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next generation sequencing analysis

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https://www.readbyqxmd.com/read/30107212/extended-hla-g-genetic-diversity-and-ancestry-composition-in-a-brazilian-admixed-population-sample-implications-for-hla-g-transcriptional-control-and-for-case-control-association-studies
#1
Maria Luiza Guimarães de Oliveira, Luciana Caricati Veiga-Castelli, Letícia Marcorin, Guilherme Debortoli, Alison Luis Eburneo Pereira, Nádia Carolina de Aguiar Fracasso, Guilherme do Valle Silva, Andréia S Souza, Juliana Doblas Massaro, Aguinaldo Luiz Simões, Audrey Sabbagh, Eduardo Antônio Donadi, Erick C Castelli, Celso Teixeira Mendes-Junior
Human leukocyte antigen-G (HLA-G) is a nonclassical Major Histocompatibility Complex (MHC) molecule with immunomodulatory function and restricted tissue expression. The genetic diversity of HLA-G has been extensively studied in several populations, however, the segment located upstream -1406 has not yet been evaluated. We characterized the nucleotide variation and haplotype structure of an extended distal region (-2635), all exons and the 3'UTR segment of HLA-G by next-generation sequencing (NGS) in a sample of 335 Brazilian individuals...
August 11, 2018: Human Immunology
https://www.readbyqxmd.com/read/30107149/the-success-of-sequence-capture-in-relation-to-phylogenetic-distance-from-a-reference-genome-a-case-study-of-avian-haemosporidian-parasites
#2
Xi Huang, Roland Hansson, Vaidas Palinauskas, Gediminas Valkiūnas, Olof Hellgren, Staffan Bensch
Genomic sequencing of avian haemosporidian parasites (Haemosporida) has been challenging due to excessive contamination from host DNA. In this study, we developed a cost-effective protocol to obtain parasite sequences from naturally infected birds, based on targeted sequence capture and next generation sequencing. With the genomic data of Haemoproteus tartakovskyi as a reference, we successfully sequenced up to 1,000 genes from each of the 15 selected samples belonging to nine different cytochrome b lineages, eight of which belong to Haemoproteus and one to Plasmodium...
August 11, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/30106960/a-pipeline-for-metabarcoding-and-diet-analysis-from-fecal-samples-developed-for-a-small-semi-aquatic-mammal
#3
Oliver Hawlitschek, Angel Fernández-González, Alfonso Balmori-de la Puente, Jose Castresana
Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms...
2018: PloS One
https://www.readbyqxmd.com/read/30106846/next-generation-sequencing-of-sporadic-vestibular-schwannoma-necessity-of-biallelic-nf2-inactivation-and-implications-of-accessory-non-nf2-variants
#4
Matthew L Carlson, James B Smadbeck, Michael J Link, Eric W Klee, George Vasmatzis, Lisa A Schimmenti
OBJECTIVES: 1) Describe the genetic alterations discovered in a series of sporadic vestibular schwannomas (VS). 2) Identify if more clinically aggressive variants possess different genetic alterations compared to more indolent-behaving VS. METHODS: Fresh frozen tumor and matched peripheral blood leukocytes from 23 individuals with sporadic VS were analyzed using whole-exome sequencing, tumor whole transcriptome expression profiling (mRNA-Seq), and tumor mate-pair analysis...
August 13, 2018: Otology & Neurotology
https://www.readbyqxmd.com/read/30106354/the-nile-river-microbiome-reveals-a-remarkably-stable-community-between-wet-and-dry-seasons-and-sampling-sites-in-a-large-urban-metropolis-cairo-egypt
#5
Walaa A Eraqi, Marwa T ElRakaiby, Salwa A Megahed, Noha H Yousef, Mostafa S Elshahed, Aymen S Yassin
World freshwater supplies are in need of microbiome diversity analyses as a first step to future ecological studies, and to monitor water safety and quality. The Nile is a major north-flowing river in Africa that displays both spatial and temporal variations in its water quality. Here, we present the first microbiome analysis of the Nile River water in two seasons: (1) summer representing the wet season, and (2) winter representing the dry season, as sampled around Cairo, the capital of Egypt. Surface river water samples were collected from selected locations along the path of river, and the microbial composition was analyzed by next-generation sequencing of the 16S rRNA gene...
August 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30105577/validation-of-the-oncomine-%C3%A2-focus-panel-for-next-generation-sequencing-of-clinical-tumour-samples
#6
Hannah L Williams, Kathy Walsh, Austin Diamond, Anca Oniscu, Zandra C Deans
The clinical utility of next-generation sequencing (NGS) for a diverse range of targets is expanding, increasing the need for multiplexed analysis of both DNA and RNA. However, translation into daily use requires a rigorous and comprehensive validation strategy. The aim of this clinical validation was to assess the performance of the Ion Torrent Personal Genome Machine (IonPGM™ ) and validate the Oncomine™ Focus DNA and RNA Fusion panels for clinical application in solid tumour testing of formalin-fixed, paraffin-embedded (FFPE) tissue...
August 13, 2018: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/30105547/genetic-basis-of-hypertrophic-cardiomyopathy-in-children
#7
Stefan Rupp, Moataz Felimban, Anne Schänzer, Dietmar Schranz, Christoph Marschall, Martin Zenker, Thushiha Logeswaran, Christoph Neuhäuser, Josef Thul, Christian Jux, Andreas Hahn
BACKGROUND: Previous investigations assessing the genetic cause of pediatric hypertrophic cardiomyopathy (HCM) found underlying genetic mutations in 50-60% of cases. The purpose of our study was to analyze whether this number can be augmented by applying next-generation sequencing and directing further diagnostics by discussing unsolved cases in a multidisciplinary board. METHODS AND RESULTS: 42 patients with the diagnoses of HCM made before age 18 years were treated in our center from 2000 to 2016...
August 13, 2018: Clinical Research in Cardiology: Official Journal of the German Cardiac Society
https://www.readbyqxmd.com/read/30105468/targeted-next-generation-sequencing-of-406-genes-identified-genetic-defects-underlying-congenital-heart-disease-in-down-syndrome-patients
#8
Khalid M Alharbi, Abdelhadi H Al-Mazroea, Atiyeh M Abdallah, Yousef Almohammadi, S Justin Carlus, Sulman Basit
Down syndrome (DS) is the most common autosomal chromosome anomaly. DS is frequently associated with congenital heart disease (CHD). Patients with DS have 40-60% chance of having CHD. It means that CHD in DS is not only due to trisomy 21 and there are some other genetic factors underlying CHD in DS children. In this study, a total of 240 DNA samples from patients were analyzed including 100 patients with CHD only, 110 patients having CHD along with DS and 30 patients with isolated DS. A cardiovascular gene panel consisting of probes for 406 genes was used to screen DNA samples of all 240 patients for mutation identification...
August 13, 2018: Pediatric Cardiology
https://www.readbyqxmd.com/read/30105228/illumina-next-generation-sequencing-for-the-analysis-of-eimeria-populations-in-commercial-broilers-and-indigenous-chickens
#9
Ankit T Hinsu, Jalpa R Thakkar, Prakash G Koringa, Vladimir Vrba, Subhash J Jakhesara, Androniki Psifidi, Javier Guitian, Fiona M Tomley, Dharamsibhai N Rank, Muthusamy Raman, Chaitanya G Joshi, Damer P Blake
Eimeria species parasites can cause the enteric disease coccidiosis, most notably in chickens where the economic and welfare implications are significant. Seven Eimeria species are recognized to infect chickens, although understanding of their regional occurrence, abundance, and population structure remains limited. Reports of Eimeria circulating in chickens across much of the southern hemisphere with cryptic genotypes and the capacity to escape current anticoccidial vaccines have revealed unexpected levels of complexity...
2018: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/30105017/asap-a-webserver-for-immunoglobulin-sequencing-analysis-pipeline
#10
Oren Avram, Anna Vaisman-Mentesh, Dror Yehezkel, Haim Ashkenazy, Tal Pupko, Yariv Wine
Reproducible and robust data on antibody repertoires are invaluable for basic and applied immunology. Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology, providing quantitative molecular information on antibody polyclonal composition. However, major computational challenges exist when analyzing antibody sequences, from error handling to hypermutation profiles and clonal expansion analyses. In this work, we developed the ASAP (A webserver for Immunoglobulin-Seq Analysis Pipeline) webserver (https://asap...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/30104702/plga-encapsulated-cpg-odn-and-campylobacter-jejuni-lysate-modulate-cecal-microbiota-composition-in-broiler-chickens-experimentally-challenged-with-c-jejuni
#11
Khaled Taha-Abdelaziz, Alexander Yitbarek, Tamiru Negash Alkie, Douglas C Hodgins, Leah R Read, J Scott Weese, Shayan Sharif
Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. Reducing Campylobacter numbers in the intestinal tract of chickens will minimize transmission to humans, thereby reducing the incidence of infection. We have previously shown that oral pre-treatment of chickens with C. jejuni lysate and Poly D, L-lactide-co-glycolide polymer nanoparticles (PLGA NPs) containing CpG oligodeoxynucleotide (ODN) can reduce the number of C. jejuni in infected chickens. In the current study, the effects of these pre-treatments on the composition and functional diversity of the cecal microbiota, in chickens experimentally infected with C...
August 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30104475/genome-sequencing-and-carbohydrate-active-enzyme-cazyme-repertoire-of-the-white-rot-fungus-flammulina-elastica
#12
Young-Jin Park, Yong-Un Jeong, Won-Sik Kong
Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous...
August 13, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/30103742/altered-mirna-profile-in-testis-of-post-cryptorchidopexy-patients-with-non-obstructive-azoospermia
#13
Dongdong Tang, Zhenyu Huang, Xiaojin He, Huan Wu, Dangwei Peng, Li Zhang, Xiansheng Zhang
BACKGROUND: Cryptorchidism is one of the most common causes of non-obstructive azoospermia (NOA) leading to male infertility. Despite various medical approaches been utilised, many patients still suffer from infertility. MicroRNAs (miRNAs) play vital roles in the progress of spermatogenesis; however, little is known about the miRNA expression profile in the testes. Therefore, the miRNA profile was assessed in the testis of post-cryptorchidopexy patients. METHODS: Three post-cryptorchidopexy testicular tissue samples from patients aged 23, 26 and 28 years old and three testis tissues from patients with obstructive azoospermia (controls) aged 24, 25 and 36 years old were used in this study...
August 13, 2018: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/30103105/three-dimensional-primary-cultures-for-selecting-human-breast-cancers-that-are-sensitive-to-the-anti-tumor-activity-of-ipatasertib-or-taselisib-in-combination-with-anti-microtubule-cytotoxic-drugs
#14
M Orditura, C M Della Corte, A Diana, V Ciaramella, E Franzese, V Famiglietti, I Panarese, R Franco, A Grimaldi, A Lombardi, M Caraglia, A Santoriello, E Procaccini, E Lieto, E Maiello, F De Vita, F Ciardiello, F Morgillo
Two inhibitors of phosphatidylinositol 3-kinase (PI3K) pathway taselisib, targeting the mutant PI3K-subunit-alpha (PI3KA) and ipatasertib, AKT-inhibitor, are currently under clinical investigation in breast cancer (BC) patients. We have previously demonstrated the anti-tumor efficacy of these anti-PI3K/AKT-inibitors in combination with anti-microtubule drugs in human BC cell lines, through a complete cytoskeleton disorganization. In this work, we generated ex-vivo three-dimensional (3D) cultures from human BC as a model to test drug efficacy and to identify new molecular biomarkers for selection of BC patients suitable for anti-PI3K/AKT-inibitors treatment...
August 4, 2018: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/30102374/comprehensive-comparative-analysis-of-methods-and-software-for-identifying-viral-integrations
#15
Xun Chen, Jason Kost, Dawei Li
Many viruses are capable of integrating in the human genome, particularly viruses involved in tumorigenesis. Viral integrations can be considered genetic markers for discovering virus-caused cancers and inferring cancer cell development. Next-generation sequencing (NGS) technologies have been widely used to screen for viral integrations in cancer genomes, and a number of bioinformatics tools have been developed to detect viral integrations using NGS data. However, there has been no systematic comparison of the methods or software...
August 8, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/30102337/fat1-somatic-mutations-in-head-and-neck-carcinoma-are-associated-with-tumor-progression-and-survival
#16
Shu-Chun Lin, Li-Han Lin, Ssu-Yu Yu, Shou-Yen Kao, Kuo-Wei Chang, Hui-Wen Cheng, Chung-Ji Liu
In recent years, the incidence and mortality rates of head and neck squamous cell carcinoma (HNSCC) have increased worldwide. Therefore, understanding genomic alterations in HNSCC carcinogenesis is crucial for appropriate diagnosis and therapy. Procadherin FAT1, which encodes 4588 amino acid residues, regulates complex mechanisms to promote oncogenesis or suppression of malignancies. Multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) revealed FAT1 somatic mutations. The clinicopathologic implications of FAT1 in HNSCC were investigated using expression assays, and the functional role of FAT1 in HNSCC pathogenesis was determined using ectopic expression and knockdown experiments...
August 9, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/30102276/combining-analysis-of-dna-in-a-crude-virion-extraction-with-the-analysis-of-rna-from-infected-leaves-to-discover-new-virus-genomes
#17
Jeanmarie Verchot, Aastha Thapa, Dulanjani Wijayasekara, Peter R Hoyt
This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low titers in their host or cannot be mechanically inoculated to another host are difficult to propagate to achieve a greater titer of infectious material. Infected leaves are ground in a mild buffer with optimal pH and ionic composition recommended for purifying most bacilliform Para retroviruses. Urea is used to break up inclusion bodies that trap virions and to dissolve cellular components...
July 27, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/30102009/impact-of-tumour-profiling-on-clinical-trials-in-salivary-gland-cancer
#18
EDITORIAL
Samuel Rack, Rizwana Rahman, Louise Carter, Craig McKay, Robert Metcalf
Salivary gland cancer is a rare disease comprising multiple biologically diverse disease entities. Clinical trials have had relatively less impact on clinical practice in comparison with other cancer types. Here we describe clinical trials recruiting in salivary gland cancer and 'basket studies' incorporating molecular analysis using next generation sequencing (NGS) to stratify patients for molecularly targeted therapies. A systematic review of clinicaltrials. gov, PUBMED and ASCO, ESMO and AACR meeting abstracts was performed to identify clinical trials recruiting either salivary gland cancer cohorts or 'basket studies' which would be suitable for salivary gland cancer patients...
August 13, 2018: Clinical Otolaryngology
https://www.readbyqxmd.com/read/30101986/massively-parallel-sequencing-techniques-for-forensics-a-review
#19
REVIEW
B B Bruijns, R M Tiggelaar, J G E Gardeniers
DNA sequencing, starting with Sanger chain termination in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as biotechnology, virology and medical diagnostics. Also in the forensic field these techniques have gained attention, reflected by the growing number of articles published over the last 2-3 years. This review contains a brief description of first, second and third generation sequencing techniques, and focuses on the recent developments in human DNA analysis applicable in the forensic field...
August 13, 2018: Electrophoresis
https://www.readbyqxmd.com/read/30101316/processing-of-big-heterogeneous-genomic-datasets-for-tertiary-analysis-of-next-generation-sequencing-data
#20
Marco Masseroli, Arif Canakoglu, Pietro Pinoli, Abdulrahman Kaitoua, Andrea Gulino, Olha Horlova, Luca Nanni, Anna Bernasconi, Stefano Perna, Eirini Stamoulakatou, Stefano Ceri
Motivation: We previously proposed a paradigm shift in genomic data management, based on the Genomic Data Model (GDM) for mediating existing data formats and on the GenoMetric Query Language (GMQL) for supporting, at a high level of abstraction, data extraction and the most common data-driven computations required by tertiary data analysis of Next Generation Sequencing datasets. Here, we present a new GMQL-based system with enhanced accessibility, portability, scalability and performance...
August 7, 2018: Bioinformatics
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