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Whole genome sequencing pathology

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https://www.readbyqxmd.com/read/29764912/mitochondrial-pitrm1-peptidase-loss-of-function-in-childhood-cerebellar-atrophy
#1
Yeshaya Langer, Adi Aran, Suleyman Gulsuner, Bassam Abu Libdeh, Paul Renbaum, Dario Brunetti, Pedro-Filipe Teixeira, Tom Walsh, Sharon Zeligson, Roberta Ruotolo, Rachel Beeri, Imad Dweikat, Maher Shahrour, Ariella Weinberg-Shukron, Fouad Zahdeh, Enrico Baruffini, Elzbieta Glaser, Mary-Claire King, Ephrat Levy-Lahad, Massimo Zeviani, Reeval Segel
OBJECTIVE: To identify the genetic basis of a childhood-onset syndrome of variable severity characterised by progressive spinocerebellar ataxia, mental retardation, psychotic episodes and cerebellar atrophy. METHODS: Identification of the underlying mutations by whole exome and whole genome sequencing. Consequences were examined in patients' cells and in yeast. RESULTS: Two brothers from a consanguineous Palestinian family presented with progressive spinocerebellar ataxia, mental retardation and psychotic episodes...
May 15, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29761480/whole-exome-sequencing-identifies-plec-exo5-and-dnah7-as-novel-susceptibility-genes-in-testicular-cancer
#2
Beatriz Paumard-Hernández, Oriol Calvete, Lucia Inglada Pérez, Héctor Tejero, Fátima Al-Shahrour, Guillermo Pita, Alicia Barroso, Juan Carlos Triviño, Miguel Urioste, Claudia Valverde, Enrique González Billalabeitia, Vanesa Quiroga, Juan Francisco Rodríguez Moreno, Antonio Fernández Aramburo, Cristina López, Pablo Maroto, Javier Sastre, María José Juan Fita, Ignacio Duran, Isabel Lorenzo-Lorenzo, Patricia Iranzo, Xavier García Del Muro, Silverio Ros, Francisco Zambrana, Ana María Autran, Javier Benítez
Testicular germ cell tumors (TGCTs) are a clinically and pathologically heterogeneous disease, and little is known of its genetic basis. Only low susceptibility risk loci have been identified for both sporadic and familial cases. Therefore, we tried to identify new susceptibility genes responsible for familial testicular cancer that may contribute to increasing our knowledge about the genetic basis of the disease. Nineteen Spanish families with at least two affected individuals with TGCT were selected. WES was performed on those individuals using an Illumina Hiseq2000 sequencing platform...
May 15, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29755957/molecular-targets-related-drug-resistance-mechanisms-in-mdr-xdr-and-tdr-mycobacterium-tuberculosis-strains
#3
REVIEW
H M Adnan Hameed, Md Mahmudul Islam, Chiranjibi Chhotaray, Changwei Wang, Yang Liu, Yaoju Tan, Xinjie Li, Shouyong Tan, Vincent Delorme, Wing W Yew, Jianxiong Liu, Tianyu Zhang
Tuberculosis (TB) is a formidable infectious disease that remains a major cause of death worldwide today. Escalating application of genomic techniques has expedited the identification of increasing number of mutations associated with drug resistance in Mycobacterium tuberculosis . Unfortunately the prevalence of bacillary resistance becomes alarming in many parts of the world, with the daunting scenarios of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and total drug-resistant tuberculosis (TDR-TB), due to number of resistance pathways, alongside some apparently obscure ones...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29755111/genomic-landscape-and-prognostic-analysis-of-mantle-cell-lymphoma
#4
Ping Yang, Weilong Zhang, Jing Wang, Yuanyuan Liu, Ran An, Hongmei Jing
To gain insight into the molecular pathogenesis of patients with mantle cell lymphoma (MCL), next-generation whole-exome sequencing of 16 MCL patients was performed. We identified recurrent mutations in genes that are well known to be functionally relevant in MCL, including ATM (37.5%), TP53 (31.3%), WHSC1 (31.3%), CCND1 (18.8%), NOTCH2 (6.3%), and CDKN2A (6.3%). We also identified somatic mutations in genes for which a functional role in MCL has not been previously suspected. These genes included CCDC15, APC, CDH1, S1PR1, ATRX, BRCA2, CASP8, and NOTCH3...
May 14, 2018: Cancer Gene Therapy
https://www.readbyqxmd.com/read/29667327/novel-west-syndrome-candidate-genes-in-a-chinese-cohort
#5
Jing Peng, Ying Wang, Fang He, Chen Chen, Li-Wen Wu, Li-Fen Yang, Yu-Ping Ma, Wen Zhang, Zi-Qing Shi, Chao Chen, Kun Xia, Hui Guo, Fei Yin, Nan Pang
AIMS: West syndrome (WS) is a classic form of early infantile epileptic encephalopathy (EIEE) characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on electroencephalography. Genetic defects play a critical role in the pathology of WS, and 54 EIEE genes have been identified till date. This study was designed to uncover new candidate genes for West syndrome. METHODS: In this study, we recruited 56 Chinese families with WS of unknown etiology...
April 17, 2018: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/29665859/morphology-and-genomic-hallmarks-of-breast-tumours-developed-by-atm-deleterious-variant-carriers
#6
Anne-Laure Renault, Noura Mebirouk, Laetitia Fuhrmann, Guillaume Bataillon, Eve Cavaciuti, Dorothée Le Gal, Elodie Girard, Tatiana Popova, Philippe La Rosa, Juana Beauvallet, Séverine Eon-Marchais, Marie-Gabrielle Dondon, Catherine Dubois d'Enghien, Anthony Laugé, Walid Chemlali, Virginie Raynal, Martine Labbé, Ivan Bièche, Sylvain Baulande, Jacques-Olivier Bay, Pascaline Berthet, Olivier Caron, Bruno Buecher, Laurence Faivre, Marc Fresnay, Marion Gauthier-Villars, Paul Gesta, Nicolas Janin, Sophie Lejeune, Christine Maugard, Sébastien Moutton, Laurence Venat-Bouvet, Hélène Zattara, Jean-Pierre Fricker, Laurence Gladieff, Isabelle Coupier, Georgia Chenevix-Trench, Janet Hall, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, Nadine Andrieu, Fabienne Lesueur
BACKGROUND: The ataxia telangiectasia mutated (ATM) gene is a moderate-risk breast cancer susceptibility gene; germline loss-of-function variants are found in up to 3% of hereditary breast and ovarian cancer (HBOC) families who undergo genetic testing. So far, no clear histopathological and molecular features of breast tumours occurring in ATM deleterious variant carriers have been described, but identification of an ATM-associated tumour signature may help in patient management. METHODS: To characterise hallmarks of ATM-associated tumours, we performed systematic pathology review of tumours from 21 participants from ataxia-telangiectasia families and 18 participants from HBOC families, as well as copy number profiling on a subset of 23 tumours...
April 17, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29665434/differential-growth-of-mycobacterium-leprae-strains-snp-genotypes-in-armadillos
#7
Rahul Sharma, Pushpendra Singh, Maria Pena, Ramesh Subramanian, Vladmir Chouljenko, Joohyun Kim, Nayong Kim, John Caskey, Marie A Baudena, Linda B Adams, Richard W Truman
Leprosy (Hansen's Disease) has occurred throughout human history, and persists today at a low prevalence in most populations. Caused by Mycobacterium leprae, the infection primarily involves the skin, mucosa and peripheral nerves. The susceptible host range for Mycobacterium leprae is quite narrow. Besides humans, nine banded armadillos (Dasypus novemcinctus) and red squirrels (Sciurus vulgaris) are the only other natural hosts for M. leprae, but only armadillos recapitulate the disease as seen in humans. Armadillos across the Southern United States harbor a single predominant genotypic strain (SNP Type-3I) of M...
April 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29650777/-mll-leukemia-induction-by-t-9-11-chromosomal-translocation-in-human-hematopoietic-stem-cells-using-genome-editing
#8
Corina Schneidawind, Johan Jeong, Dominik Schneidawind, In-Suk Kim, Jesús Duque-Afonso, Stephen Hon Kit Wong, Masayuki Iwasaki, Erin H Breese, James L Zehnder, Matthew Porteus, Michael L Cleary
Genome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks. However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development. Here, we used transcription activator-like effector nucleases to generate t(9;11) chromosomal translocations encoding MLL-AF9 and reciprocal AF9-MLL fusion products in CD34+ human cord blood cells...
April 24, 2018: Blood Advances
https://www.readbyqxmd.com/read/29643404/canine-napepld-associated-models-of-human-myelin-disorders
#9
K M Minor, A Letko, D Becker, M Drögemüller, P J J Mandigers, S R Bellekom, P A J Leegwater, Q E M Stassen, K Putschbach, A Fischer, T Flegel, K Matiasek, K J Ekenstedt, E Furrow, E E Patterson, S R Platt, P A Kelly, J P Cassidy, G D Shelton, K Lucot, D L Bannasch, H Martineau, C F Muir, S L Priestnall, D Henke, A Oevermann, V Jagannathan, J R Mickelson, C Drögemüller
Canine leukoencephalomyelopathy (LEMP) is a juvenile-onset neurodegenerative disorder of the CNS white matter currently described in Rottweiler and Leonberger dogs. Genome-wide association study (GWAS) allowed us to map LEMP in a Leonberger cohort to dog chromosome 18. Subsequent whole genome re-sequencing of a Leonberger case enabled the identification of a single private homozygous non-synonymous missense variant located in the highly conserved metallo-beta-lactamase domain of the N-acyl phosphatidylethanolamine phospholipase D (NAPEPLD) gene, encoding an enzyme of the endocannabinoid system...
April 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29626926/interpreting-chromosomal-rearrangements-in-the-context-of-3-dimentional-genome-organization-a-practical-guide-for-medical-genetics
#10
REVIEW
V S Fishman, P A Salnikov, N R Battulin
In this exciting era of "next-gen cytogenetics", the use of novel molecular methods such as comparative genome hybridization and whole genome and whole exome sequencing becomes more and more common in clinics. This results in generation of large amounts of high-resolution patient-specific data and challenges the development of new approaches for interpretation of obtained information. Usually, interpretation of chromosomal rearrangements is focused on alterations of linear genome sequence, underestimating the role of spatial chromatin organization...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626081/recognition-of-the-polycistronic-nature-of-human-genes-is-critical-to-understanding-the-genotype-phenotype-relationship
#11
Marie A Brunet, Sébastien A Levesque, Darel J Hunting, Alan A Cohen, Xavier Roucou
Technological advances promise unprecedented opportunities for whole exome sequencing and proteomic analyses of populations. Currently, data from genome and exome sequencing, or proteomic studies are searched against reference genome annotations. This provides the foundation for research and clinical screening for genetic causes of pathologies. However, current genome annotations substantially underestimate the proteomic information encoded within a gene. Numerous studies have now demonstrated the expression and function of alternative (mainly small, sometimes overlapping) ORFs within mature gene transcripts...
April 6, 2018: Genome Research
https://www.readbyqxmd.com/read/29615506/coexistence-of-multiple-endemic-and-pandemic-lineages-of-the-rice-blast-pathogen
#12
Pierre Gladieux, Sébastien Ravel, Adrien Rieux, Sandrine Cros-Arteil, Henri Adreit, Joëlle Milazzo, Maud Thierry, Elisabeth Fournier, Ryohei Terauchi, Didier Tharreau
The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae ) is both a threat to global food security and a model for plant pathology. Molecular pathologists need an accurate understanding of the origins and line of descent of M. oryzae populations in order to identify the genetic and functional bases of pathogen adaptation and to guide the development of more effective control strategies. We used a whole-genome sequence analysis of samples from different times and places to infer details about the genetic makeup of M...
April 3, 2018: MBio
https://www.readbyqxmd.com/read/29610392/personalized-oncogenomic-analysis-of-metastatic-adenoid-cystic-carcinoma-using-whole-genome-sequencing-to-inform-clinical-decision-making
#13
Manik Chahal, Erin Pleasance, Jasleen Grewal, Eric Zhao, Tony Ng, Erin Chapman, Martin R Jones, Yaoqing Shen, Karen L Mungall, Melika Bonakdar, Gregory A Taylor, Yussanne Ma, Andrew J Mungall, Richard A Moore, Howard Lim, Daniel Renouf, Stephen Yip, Steven J M Jones, Marco A Marra, Janessa Laskin
Metastatic adenoid cystic carcinomas (ACCs) can cause significant morbidity and mortality. Because of their slow growth and relative rarity, there is limited evidence for systemic therapy regimens. Recently, molecular profiling studies have begun to reveal the genetic landscape of these poorly understood cancers, and new treatment possibilities are beginning to emerge. The objective is to use whole-genome and transcriptome sequencing and analysis to better understand the genetic alterations underlying the pathology of metastatic and rare ACCs and determine potentially actionable therapeutic targets...
April 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29608913/shallow-whole-genome-sequencing-for-robust-copy-number-profiling-of-formalin-fixed-paraffin-embedded-breast-cancers
#14
Suet-Feung Chin, Angela Santonja, Marta Grzelak, Soomin Ahn, Stephen-John Sammut, Harry Clifford, Oscar M Rueda, Michelle Pugh, Mae A Goldgraben, Helen A Bardwell, Eun Yoon Cho, Elena Provenzano, Federico Rojo, Emilio Alba, Carlos Caldas
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98...
March 30, 2018: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/29574826/antibody-repertoire-analysis-in-polygenic-autoimmune-diseases
#15
REVIEW
Rachael J M Bashford-Rogers, Kenneth G C Smith, David C Thomas
High-throughput sequencing of the DNA/RNA encoding antibody heavy and light chains is rapidly transforming the field of adaptive immunity. It can address key questions including (i) how the B-cell repertoire differs in health and disease and (ii) if it does differ, the point(s) in B-cell development at which this occurs. The advent of technologies, such as whole genome sequencing, offers the chance to link abnormalities in the B-cell antibody repertoire to specific genomic variants and polymorphisms. Here, we discuss the current research using B-cell antibody repertoire sequencing in three polygenic autoimmune diseases where there is good evidence for a pathological role for B-cells, namely systemic lupus erythematosus, multiple sclerosis and rheumatoid arthritis...
March 25, 2018: Immunology
https://www.readbyqxmd.com/read/29572210/a-novel-glaesserella-sp-isolated-from-severe-respiratory-infections-in-pigs-has-a-mosaic-genome-with-virulence-factors-putatively-acquired-by-horizontal-transfer
#16
Anne E Watt, Glenn F Browning, Alistair R Legione, Rhys N Bushell, Andrew Stent, Ross S Cutler, Neil D Young, Marc S Marenda
An unknown member of the family Pasteurellaceae was repeatedly isolated from severe pulmonary lesions in 20-24 week old pigs reared on the same farm in Victoria, Australia. The aetiological diagnosis of the disease was inconclusive. The complete genome sequence analysis of one strain, 15-184, revealed some phylogenic proximity to Glaesserella (Haemophilus) parasuis , the cause of Glasser's disease. However, sequences of the 16S rRNA and housekeeping genes, as well as average nucleotide identity scores, differed from all other known species in the family Pasteurellaceae The protein content of 15-184 was composite, with 60% of coding sequences matching known G...
March 23, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29570912/a-case-of-severe-soft-tissue-infection-due-to-streptococcus-tigurinus-diagnosed-by-necropsy-in-which-genomic-analysis-was-useful-for-clarifying-its-pathogenicity
#17
Hidenori Yoshizawa, Daisuke Motooka, Yuki Matsumoto, Ryuichi Katada, Shota Nakamura, Eiichi Morii, Tetsuya Iida, Hiroshi Matsumoto
Post-mortem detection of pathogenetic microorganisms in severe infectious death is significantly important for diagnosing the cause of death as well as for public health. However, it is difficult to recognize whether a microorganism detected from post-mortem materials is truly pathogenic or not. We report a case of severe soft tissue infection due to Streptococcus oralis subsp. tigurinus (S. tigurinus), a recently reported species, in which whole-genome analysis was performed to clarify its pathogenicity. A 46-year-old woman had died with symptoms of a severe infectious disease...
March 23, 2018: Pathology International
https://www.readbyqxmd.com/read/29569666/circulating-tumor-dna-and-liquid-biopsy-opportunities-challenges-and-recent-advances-in-detection-technologies
#18
REVIEW
Lena Gorgannezhad, Muhammad Umer, Md Nazmul Islam, Nam-Trung Nguyen, Muhammad J A Shiddiky
Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer...
March 23, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29555671/a-screening-approach-to-identify-clinically-actionable-variants-causing-congenital-heart-disease-in-exome-data
#19
Justin O Szot, Hartmut Cuny, Gillian M Blue, David T Humphreys, Eddie Ip, Katrina Harrison, Gary F Sholler, Eleni Giannoulatou, Paul Leo, Emma L Duncan, Duncan B Sparrow, Joshua W K Ho, Robert M Graham, Nicholas Pachter, Gavin Chapman, David S Winlaw, Sally L Dunwoodie
BACKGROUND: Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD. METHODS: Whole-exome sequencing was performed with the DNA of multiple family members...
March 2018: Circulation. Genomic and precision medicine
https://www.readbyqxmd.com/read/29511670/whole-exome-sequencing-identified-a-novel-compound-heterozygous-mutation-of-lrrc6-in-a-chinese-primary-ciliary-dyskinesia-patient
#20
Lv Liu, Hong Luo
Primary ciliary dyskinesia (PCD) is a clinical rare peculiar disorder, mainly featured by respiratory infection, tympanitis, nasosinusitis, and male infertility. Previous study demonstrated it is an autosomal recessive disease and by 2017 almost 40 pathologic genes have been identified. Among them are the leucine-rich repeat- (LRR-) containing 6 (LRRC6) codes for a 463-amino-acid cytoplasmic protein, expressed distinctively in motile cilia cells, including the testis cells and the respiratory epithelial cells...
2018: BioMed Research International
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