The UCSC Genome Browser database: 2015 update

“…The non-overlapping set of RefSeq (Pruitt et al 2014) and Mammalian Gene Collection (Team MGCP 2009) genes (18,814) was downloaded from UCSC (Rosenbloom et al 2015) (http://hgdownload.soe.ucsc. edu/downloads.html, ftp://hgdownload.soe.ucsc.edu/ goldenPath/currentGenomes/Rattus_norvegicus/ database/) for the most recent build of the rat genome (Rnor_6.0; https://www.hgsc.bcm.edu/rat-genomeproject; July 2014 (Rosenbloom et al 2015)).…”

Section: Probe Designmentioning

confidence: 99%

“…edu/downloads.html, ftp://hgdownload.soe.ucsc.edu/ goldenPath/currentGenomes/Rattus_norvegicus/ database/) for the most recent build of the rat genome (Rnor_6.0; https://www.hgsc.bcm.edu/rat-genomeproject; July 2014 (Rosenbloom et al 2015)). Transcription start sites (TSS) were used to set Bpromoter regionsâ t 4000 bp upstream plus 1000 bp downstream of each TSS.…”

Section: Probe Designmentioning

confidence: 99%

“…Transcription start sites (TSS) were used to set Bpromoter regionsâ t 4000 bp upstream plus 1000 bp downstream of each TSS. CG islands (Gardiner-Garden and Frommer 1987) not present in repeat regions (18,411), i.e., masked CG islands, were downloaded from UCSC (Rosenbloom et al 2015), and CG island shores and shelves (Irizarry et al 2009;Sandoval et al 2011) were defined as 4000 bp up and downstream of the masked CG islands (Fig. 1a).…”

Section: Probe Designmentioning

confidence: 99%

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Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

Masser

Stanford

Hadad

et al. 2016

AGE

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Epigenetic regulation through DNA methylation (5mC) plays an important role in development, aging, and a variety of diseases. Genome-wide studies of base-and strand-specific 5mC are limited by the extensive sequencing required. Targeting bisulfite sequencing to specific genomic regions through sequence AGE (2016) capture with complimentary oligonucleotide probes retains the advantages of bisulfite sequencing while focusing sequencing reads on regions of interest, enables analysis of more samples by decreasing the amount of sequence required per sample, and provides base-and strand-specific absolute quantitation of CG and non-CG methylation levels. As an example, an oligonucleotide capture set to interrogate 5mC levels in all rat RefSeq gene promoter regions (18,814) and CG islands, shores, and shelves (18,411) was generated. Validation using whole-genome methylation standards and biological samples demonstrates enrichment of the targeted regions and accurate base-specific quantitation of CG and non-CG methylation for both forward and reverse genomic strands. A total of 170 Mb of the rat genome is covered including 6.6 million CGs and over 67 million non-CG sites, while reducing the amount of sequencing required by~85 % as compared to existing wholegenome sequencing methods. This oligonucleotide capture targeting approach and quantitative validation workflow can also be applied to any genome of interest.

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“…Candidate variants genome wide and in the region of association and their depth of coverage were identified using dynamic filters based on phenotype‐specific allele frequencies in the Variant Explorer tool on the maverix analytic platform (maverixbio.com) and viewed using the UCSC Genome Browser (Rosenbloom et al . 2015). …”

mentioning

confidence: 99%

COLQ variant associated with Devon Rex and Sphynx feline hereditary myopathy

et al. 2015

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SummarySome Devon Rex and Sphynx cats have a variably progressive myopathy characterized by appendicular and axial muscle weakness, megaesophagus, pharyngeal weakness and fatigability with exercise. Muscle biopsies from affected cats demonstrated variable pathological changes ranging from dystrophic features to minimal abnormalities. Affected cats have exacerbation of weakness following anticholinesterase dosing, a clue that there is an underlying congenital myasthenic syndrome (CMS). A genome‐wide association study and whole‐genome sequencing suggested a causal variant for this entity was a c.1190G>A variant causing a cysteine to tyrosine substitution (p.Cys397Tyr) within the C‐terminal domain of collagen‐like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase (COLQ). Alpha‐dystroglycan expression, which is associated with COLQ anchorage at the motor end‐plate, has been shown to be deficient in affected cats. Eighteen affected cats were identified by genotyping, including cats from the original clinical descriptions in 1993 and subsequent publications. Eight Devon Rex and one Sphynx not associated with the study were identified as carriers, suggesting an allele frequency of ~2.0% in Devon Rex. Over 350 tested cats from other breeds did not have the variant. Characteristic clinical features and variant presence in all affected cats suggest a model for COLQ CMS. The association between the COLQ variant and this CMS affords clinicians the opportunity to confirm diagnosis via genetic testing and permits owners and breeders to identify carriers in the population. Moreover, accurate diagnosis increases available therapeutic options for affected cats based on an understanding of the pathophysiology and experience from human CMS associated with COLQ variants.

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The UCSC Genome Browser database: 2015 update

Cited by 874 publications

References 61 publications

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation

Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

COLQ variant associated with Devon Rex and Sphynx feline hereditary myopathy

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