scholarly journals The GeneCards Suite

Author(s):  
Marilyn Safran ◽  
Naomi Rosen ◽  
Michal Twik ◽  
Ruth BarShir ◽  
Tsippi Iny Stein ◽  
...  

AbstractThe GeneCards® database of human genes was launched in 1997 and has expanded since then to encompass gene-centric, disease-centric, and pathway-centric entities and relationships within the GeneCards Suite, effectively navigating the universe of human biological data—genes, proteins, cells, regulatory elements, biological pathways, and diseases—and the connections among them. The knowledgebase amalgamates information from >150 selected sources related to genes, proteins, ncRNAs, regulatory elements, chemical compounds, drugs, splice variants, SNPs, signaling molecules, differentiation protocols, biological pathways, stem cells, genetic tests, clinical trials, diseases, publications, and more and empowers the suite’s Next Generation Sequencing (NGS), gene set, shared descriptors, and batch query analysis tools.

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 416
Author(s):  
Lorena Landuzzi ◽  
Maria Cristina Manara ◽  
Pier-Luigi Lollini ◽  
Katia Scotlandi

Osteosarcoma (OS) is a rare malignant primary tumor of mesenchymal origin affecting bone. It is characterized by a complex genotype, mainly due to the high frequency of chromothripsis, which leads to multiple somatic copy number alterations and structural rearrangements. Any effort to design genome-driven therapies must therefore consider such high inter- and intra-tumor heterogeneity. Therefore, many laboratories and international networks are developing and sharing OS patient-derived xenografts (OS PDX) to broaden the availability of models that reproduce OS complex clinical heterogeneity. OS PDXs, and new cell lines derived from PDXs, faithfully preserve tumor heterogeneity, genetic, and epigenetic features and are thus valuable tools for predicting drug responses. Here, we review recent achievements concerning OS PDXs, summarizing the methods used to obtain ectopic and orthotopic xenografts and to fully characterize these models. The availability of OS PDXs across the many international PDX platforms and their possible use in PDX clinical trials are also described. We recommend the coupling of next-generation sequencing (NGS) data analysis with functional studies in OS PDXs, as well as the setup of OS PDX clinical trials and co-clinical trials, to enhance the predictive power of experimental evidence and to accelerate the clinical translation of effective genome-guided therapies for this aggressive disease.


2015 ◽  
Vol 97 ◽  
Author(s):  
TAHIR ATIK ◽  
GUNEY BADEMCI ◽  
OSCAR DIAZ-HORTA ◽  
SUSAN H. BLANTON ◽  
MUSTAFA TEKIN

SummaryNext-generation sequencing (NGS) technologies have played a central role in the genetic revolution. These technologies, especially whole-exome sequencing, have become the primary tool of geneticists to identify the causative DNA variants in Mendelian disorders, including hereditary deafness. Current research estimates that 1% of all human genes have a function in hearing. To date, mutations in over 80 genes have been reported to cause nonsyndromic hearing loss (NSHL). Strikingly, more than a quarter of all known genes related to NSHL were discovered in the past 5 years via NGS technologies. In this article, we review recent developments in the usage of NGS for hereditary deafness, with an emphasis on whole-exome sequencing.


2015 ◽  
Vol 35 (12) ◽  
pp. 2203-2214 ◽  
Author(s):  
Muhammad Sohail ◽  
Jiuyong Xie

Alternative splicing contributes greatly to the diversification of mammalian proteomes, but the molecular basis for the evolutionary emergence of splice variants remains poorly understood. We have recently found a novel class of splicing regulatory elements between the polypyrimidine tract (Py) and 3′ AG (REPA) at intron ends in many human genes, including the multifunctionalPRMT5(for protein arginine methyltransferase 5) gene. The PRMT5 element is comprised of two G tracts that arise in most mammals and accompany significant exon skipping in human transcripts. The G tracts inhibit splicing by recruiting heterogeneous nuclear ribonucleoprotein (hnRNP) H and F (H/F) to reduce U2AF65 binding to the Py, causing exon skipping. The resulting novel shorter variant PRMT5S exhibits a histone H4R3 methylation effect similar to that seen with the original longer PRMT5L isoform but exhibits a distinct localization and preferential control of critical genes for cell cycle arrest at interphase in comparison to PRMT5L. This report thus provides a molecular mechanism for the evolutionary emergence of a novel splice variant with an opposite function in a fundamental cell process. The presence of REPA elements in a large group of genes implies their wider impact on different cellular processes for increased protein diversity in humans.


Author(s):  
Naiyar Iqbal ◽  
Pradeep Kumar

Disease classification based on biological data is an important area in bioinformatics and biomedical research. It helps the doctors and medical practitioners for the early detection of disease and support them as a computer-aided diagnostic tool for accurate diagnosis, prognosis, and treatment of disease. Earlier Microarray gene expression data have wide application for the classification of disease, but now Next-generation sequencing (NGS) has replaced the Microarray technology. From the last few years, RNA sequence (RNA-Seq) data are widely used for the transcriptomic analysis. Hence, RNA-Seq based classification of disease is in its infancy. In this article, we present a general framework for the classification of disease constructed on RNA-Seq data. This framework will guide the researchers to process RNA-Seq, extract relevant features and apply the appropriate classifier to classify any kind of disease.


2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15043-e15043
Author(s):  
Nadia Ashai ◽  
Matthew Stuart ◽  
Mateo Mejia Saldarriaga ◽  
Wei Zhang ◽  
Renee Huang ◽  
...  

e15043 Background: Upfront testing for MSI, and mutations in KRAS, NRAS, and BRAF is recommended. The most cost-effective way of obtaining this information remains unclear. We examined cost of broad next generation sequencing (NGS), in comparison to hotspot (HT) and individual target (IT) testing in patients with mCRC with Medicare (MC) and commercial insurance (CI) at MMC. As a surrogate of effectiveness, we hypothesize that patients with NGS are more likely to enroll in clinical trials. Methods: Cost of individual and hotspot tests were derived from known reimbursement rates with insurances affiliated with MMC. Due to ongoing changes in current procedural terminology for NGS, we used known reimbursement amounts from our patients. We applied these costs to a model population of 1,000,000 people. We then evaluated clinical trial enrollment of patients who had either NGS or hotspot/individual testing. Results: MC costs for IT, HT, NGS testing were $1,504, $752, and $4,680 respectively. CI costs were $1,910, $814, $2,366 for IT, HT, and NGS testing respectively. When applied to our model population, NGS cost $914,604 and $1,131,016 more than individual and hot spot testing respectively for MC patients, and $21,432 and $72,924 more for CI patients. Analysis of effectiveness included 136 patients, wherein 8% of those with NGS (n = 5/61) were enrolled in clinical trials as a result of testing compared to 1% of those with HT/IT (n = 1/75). Conclusions: Broad spectrum NGS costs more than individual or hot spot testing in mCRC. However, patients with NGS testing were more likely to be enrolled in clinical trials, suggesting the need for studies to further evaluate ideal testing modality. [Table: see text]


2021 ◽  
Author(s):  
Hyungtaek Jung ◽  
Brendan Jeon ◽  
Daniel Ortiz-Barrientos

Storing and manipulating Next Generation Sequencing (NGS) file formats is an essential but difficult task in biological data analysis. The easyfm ( easy f ile m anipulation) toolkit ( https://github.com/TaekAndBrendan/easyfm ) makes manipulating commonly used NGS files more accessible to biologists. It enables them to perform end-to-end reproducible data analyses using a free standalone desktop application (available on Windows, Mac and Linux). Unlike existing tools (e.g. Galaxy), the Graphical User Interface (GUI)-based easyfm is not dependent on any high-performance computing (HPC) system and can be operated without an internet connection. This specific benefit allow easyfm to seamlessly integrate visual and interactive representations of NGS files, supporting a wider scope of bioinformatics applications in the life sciences.


Author(s):  
Sue Espe

MalaCards: The Human Disease Database is a robust database designed to enable genomic and genetic researchers, investigators, and scholars to efficiently navigate the universe of human genes, genetic variants, proteins, cells, and biological pathways related to various human diseases.


2018 ◽  
Vol 399 (9) ◽  
pp. 1065-1071 ◽  
Author(s):  
Panagiotis G. Adamopoulos ◽  
Christos K. Kontos ◽  
Andreas Scorilas

AbstractTissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional characteristics. In this study, we describe the molecular cloning of four novel splice variants of the humanKLK11andKLK12genes, discovered by combining 3′ rapid amplification of cDNA ends (3′ RACE), next-generation sequencing (NGS) technology, advanced bioinformatic analysis and Sanger sequencing. Expression analysis of these new transcripts in cell lines originating from 17 cancerous and two normal tissues revealed the expression pattern of each transcript. These novelKLK11andKLK12splice variants represent new potential cancer biomarkers.


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