The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation

Kocher, Jean-Pierre A.; Quest, Daniel J.; Duffy, Patrick H.; Meiners, Michael A.; Moore, Raymond M.; Rider, David N.; Hossain, Asif; Hart, Steven N.; Dinu, Valentin

doi:10.1093/bioinformatics/btu137

Cited by 72 publications

(58 citation statements)

References 8 publications

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“…Mutation analysis was performed by using Ion Reporter Software v4.4 (Thermo-Fisher), and further data curation was performed by using the Biological Reference Repository (BioR, Mayo Clinic, Rochester, MN). 26 27 ; and PolyPhen-2 (Harvard Medical School). 28 Germ line variants were filtered out by comparing each tumor sample with its germ line counterpart.…”

Section: Targeted Sequencingmentioning

confidence: 99%

Targeted sequencing of refractory myeloma reveals a high incidence of mutations in CRBN and Ras pathway genes

Kortüm

Elias

Hanafiah

et al. 2016

Blood

207

191

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• The incidence of mutations within the MAPK pathway, the CRBN pathway, and TP53 is significantly increased in drug-refractory MM.• Mutations in CRBN might contribute to IMiD resistance in drug-refractory MM.In this study, targeted sequencing to screen 50 multidrug refractory multiple myeloma (rMM) patients was performed by using the Multiple Myeloma Mutation Panel. Patients were pretreated with both immunomodulatory drugs (IMiDs) and proteasome inhibitors (PIs), and 88%, 78%, and 68% were refractory to an IMiD, a PI, or both, respectively. The majority of patients had progressive (82%) or refractory (78%) disease immediately before sampling, with 43% being IMiD refractory and 46% being PI refractory in the most recent line of therapy. Compared with newly diagnosed MM, an increased prevalence of mutations in the Ras pathway genes KRAS, NRAS, and/or BRAF (72%), as well as TP53 (26%), CRBN (12%), and CRBN pathway genes (10%) was observed. Longitudinal analyses performed in 3 patients with CRBN mutations at time of IMiD resistance confirmed that these mutations were undetectable at earlier, IMiD-sensitive time points. Furthermore, the functional introduction of these mutations in MM cells conferred lenalidomide resistance in vitro. These data indicate a differential genetic landscape in rMM associated with drug response. (Blood. 2016;128(9):1226-1233

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Section: Targeted Sequencingmentioning

confidence: 99%

Targeted sequencing of refractory myeloma reveals a high incidence of mutations in CRBN and Ras pathway genes

Kortüm

Elias

Hanafiah

et al. 2016

Blood

207

191

View full text Add to dashboard Cite

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“…Variants that occurred at locations present in dbSNP (build137), BGI 62 or ESP6500 (http://evs.gs.washington.edu/EVS), 1,000 genome 63,64 databases were removed from consideration. Annotation variant analysis was carried out with the BioR variant annotation platform 65 against Ensembl v.70 and consequence prediction using SNPeffect (v.2.0.5d) and VEP (v.2.7).…”

Section: Methodsmentioning

confidence: 99%

ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors

Skamagki

Correia

Yeung³

et al. 2017

Nat Cell Biol

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Induced pluripotent stem cells (iPSCs), which are used to produce transplantable tissues, may particularly benefit older patients, who are more likely to suffer from degenerative diseases. However, iPSCs generated from aged donors (A-iPSCs) exhibit higher genomic instability, defects in apoptosis and a blunted DNA damage response compared with iPSCs generated from younger donors. We demonstrated that A-iPSCs exhibit excessive glutathione-mediated reactive oxygen species (ROS) scavenging activity, which blocks the DNA damage response and apoptosis and permits survival of cells with genomic instability. We found that the pluripotency factor ZSCAN10 is poorly expressed in A-iPSCs and addition of ZSCAN10 to the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) during A-iPSC reprogramming normalizes ROS–glutathione homeostasis and the DNA damage response, and recovers genomic stability. Correcting the genomic instability of A-iPSCs will ultimately enhance our ability to produce histocompatible functional tissues from older patients’ own cells that are safe for transplantation.

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“…First, orthologues between the annotated and sample genome were identified by predicting genes (using Prodigal v2.6), and the resulting amino acid sequences were compared using BLASTϩ v2.2.26 (27). BioR v2.4.1 was used to annotate the sample genomes and identify orthologous genes (28). These genes were used to assemble the nucleotide version of a given gene for all samples.…”

Section: Methodsmentioning

confidence: 99%

Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks

et al. 2017

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Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus. Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied. Near-complete genomes, assembled de novo with paired-end and long-mate-pair (8 kb) libraries were first assembled and analyzed utilizing an in-house assembly and analytical informatics pipeline. In addition, pairedend data were assembled and analyzed using a commercial software package. Single nucleotide variant (SNP) analysis was performed using the in-house pipeline. Two assembly strategies were used to generate core genome multilocus sequence typing (cgMLST) data. First, the near-complete genome data generated with the inhouse pipeline were imported into the commercial software and used to perform cgMLST analysis. Second, the commercial software was used to assemble paired-end data, and resolved assemblies were used to perform cgMLST. Similar isolate clustering was observed using SNP calling and cgMLST, regardless of data assembly strategy. All methods provided more discrimination between outbreaks than did PFGE. Overall, all of the evaluated WGS strategies yielded statistically similar results for S. aureus typing.KEYWORDS MRSA, PFGE, Staphylococcus aureus, molecular typing, whole-genome sequencing M ethicillin-resistant Staphylococcus aureus (MRSA) infections are associated with high morbidity and mortality. MRSA transmission poses a challenge to hospital infection prevention and control practitioners and public health professionals. The Centers for Disease Control and Prevention's Active Bacterial Surveillance Report estimated that there were 72,444 cases of invasive MRSA infection in 2014, the majority of which were health care associated (HCA) (1). Proactive screening strategies (molecular and culture based) are emphasized in many institutions and are mandatory in some states. Despite these measures, HCA-MRSA outbreaks continue to occur. Thorough investigation of outbreaks is essential for confirming that an outbreak is occurring, understanding transmission patterns and reservoirs, and intervening to interrupt out-

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The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation

Cited by 72 publications

References 8 publications

Targeted sequencing of refractory myeloma reveals a high incidence of mutations in CRBN and Ras pathway genes

Targeted sequencing of refractory myeloma reveals a high incidence of mutations in CRBN and Ras pathway genes

ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors

Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks

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