Visualizing next-generation sequencing data with JBrowse

Westesson, Oscar; Skinner, Mitchell E.; Holmes, Ian

doi:10.1093/bib/bbr078

Cited by 61 publications

(59 citation statements)

References 12 publications

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“…JBrowse is an open-source project for genome browser [118]. We have facilitated visualization of external data (such as genome variants reported in DGV [50] and dbSNP [47]) along with the genomes from the two KWS individuals.…”

Section: Methodsmentioning

confidence: 99%

Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry

et al. 2014

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Population of the State of Kuwait is composed of three genetic subgroups of inferred Persian, Saudi Arabian tribe and Bedouin ancestry. The Saudi Arabian tribe subgroup traces its origin to the Najd region of Saudi Arabia. By sequencing two whole genomes and thirteen exomes from this subgroup at high coverage (>40X), we identify 4,950,724 Single Nucleotide Polymorphisms (SNPs), 515,802 indels and 39,762 structural variations. Of the identified variants, 10,098 (8.3%) exomic SNPs, 139,923 (2.9%) non-exomic SNPs, 5,256 (54.3%) exomic indels, and 374,959 (74.08%) non-exomic indels are ‘novel’. Up to 8,070 (79.9%) of the reported novel biallelic exomic SNPs are seen in low frequency (minor allele frequency <5%). We observe 5,462 known and 1,004 novel potentially deleterious nonsynonymous SNPs. Allele frequencies of common SNPs from the 15 exomes is significantly correlated with those from genotype data of a larger cohort of 48 individuals (Pearson correlation coefficient, 0.91; p <2.2×10−16). A set of 2,485 SNPs show significantly different allele frequencies when compared to populations from other continents. Two notable variants having risk alleles in high frequencies in this subgroup are: a nonsynonymous deleterious SNP (rs2108622 [19:g.15990431C>T] from CYP4F2 gene [MIM:*604426]) associated with warfarin dosage levels [MIM:#122700] required to elicit normal anticoagulant response; and a 3′ UTR SNP (rs6151429 [22:g.51063477T>C]) from ARSA gene [MIM:*607574]) associated with Metachromatic Leukodystrophy [MIM:#250100]. Hemoglobin Riyadh variant (identified for the first time in a Saudi Arabian woman) is observed in the exome data. The mitochondrial haplogroup profiles of the 15 individuals are consistent with the haplogroup diversity seen in Saudi Arabian natives, who are believed to have received substantial gene flow from Africa and eastern provenance. We present the first genome resource imperative for designing future genetic studies in Saudi Arabian tribe subgroup. The full-length genome sequences and the identified variants are available at ftp://dgr.dasmaninstitute.org and http://dgr.dasmaninstitute.org/DGR/gb.html.

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Section: Methodsmentioning

confidence: 99%

Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry

et al. 2014

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“…Some of the more recent genome releases are also available on JBrowse (Westesson, et al 2013). Both XenMine and UTexas support the recent X. laevis genome in JBrowse, and Xenbase is also currently adding this browser.…”

Section: Browsing Xenopus Genomes In Xenbasementioning

confidence: 99%

Xenopus genomic data and browser resources

Vize

Zorn

2017

Developmental Biology

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The two species of Xenopus most commonly used in biomedical research are the diploid Xenopus (Silurana) tropicalis and the tetraploid Xenopus laevis. The X. tropicalis genome sequence has been available since 2010 and this year the X. laevis, genome from two distinct genetic backgrounds has been published. Multiple genome assemblies available for both species and transcriptomic and epigenetic data sets are growing rapidly, all of which are available from a variety of web resources. This review describes the contents of these resources, how to locate and download genomic data, and also how to view and manipulate these data on various public genome browsers, with an emphasis on Xenbase, the Xenopus model organism database.

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“…MuTect 23 was used for SNV detection and Oncotator was used for mutation annotation (http://www.broadinstitute.org/oncotator, last accessed May 6, 2015). A minimum threshold of five unique reads that supported the canonical mutation and visualization in JBrowse 24 were required to make a variant call.…”

Section: Targeted Dna-seq Using Anchored Multiplex Pcrmentioning

confidence: 99%

Detection of Dual IDH1 and IDH2 Mutations by Targeted Next-Generation Sequencing in Acute Myeloid Leukemia and Myelodysplastic Syndromes

Platt

Fathi

Borger

et al. 2015

The Journal of Molecular Diagnostics

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Studies in myeloid neoplasms have described recurrent IDH1 and IDH2 mutations as primarily mutually exclusive. Over a 6-month period of clinical testing with a targeted next-generation sequencing assay, we evaluated 92 patients with acute myeloid leukemia, myelodysplastic syndrome, and chronic myelomonocytic leukemia and identified a subset of 21 patients (23%) who harbored mutations in either IDH1 or IDH2. Of the 21 patients with IDH mutations, 4 (19%) were found to have single nucleotide variants in both IDH1 and IDH2. An additional patient included in the study was found to have two different IDH2 mutations. The mutations were typically present at different variant allelic frequencies, with one predominating over the other, consistent with the presence of multiple subclones in a single patient. In one case, the variant allelic frequencies in both IDH1 and IDH2 were equally low in the setting of a high percentage of blasts, suggesting that the IDH mutations were unlikely to be present in the founding clone. Given these data, we conclude that dual IDH1/2 mutations likely were previously underestimated, a finding that may carry important treatment implications. (J Mol Diagn 2015, 17: 661e668; http://dx.doi.org/10.1016/j.jmoldx.2015 In recent years, whole-genome sequencing of acute myeloid leukemias (AMLs) led to the identification of frequent heterozygous mutations in isocitrate dehydrogenase 1 gene (IDH1).1,2 Subsequent exome sequencing and targeted resequencing studies in AML also identified frequent IDH2 mutations. 3,4 Overall, approximately 15% to 30% of AML have mutations in IDH1 or IDH2, almost exclusively at codon Arg132 for IDH1 and at codons Arg140 and Arg172 for IDH2.1,3e6 Patients with cytogenetically normal AML are enriched for these mutations. The mutations confer neomorphic enzyme activity through the NADPH-dependent reduction of the normal end-product a-ketoglutarate to the putative oncometabolite 2-hydroxyglutarate. The accumulation of high levels of 2-hydroxyglutarate in the IDH1/2-mutant tumor provides an important mechanism of cellular transformation through the targeting of epigenetic regulators. 7IDH mutations were also identified in preleukemic clonal malignancies, including myelodysplastic syndromes (MDSs) and myeloproliferative neoplasms (approximately 5% of MDS/myeloproliferative neoplasm and approximately 20% of AML arising from MDS or myeloproliferative neoplasm).

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Visualizing next-generation sequencing data with JBrowse

Cited by 61 publications

References 12 publications

Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry

Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry

Xenopus genomic data and browser resources

Detection of Dual IDH1 and IDH2 Mutations by Targeted Next-Generation Sequencing in Acute Myeloid Leukemia and Myelodysplastic Syndromes

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