cm³ tumors in SCID Balb/c mice (take rate 100%), NOD-scid IL2Rgnull (NSG) mice (100%) and C57BL/6 pfp-/- /rag2-/- mice (66%)...
December 3, 2018: Scientific Reports
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"