Biochemical Study of Tumors of the Nervous System

Allen, Nicholas

doi:10.1007/978-1-4615-7754-6_1

Cited by 2 publications

(1 citation statement)

References 91 publications

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“…The C6 rat glioma tumor cell line, chemically induced by N,N-nitrosomethylurea in an outbred Wistar rat [ 18 ] and morphologically similar to gliobastoma multiforme, is an important human translational research model for malignant glial neoplasms [ 19 , 20 ]. Exome sequencing of the C6 glioma captured 3864 non-annotated variants of which 3447 were designated as SNPs and 417 as INDELs.…”

Section: Resultsmentioning

confidence: 99%

Whole exome sequencing in the rat

Foley

Phadke²,

Hardy

et al. 2018

BMC Genomics

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BackgroundThe rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and testing of a probe set for whole exome sequencing (WES) to detect sequence variants in exons and UTRs of the rat genome. Using an in-silico approach, we designed probes targeting the rat exome and compared captured mutations in cancer-related genes from four chemically induced rat tumor cell lines (C6, FAT7, DSL-6A/C1, NBTII) to validated cancer genes in the human database, Catalogue of Somatic Mutations in Cancer (COSMIC) as well as normal rat DNA. Paired, fresh frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) liver tissue from naive rats were sequenced to confirm known dbSNP variants and identify any additional variants.ResultsInformatics analysis of available gene annotation from rat RGSC6.0/rn6 RefSeq and Ensembl transcripts provided 223,636 unique exons representing a total of 26,365 unique genes and untranslated regions. Using this annotation and the Rn6 reference genome, an in-silico probe design generated 826,878 probe sequences of which 94.2% were uniquely aligned to the rat genome without mismatches. Further informatics analysis revealed 25,249 genes (95.8%) covered by at least one probe and 23,603 genes (93.5%) had every exon covered by one or more probes. We report high performance metrics from exome sequencing of our probe set and Sanger validation of annotated, highly relevant, cancer gene mutations as cataloged in the human COSMIC database, in addition to several exonic variants in cancer-related genes.ConclusionsAn in-silico probe set was designed to enrich the rat exome from isolated DNA. The platform was tested on rat tumor cell lines and normal FF and FFPE liver tissue. The method effectively captured target exome regions in the test DNA samples with exceptional sensitivity and specificity to obtain reliable sequencing data representing variants that are likely chemically induced somatic mutations. Genomic discovery conducted by means of high throughput WES queries should benefit investigators in discovering rat genomic variants in disease etiology and in furthering human translational research.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4858-8) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Whole exome sequencing in the rat

Foley

Phadke²,

Hardy

et al. 2018

BMC Genomics

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An improved rat brain-tumor model

Kobayashi¹,

Allen²,

Clendenon³

et al. 1980

Journal of Neurosurgery

126

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In order to correct the shortcomings of the former brain storage model, an improved brain storage model was proposed, it consisted of a memory bank and a series of sub-storages. These sub-storages were concluding sub-storage, effective search sub-storage, storing sub-storage, recalls sub-storage and forgetting sub-storage. The input formation of the improved brain storage model was single fuzzy cognitive unit event. Experimental results demonstrated that the model was able to simulate storage functions of the brain, such as concluding, storing, recalling and forgetting. So the improved brain storage model is optimal.

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Biochemical Study of Tumors of the Nervous System

Cited by 2 publications

References 91 publications

Whole exome sequencing in the rat

Whole exome sequencing in the rat

An improved rat brain-tumor model

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