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https://www.readbyqxmd.com/read/28068558/targeted-next-generation-sequencing-of-the-entire-vitamin-d-receptor-gene-reveals-polymorphisms-correlated-with-vitamin-d-deficiency-among-older-filipino-women-with-and-without-fragility-fracture
#1
Mark Pretzel Zumaraga, Paul Julius Medina, Juan Miguel Recto, Lauro Abrahan, Edelyn Azurin, Celeste C Tanchoco, Cecilia A Jimeno, Cynthia Palmes-Saloma
This study aimed to discover genetic variants in the entire 101 kB vitamin D receptor (VDR) gene for vitamin D deficiency in a group of postmenopausal Filipino women using targeted next generation sequencing (TNGS) approach in a case-control study design. A total of 50 women with and without osteoporotic fracture seen at the Philippine Orthopedic Center were included. Blood samples were collected for determination of serum vitamin D, calcium, phosphorus, glucose, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase and as primary source for targeted VDR gene sequencing using the Ion Torrent Personal Genome Machine...
December 21, 2016: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28056804/indelseek-detection-of-complex-insertions-and-deletions-from-next-generation-sequencing-data
#2
Chun Hang Au, Anskar Y H Leung, Ava Kwong, Tsun Leung Chan, Edmond S K Ma
BACKGROUND: Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. RESULTS: INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of "pileup" of each reference position across multiple alignments...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049408/detailed-simulation-of-cancer-exome-sequencing-data-reveals-differences-and-common-limitations-of-variant-callers
#3
Ariane L Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
BACKGROUND: Next-generation sequencing of matched tumor and normal biopsy pairs has become a technology of paramount importance for precision cancer treatment. Sequencing costs have dropped tremendously, allowing the sequencing of the whole exome of tumors for just a fraction of the total treatment costs. However, clinicians and scientists cannot take full advantage of the generated data because the accuracy of analysis pipelines is limited. This particularly concerns the reliable identification of subclonal mutations in a cancer tissue sample with very low frequencies, which may be clinically relevant...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28045987/high-throughput-resequencing-of-maize-landraces-at-genomic-regions-associated-with-flowering-time
#4
Tiffany M Jamann, Shilpa Sood, Randall J Wisser, James B Holland
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions...
2017: PloS One
https://www.readbyqxmd.com/read/28035032/using-genotype-array-data-to-compare-multi-and-single-sample-variant-calls-and-improve-variant-call-sets-from-deep-coverage-whole-genome-sequencing-data
#5
Suyash S Shringarpure, Rasika A Mathias, Ryan D Hernandez, Timothy D O'Connor, Zachary A Szpiech, Raul Torres, Francisco M De La Vega, Carlos D Bustamante, Kathleen C Barnes, Margaret A Taub
MOTIVATION: Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X)...
December 29, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28008336/micado-looking-for-mutations-in-targeted-pacbio-cancer-data-an-alignment-free-method
#6
Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, Jonas Bergh, Macha Nikolski
Targeted sequencing is commonly used in clinical application of NGS technology since it enables generation of sufficient sequencing depth in the targeted genes of interest and thus ensures the best possible downstream analysis. This notwithstanding, the accurate discovery and annotation of disease causing mutations remains a challenging problem even in such favorable context. The difficulty is particularly salient in the case of third generation sequencing technology, such as PacBio. We present MICADo, a de Bruijn graph based method, implemented in python, that makes possible to distinguish between patient specific mutations and other alterations for targeted sequencing of a cohort of patients...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27964748/non-coding-single-nucleotide-variants-affecting-estrogen-receptor-binding-and-activity
#7
Amir Bahreini, Kevin Levine, Lucas Santana-Santos, Panayiotis V Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich, Adrian V Lee
BACKGROUND: Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic changes in different breast cancer models. We investigated whether single nucleotide variants (SNVs) in ER binding sites (regSNVs) contribute to ER action through changes in the ER cistrome, thereby affecting disease progression. Here we developed a computational pipeline to identify SNVs in ER binding sites using chromatin immunoprecipitation sequencing (ChIP-seq) data from ER+ breast cancer models...
December 13, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27928499/whole-genome-resequencing-of-a-laboratory-adapted-drosophila-melanogaster
#8
William P Gilks, Tanya M Pennell, Ilona Flis, Matthew T Webster, Edward H Morrow
As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LH M). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes...
2016: F1000Research
https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#9
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27807805/identification-of-heterozygous-single-and-multi-exon-deletions-in-il7r-by-whole-exome-sequencing
#10
Karin R Engelhardt, Yaobo Xu, Angela Grainger, Mila G C Germani Batacchi, David J Swan, Joseph D P Willet, Intan J Abd Hamid, Philipp Agyeman, Dawn Barge, Shahnaz Bibi, Lucy Jenkins, Terence J Flood, Mario Abinun, Mary A Slatter, Andrew R Gennery, Andrew J Cant, Mauro Santibanez Koref, Kimberly Gilmour, Sophie Hambleton
PURPOSE: We aimed to achieve a retrospective molecular diagnosis by applying state-of-the-art genomic sequencing methods to past patients with T-B+NK+ severe combined immunodeficiency (SCID). We included identification of copy number variations (CNVs) by whole exome sequencing (WES) using the CNV calling method ExomeDepth to detect gene alterations for which routine Sanger sequencing analysis is not suitable, such as large heterozygous deletions. METHODS: Of a total of 12 undiagnosed patients with T-B+NK+ SCID, we analyzed eight probands by WES, using GATK to detect single nucleotide variants (SNVs) and small insertions and deletions (INDELs) and ExomeDepth to detect CNVs...
November 2, 2016: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/27769321/single-exome-sequencing-identified-a-novel-rp2-mutation-in-a-child-with-x-linked-retinitis-pigmentosa
#11
Hassol Lim, Young-Mi Park, Jong-Keuk Lee, Hyun Taek Lim
OBJECTIVE: To present an efficient and successful application of a single-exome sequencing study in a family clinically diagnosed with X-linked retinitis pigmentosa. DESIGN: Exome sequencing study based on clinical examination data. PARTICIPANTS: An 8-year-old proband and his family. METHODS: The proband and his family members underwent comprehensive ophthalmologic examinations. Exome sequencing was undertaken in the proband using Agilent SureSelect Human All Exon Kit and Illumina HiSeq 2000 platform...
October 2016: Canadian Journal of Ophthalmology. Journal Canadien D'ophtalmologie
https://www.readbyqxmd.com/read/27764769/establishing-the-involvement-of-the-novel-gene-agbl5-in-retinitis-pigmentosa-by-whole-genome-sequencing
#12
Kari Branham, Hiroko Matsui, Pooja Biswas, Aditya A Guru, Michael Hicks, John J Suk, He Li, David Jakubosky, Tao Long, Amalio Telenti, Naoki Nariai, John R Heckenlively, Kelly A Frazer, Paul A Sieving, Radha Ayyagari
While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40-50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of IRD in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10...
December 1, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/27716037/impact-of-post-alignment-processing-in-variant-discovery-from-whole-exome-data
#13
Shulan Tian, Huihuang Yan, Michael Kalmbach, Susan L Slager
BACKGROUND: GATK Best Practices workflows are widely used in large-scale sequencing projects and recommend post-alignment processing before variant calling. Two key post-processing steps include the computationally intensive local realignment around known INDELs and base quality score recalibration (BQSR). Both have been shown to reduce erroneous calls; however, the findings are mainly supported by the analytical pipeline that incorporates BWA and GATK UnifiedGenotyper. It is not known whether there is any benefit of post-processing and to what extent the benefit might be for pipelines implementing other methods, especially given that both mappers and callers are typically updated...
October 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27633116/investigation-of-rare-and-low-frequency-variants-using-high-throughput-sequencing-with-pooled-dna-samples
#14
Jingwen Wang, Tiina Skoog, Elisabet Einarsdottir, Tea Kaartokallio, Hannele Laivuori, Anna Grauers, Paul Gerdhem, Marjo Hytönen, Hannes Lohi, Juha Kere, Hong Jiao
High-throughput sequencing using pooled DNA samples can facilitate genome-wide studies on rare and low-frequency variants in a large population. Some major questions concerning the pooling sequencing strategy are whether rare and low-frequency variants can be detected reliably, and whether estimated minor allele frequencies (MAFs) can represent the actual values obtained from individually genotyped samples. In this study, we evaluated MAF estimates using three variant detection tools with two sets of pooled whole exome sequencing (WES) and one set of pooled whole genome sequencing (WGS) data...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27632638/beta-binomial-model-for-the-detection-of-rare-mutations-in-pooled-next-generation-sequencing-experiments
#15
Audrone Jakaitiene, Mariano Avino, Mario Rosario Guarracino
Against diminishing costs, next-generation sequencing (NGS) still remains expensive for studies with a large number of individuals. As cost saving, sequencing genome of pools containing multiple samples might be used. Currently, there are many software available for the detection of single-nucleotide polymorphisms (SNPs). Sensitivity and specificity depend on the model used and data analyzed, indicating that all software have space for improvement. We use beta-binomial model to detect rare mutations in untagged pooled NGS experiments...
September 15, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27612449/a-hybrid-computational-strategy-to-address-wgs-variant-analysis-in-5000-samples
#16
Zhuoyi Huang, Navin Rustagi, Narayanan Veeraraghavan, Andrew Carroll, Richard Gibbs, Eric Boerwinkle, Manjunath Gorentla Venkata, Fuli Yu
BACKGROUND: The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies...
September 10, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27604516/from-wet-lab-to-variations-concordance-and-speed-of-bioinformatics-pipelines-for-whole-genome-and-whole-exome-sequencing
#17
Steve Laurie, Marcos Fernandez-Callejo, Santiago Marco-Sola, Jean-Remi Trotta, Jordi Camps, Alejandro Chacón, Antonio Espinosa, Marta Gut, Ivo Gut, Simon Heath, Sergi Beltran
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample...
December 2016: Human Mutation
https://www.readbyqxmd.com/read/27590916/an-analytical-workflow-for-accurate-variant-discovery-in-highly-divergent-regions
#18
Shulan Tian, Huihuang Yan, Claudia Neuhauser, Susan L Slager
BACKGROUND: Current variant discovery methods often start with the mapping of short reads to a reference genome; yet, their performance deteriorates in genomic regions where the reads are highly divergent from the reference sequence. This is particularly problematic for the human leukocyte antigen (HLA) region on chromosome 6p21.3. This region is associated with over 100 diseases, but variant calling is hindered by the extreme divergence across different haplotypes. RESULTS: We simulated reads from chromosome 6 exonic regions over a wide range of sequence divergence and coverage depth...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27585926/bioinformatic-analysis-of-genotype-by-sequencing-gbs-data-with-ngsep
#19
Claudia Perea, Juan Fernando De La Hoz, Daniel Felipe Cruz, Juan David Lobaton, Paulo Izquierdo, Juan Camilo Quintero, Bodo Raatz, Jorge Duitama
BACKGROUND: Therecent development and availability of different genotype by sequencing (GBS) protocols provided a cost-effective approach to perform high-resolution genomic analysis of entire populations in different species. The central component of all these protocols is the digestion of the initial DNA with known restriction enzymes, to generate sequencing fragments at predictable and reproducible sites. This allows to genotype thousands of genetic markers on populations with hundreds of individuals...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27562535/transcriptomic-snp-discovery-for-custom-genotyping-arrays-impacts-of-sequence-data-snp-calling-method-and-genotyping-technology-on-the-probability-of-validation-success
#20
Emily Humble, Michael A S Thorne, Jaume Forcada, Joseph I Hoffman
BACKGROUND: Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context...
August 26, 2016: BMC Research Notes
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