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https://www.readbyqxmd.com/read/29764365/towards-pan-genome-read-alignment-to-improve-variation-calling
#1
Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen
BACKGROUND: Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29762754/optimized-distributed-systems-achieve-significant-performance-improvement-on-sorted-merging-of-massive-vcf-files
#2
Xiaobo Sun, Jingjing Gao, Peng Jin, Celeste Eng, Esteban G Burchard, Terri H Beaty, Ingo Ruczinski, Rasika A Mathias, Kathleen C Barnes, Fusheng Wang, Zhaohui Qin
Background: Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of Variant Call Format (VCF) files is frequently required in large scale whole genome sequencing or whole exome sequencing projects. Traditional single machine based methods become increasingly inefficient when processing large numbers of VCF files due to the excessive computation time and I/O bottleneck...
May 11, 2018: GigaScience
https://www.readbyqxmd.com/read/29751582/whole-exome-sequencing-identifies-new-host-genomic-susceptibility-factors-in-empyema-caused-by-streptococcus-pneumoniae-in-children-a-pilot-study
#3
Antonio Salas, Jacobo Pardo-Seco, Ruth Barral-Arca, Miriam Cebey-López, Alberto Gómez-Carballa, Irene Rivero-Calle, Sara Pischedda, María-José Currás-Tuala, Jorge Amigo, José Gómez-Rial, Federico Martinón-Torres
Pneumonia is the leading cause of death amongst infectious diseases. Streptococcus pneumoniae is responsible for about 25% of pneumonia cases worldwide, and it is a major cause of childhood mortality. We carried out a whole exome sequencing (WES) study in eight patients with complicated cases of pneumococcal pneumonia (empyema). An initial assessment of statistical association of WES variation with pneumonia was carried out using data from the 1000 Genomes Project (1000G) for the Iberian Peninsula (IBS) as reference controls...
May 3, 2018: Genes
https://www.readbyqxmd.com/read/29705498/whole-exome-sequencing-in-an-italian-family-with-isolated-maxillary-canine-agenesis-and-canine-eruption-anomalies
#4
Ersilia Barbato, Alice Traversa, Rosanna Guarnieri, Agnese Giovannetti, Maria Luce Genovesi, Maria Rosa Magliozzi, Stefano Paolacci, Andrea Ciolfi, Simone Pizzi, Roberto Di Giorgio, Marco Tartaglia, Antonio Pizzuti, Viviana Caputo
OBJECTIVE: The aim of this study was the clinical and molecular characterization of a family segregating a trait consisting of a phenotype specifically involving the maxillary canines, including agenesis, impaction and ectopic eruption, characterized by incomplete penetrance and variable expressivity. DESIGN: Clinical standardized assessment of 14 family members and a whole-exome sequencing (WES) of three affected subjects were performed. WES data analyses (sequence alignment, variant calling, annotation and prioritization) were carried out using an in-house implemented pipeline...
April 21, 2018: Archives of Oral Biology
https://www.readbyqxmd.com/read/29700676/ffpe-breast-tumour-blocks-provide-reliable-sources-of-both-germline-and-malignant-dna-for-investigation-of-genetic-determinants-of-individual-tumour-responses-to-treatment
#5
Anna Wilkins, Ritika Chauhan, Alistair Rust, Alex Pearson, Frances Daley, Floriana Manodoro, Kerry Fenwick, Judith Bliss, John Yarnold, Navita Somaiah
BACKGROUND: Bio-banked formalin-fixed paraffin-embedded (FFPE) tissues provide an excellent opportunity for translational genomic research. Historically matched blood has not always been collected as a source of germline DNA. This project aimed to establish if normal FFPE breast tissue could be used as an alternative to blood. METHODS: Exome sequencing was carried out on matched tumour tissue, normal breast tissue and blood on five patients in the START trial. Retrieved samples had been archived at different centres for at least 13 years...
April 26, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29697369/eagle-explicit-alternative-genome-likelihood-evaluator
#6
Tony Kuo, Martin C Frith, Jun Sese, Paul Horton
BACKGROUND: Reliable detection of genome variations, especially insertions and deletions (indels), from single sample DNA sequencing data remains challenging, partially due to the inherent uncertainty involved in aligning sequencing reads to the reference genome. In practice a variety of ad hoc quality filtering methods are employed to produce more reliable lists of putative variants, but the resulting lists typically still include numerous false positives. Thus it would be desirable to be able to rigorously evaluate the degree to which each putative variant is supported by the data...
April 20, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29694377/a-framework-for-the-estimation-of-the-proportion-of-true-discoveries-in-single-nucleotide-variant-detection-studies-for-human-data
#7
Nik Tuzov
Any single nucleotide variant detection study could benefit from a fast and cheap method of measuring the quality of variant call list. It is advantageous to be able to see how the call list quality is affected by different variant filtering thresholds and other adjustments to the study parameters. Here we look into a possibility of estimating the proportion of true positives in a single nucleotide variant call list for human data. Using whole-exome and whole-genome gold standard data sets for training, we focus on building a generic model that only relies on information available from any variant caller...
2018: PloS One
https://www.readbyqxmd.com/read/29689380/mpa-a-free-accessible-and-efficient-pipeline-for-single-nucleotide-variant-annotation-and-prioritization-for-next-generation-sequencing-routine-molecular-diagnosis
#8
Kevin Yauy, David Baux, Henri Pegeot, Charles Van Goethem, Charly Mathieu, Thomas Guignard, Raul Juntas Morales, Delphine Lacourt, Martin Krahn, Vilma-Lotta Lehtokari, Gisele Bonne, Sylvie Tuffery-Giraud, Michel Koenig, Mireille Cossée
Interpretation of next-generation sequencing data constitutes the main limitation in molecular genetics diagnosis. In diagnosis of myopathies and muscular dystrophies (MMD), another major issue is to efficiently predict pathogenicity of variants identified in large genes, especially TTN, since current in silico prediction tools show limitations to predict and rank the numerous variants of such genes. We propose a unique variant prioritization score called mobidic prioritization algorithm (MPA) based on curated interpretation for previously reported variants, biological assumptions, and splice and missense predictors to prioritize all types of single nucleotide variants...
April 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29673316/a-study-on-fast-calling-variants-from-next-generation-sequencing-data-using-decision-tree
#9
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29668842/garfield-ngs-genomic-variants-filtering-by-deep-learning-models-in-ngs
#10
Viola Ravasio, Marco Ritelli, Andrea Legati, Edoardo Giacopuzzi
Summary: Exome sequencing approach is extensively used in research and diagnostic laboratories to discover pathological variants and study genetic architecture of human diseases. However, a significant proportion of identified genetic variants are actually false positive calls, and this pose serious challenges for variants interpretation. Here, we propose a new tool named GARFIELD-NGS (Genomic vARiants FIltering by dEep Learning moDels in NGS), which rely on deep learning models to dissect false and true variants in exome sequencing experiments performed with Illumina or ION platforms...
April 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29661148/identification-of-missing-variants-by-combining-multiple-analytic-pipelines
#11
Yingxue Ren, Joseph S Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P Sinnwell, Shannon K McDonnell, Joanna M Biernacka, Minerva M Carrasquillo, Owen A Ross, Nilüfer Ertekin-Taner, Rosa Rademakers, Matthew Hudson, Liudmila Sergeevna Mainzer, Yan W Asmann
BACKGROUND: After decades of identifying risk factors using array-based genome-wide association studies (GWAS), genetic research of complex diseases has shifted to sequencing-based rare variants discovery. This requires large sample sizes for statistical power and has brought up questions about whether the current variant calling practices are adequate for large cohorts. It is well-known that there are discrepancies between variants called by different pipelines, and that using a single pipeline always misses true variants exclusively identifiable by other pipelines...
April 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29648622/deep-learning-of-genomic-variation-and-regulatory-network-data
#12
Amalio Telenti, Christoph Lippert, Pi-Chuan Chang, Mark DePristo
The human genome is now investigated through high throughput functional assays, and through the generation of population genomic data. These advances support the identification of functional genetic variants and the prediction of traits (eg. deleterious variants and disease). This review summarizes lessons learned from the large-scale analyses of genome and exome datasets, modeling of population data and machine learning strategies to solve complex genomic sequence regions. The review also portrays the rapid adoption of artificial intelligence/deep neural networks in genomics; in particular, deep learning approaches are well suited to model the complex dependencies in the regulatory landscape of the genome, and to provide predictors for genetic variant calling and interpretation...
April 10, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29621323/performance-comparison-of-three-dna-extraction-kits-on-human-whole-exome-data-from-formalin-fixed-paraffin-embedded-normal-and-tumor-samples
#13
Eric Bonnet, Marie-Laure Moutet, Céline Baulard, Delphine Bacq-Daian, Florian Sandron, Lilia Mesrob, Bertrand Fin, Marc Delépine, Marie-Ange Palomares, Claire Jubin, Hélène Blanché, Vincent Meyer, Anne Boland, Robert Olaso, Jean-François Deleuze
Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling...
2018: PloS One
https://www.readbyqxmd.com/read/29610677/potential-association-of-lmna-associated-generalized-lipodystrophy-with-juvenile-dermatomyositis
#14
Melis Sahinoz, Shafaq Khairi, Ashley Cuttitta, Graham F Brady, Amit Rupani, Rasimcan Meral, Marwan K Tayeh, Peedikayil Thomas, Meredith Riebschleger, Sandra Camelo-Piragua, Jeffrey W Innis, M Bishr Omary, Daniel E Michele, Elif A Oral
Background: Juvenile dermatomyositis (JDM) is an auto-immune muscle disease which presents with skin manifestations and muscle weakness. At least 10% of the patients with JDM present with acquired lipodystrophy. Laminopathies are caused by mutations in the lamin genes and cover a wide spectrum of diseases including muscular dystrophies and lipodystrophy. The p.T10I LMNA variant is associated with a phenotype of generalized lipodystrophy that has also been called atypical progeroid syndrome...
2018: Clinical Diabetes and Endocrinology
https://www.readbyqxmd.com/read/29596782/scalable-open-science-approach-for-mutation-calling-of-tumor-exomes-using-multiple-genomic-pipelines
#15
Kyle Ellrott, Matthew H Bailey, Gordon Saksena, Kyle R Covington, Cyriac Kandoth, Chip Stewart, Julian Hess, Singer Ma, Kami E Chiotti, Michael McLellan, Heidi J Sofia, Carolyn Hutter, Gad Getz, David Wheeler, Li Ding
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time...
March 28, 2018: Cell Systems
https://www.readbyqxmd.com/read/29593270/sample-index-misassignment-impacts-tumour-exome-sequencing
#16
Daniel Vodák, Susanne Lorenz, Sigve Nakken, Lars Birger Aasheim, Harald Holte, Baoyan Bai, Ola Myklebost, Leonardo A Meza-Zepeda, Eivind Hovig
Sample pooling enabled by dedicated indexes is a common strategy for cost-effective and robust high-throughput sequencing. Index misassignment leading to mutual contamination between pooled samples has however been described as a general problem of the latest Illumina sequencing instruments utilizing exclusion amplification. Using real-life data from multiple tumour sequencing projects, we demonstrate that index misassignment can induce artefactual variant calls closely resembling true, high-quality somatic variants...
March 28, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29590101/bamgineer-introduction-of-simulated-allele-specific-copy-number-variants-into-exome-and-targeted-sequence-data-sets
#17
Soroush Samadian, Jeff P Bruce, Trevor J Pugh
Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments...
March 28, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29582136/unexplained-cardiac-arrest-a-tale-of-conflicting-interpretations-of-kcnq1-genetic-test-results
#18
Han Chow Chua, Helge Servatius, Babken Asatryan, André Schaller, Claudine Rieubland, Fabian Noti, Jens Seiler, Laurent Roten, Samuel H Baldinger, Hildegard Tanner, Juerg Fuhrer, Andreas Haeberlin, Anna Lam, Stephan A Pless, Argelia Medeiros-Domingo
OBJECTIVE: Unexplained cardiac arrest (UCA) is often the first manifestation of an inherited arrhythmogenic disease. Genetic testing in UCA is challenging due to the complexities of variant interpretation in the absence of supporting cardiac phenotype. We aimed to investigate if a KCNQ1 variant [p.(Pro64_Pro70del)], previously reported as pathogenic, contributes to the long-QT syndrome phenotype, co-segregates with disease or affects KCNQ1 function in vitro. METHODS: DNA was extracted from peripheral blood of a 22-year-old male after resuscitation from UCA...
March 26, 2018: Clinical Research in Cardiology: Official Journal of the German Cardiac Society
https://www.readbyqxmd.com/read/29565419/whole-genome-sequencing-offers-additional-but-limited-clinical-utility-compared-with-reanalysis-of-whole-exome-sequencing
#19
Ahmed Alfares, Taghrid Aloraini, Lamia Al Subaie, Abdulelah Alissa, Ahmed Al Qudsi, Ahmed Alahmad, Fuad Al Mutairi, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Mohammed Albalwi, Saeed Alturki, Majid Alfadhel
PurposeWhole-exome sequencing (WES) and whole-genome sequencing (WGS) are used to diagnose genetic and inherited disorders. However, few studies comparing the detection rates of WES and WGS in clinical settings have been performed.MethodsVariant call format files were generated and raw data analysis was performed in cases in which the final molecular results showed discrepancies. We classified the possible explanations for the discrepancies into three categories: the time interval between the two tests, the technical limitations of WES, and the impact of the sequencing system type...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29558889/naa10-dysfunction-with-normal-nata-complex-activity-in-a-girl-with-non-syndromic-id-and-a-de-novo-naa10-p-v111g-variant-a-case-report
#20
Nina McTiernan, Svein Isungset Støve, Ingvild Aukrust, Marita Torrisen Mårli, Line M Myklebust, Gunnar Houge, Thomas Arnesen
BACKGROUND: The NAA10-NAA15 (NatA) protein complex is an N-terminal acetyltransferase responsible for acetylating ~ 40% of eukaryotic proteins. In recent years, NAA10 variants have been found in patients with an X-linked developmental disorder called Ogden syndrome in its most severe form and, in other familial or de novo cases, with variable degrees of syndromic intellectual disability (ID) affecting both sexes. CASE PRESENTATION: Here we report and functionally characterize a novel and de novo NAA10 (NM_003491...
March 20, 2018: BMC Medical Genetics
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