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Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics.

ABSTRACT: The goal of this study was to perform candidate gene association with cytotoxicity of chemotherapeutics in cell line models through resequencing and discovery of rare and low frequency variants along with common variations. Here, an association study of cytotoxicity response to 30 FDA approved drugs was conducted and we applied next generation targeted sequencing technology to discover variants from 103 candidate genes in 95 lymphoblastoid cell lines from 14 CEPH pedigrees. In this article, we called variants across 95 cell lines and performed association analysis for cytotoxic response using the Family Based Association Testing method and software.We called 2281 variable SNP genotypes across the 103 genes for these cell lines and identified three genes of significant association within this marker set. Specifically, ATP-binding cassette, sub-family C, member 5 (ABCC5), metallothionein 1A (MT1A) and NAD(P)H dehydrogenase quinone1 (NQO1) were significantly associated with oxaliplatin drug response. The significant SNP on NQO1 (rs1800566) has been linked with poor survival rates in patients with non-small cell lung cancer treated with cisplatin (which belongs to the same class of drugs as oxaliplatin). A SNP (rs1846692) near the 5' region of MT1A was associated with arsenic trioxide.The results from this study are promising and this serves as a proof-of-principle demonstration of the use of sequencing data in the cytotoxicity models of human cell lines. With increased sample sizes, such studies will be a fast and powerful way to associate common and rare variants with drug response; while overcoming the cost and time limitations to recruit cohorts for association study.

SUBMITTER: Hariani GD

PROVIDER: S-EPMC4068968 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics.

Hariani Gunjan D GD Lam Ernest T ET Havener Tammy T Kwok Pui-Yan PY McLeod Howard L HL Wagner Michael J MJ Motsinger-Reif Alison A AA

BMC research notes 20140612

<h4>Background</h4>The goal of this study was to perform candidate gene association with cytotoxicity of chemotherapeutics in cell line models through resequencing and discovery of rare and low frequency variants along with common variations. Here, an association study of cytotoxicity response to 30 FDA approved drugs was conducted and we applied next generation targeted sequencing technology to discover variants from 103 candidate genes in 95 lymphoblastoid cell lines from 14 CEPH pedigrees. In ...[more]

PMID: 24924344

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Project description:Identifying the Mechanism of Action (MoA) of drugs is critical for the development of new drugs, understanding their side effects, and drug repositioning. However, identifying drug MoA has been challenging and has been traditionally attempted only though large experimental setups with little success. While advances in computational power offers the opportunity to achieve this in-silico, methods to exploit existing computational resources are still in their infancy. To overcome this, we developed a novel method to identify Drug Mechanism of Action using Network Dysregulation (DeMAND). The method is based on the realization that drugs affect the protein activity of their targets, but not necessarily their mRNA expression levels. In contrast, the change in protein activity directly affects the mRNA expression levels of downstream genes. Based on this hypothesis, DeMAND identifies drug MoA by comparing gene expression profiles following drug perturbation with control samples, and computing the change in the individual interactions within a pre-determined integrated transcriptional and post-translational regulatory model (interactome). This dataset includes GEPs in 3 different B-cell lymphoma cell lines (OCI-LY3, OCI-LY7 and U2932) at 6, 12, and 24hrs. 92 FDA approved compounds were used at a concentration of IC20 at 24h. DMSO was used as control at each time-point. A total of 828 samples and 29 control samples were available for analysis. Total RNA was isolated with the RNAqueous-96 Automated Kit (Ambion) on the Janus automated liquid handling system (Perkin Elmer Inc.), quantified by NanoDrop 6000 spectrophotometer and quality checked by Agilent Bioanalyzer. 300ng of each of the samples with RIN value >7 were converted to biotinylated cRNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) using a standard T7-based amplification protocol and hybridized on the Human Genome U219 96-Array Plate (Affymetrix). Hybridization, washing, staining and scanning of the array plates were performed on the GeneTitan Instrument (Affymetrix) according to manufacturer’s protocols.

Project description:BackgroundMedication guides are required documents to be distributed to patients in order to convey serious risks associated with certain prescribed medicines. Little is known about the effectiveness of this information to adequately inform patients on safe use.ObjectiveTo examine the readability, suitability, and comprehensibility of medication guides, particularly for those with limited literacy.DesignAssessments of suitability and readability of 185 medication guides, and a sub-study examining change in suitability and readability from 2006 to 2010 among 32 of the medication guides (Study 1); 'open book' comprehension assessment of medication guides (Study 2).SettingTwo general internal medicine clinics in Chicago, IL.PatientsFour hundred and forty-nine adults seeking primary care services, ages 18-85.MeasurementsFor Study 1, the Suitability Assessment of Materials (SAM) and Lexile score for readability. For Study 2, a tailored comprehension assessment of content found in three representative medication guides.ResultsThe 185 analyzed medication guides were on average 1923 words (SD = 1022), with a mean reading level of 10-11th grade. Only one medication guide was deemed suitable in SAM analyses. None provided summaries or reviews, or framed the context first, while very few were rated as having made the purpose evident (8 %), or limited the scope of content (22 %). For Study 2, participants' comprehension of medication guides was poor (M = 52.7 % correct responses, SD = 22.6). In multivariable analysis, low and marginal literacy were independently associated with poorer understanding (β = -14.3, 95 % CI -18.0 - -10.6, p < 0.001; low: β = -23.7, 95 % CI -28.3 - -19.0, p < 0.001).ConclusionCurrent medication guides are of little value to patients, as they are too complex and difficult to understand especially for individuals with limited literacy. Explicit guidance is offered for improving these print materials.

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Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics.

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Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics.

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