A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges.

PubWeight™: 0.98‹?› | Rank: Top 15%

🔗 View Article (PMC 3813699)

Published in PLoS One on October 30, 2013

Authors

Glen J Weiss1, Winnie S Liang, Michael J Demeure, Jeff A Kiefer, Galen Hostetter, Tyler Izatt, Shripad Sinari, Alexis Christoforides, Jessica Aldrich, Ahmet Kurdoglu, Lori Phillips, Hollie Benson, Rebecca Reiman, Angela Baker, Vickie Marsh, Daniel D Von Hoff, John D Carpten, David W Craig

Author Affiliations

1: Virginia G. Piper Cancer Center Clinical Trials at Scottsdale Healthcare (VGPCC), Scottsdale, Arizona, United States of America ; The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.

Associated clinical trials:

An Ancillary Pilot Trial Using Whole Genome Sequencing In Patients With Advance Refractory Cancer | NCT01443390

Articles cited by this

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med (2012) 44.56

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2000) 34.79

Risks and benefits of phase 1 oncology trials, 1991 through 2002. N Engl J Med (2005) 8.25

Pilot study using molecular profiling of patients' tumors to find potential targets and select treatments for their refractory cancers. J Clin Oncol (2010) 6.34

Personalized medicine in a phase I clinical trials program: the MD Anderson Cancer Center initiative. Clin Cancer Res (2012) 3.14

Therapeutic response in phase I trials of antineoplastic agents. Cancer Treat Rep (1986) 1.91

Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities. Mol Cancer Ther (2012) 1.72

Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing. PLoS One (2012) 1.21

Aprataxin tumor levels predict response of colorectal cancer patients to irinotecan-based treatment. Clin Cancer Res (2010) 1.12

Design and results of phase I cancer clinical trials: three-year experience at M.D. Anderson Cancer Center. J Clin Oncol (1996) 1.10

Molecular disruption of RAD50 sensitizes human tumor cells to cisplatin-based chemotherapy. J Clin Invest (2009) 1.07

Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma. PLoS One (2012) 0.95

Clonal evolution of a case of treatment refractory maxillary sinus carcinoma. PLoS One (2012) 0.82

Articles by these authors

Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet (2008) 20.38

Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28

Cumulative association of five genetic variants with prostate cancer. N Engl J Med (2008) 15.34

A survey of genetic human cortical gene expression. Nat Genet (2007) 12.04

A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature (2007) 10.98

High frequency of BRAF mutations in nevi. Nat Genet (2002) 9.95

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02

Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function. Proc Natl Acad Sci U S A (2004) 7.70

Enzymatic targeting of the stroma ablates physical barriers to treatment of pancreatic ductal adenocarcinoma. Cancer Cell (2012) 7.57

Promiscuous mutations activate the noncanonical NF-kappaB pathway in multiple myeloma. Cancer Cell (2007) 7.24

A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease. J Clin Psychiatry (2007) 7.23

Treatment of medulloblastoma with hedgehog pathway inhibitor GDC-0449. N Engl J Med (2009) 7.23

GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers. Neuron (2007) 6.88

Germline mutations in HOXB13 and prostate-cancer risk. N Engl J Med (2012) 5.49

Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma. Cancer Cell (2002) 5.23

Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP. J Natl Cancer Inst (2007) 4.85

American Society of Clinical Oncology Technology Assessment: chemotherapy sensitivity and resistance assays. J Clin Oncol (2004) 4.48

Clonal competition with alternating dominance in multiple myeloma. Blood (2012) 4.39

Association between two unlinked loci at 8q24 and prostate cancer risk among European Americans. J Natl Cancer Inst (2007) 4.24

Phase I trial of hedgehog pathway inhibitor vismodegib (GDC-0449) in patients with refractory, locally advanced or metastatic solid tumors. Clin Cancer Res (2011) 4.05

Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med (2012) 3.92

Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet (2010) 3.91

RNASEL Arg462Gln variant is implicated in up to 13% of prostate cancer cases. Nat Genet (2002) 3.87

Common sequence variants on 20q11.22 confer melanoma susceptibility. Nat Genet (2008) 3.79

Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies. Am J Hum Genet (2006) 3.67

Tumor-stroma interactions in pancreatic ductal adenocarcinoma. Mol Cancer Ther (2007) 3.61

The secreted glycoprotein lubricin protects cartilage surfaces and inhibits synovial cell overgrowth. J Clin Invest (2005) 3.56

Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet (2009) 3.35

Whole-genome analysis of sporadic amyotrophic lateral sclerosis. N Engl J Med (2007) 3.33

Common Kibra alleles are associated with human memory performance. Science (2006) 3.30

Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. Neuroimage (2010) 3.27

Somatic and germ-line mutations of the HRPT2 gene in sporadic parathyroid carcinoma. N Engl J Med (2003) 3.07

Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides. Blood (2012) 2.98

Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans. Alzheimers Dement (2010) 2.79

Germline mutations and sequence variants of the macrophage scavenger receptor 1 gene are associated with prostate cancer risk. Nat Genet (2002) 2.76

Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma. Nat Genet (2009) 2.73

Treatment and prevention of intraepithelial neoplasia: an important target for accelerated new agent development. Clin Cancer Res (2002) 2.71

Voxelwise genome-wide association study (vGWAS). Neuroimage (2010) 2.69

Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. Cancer Res (2002) 2.55

Phase I and pharmacokinetics trial of ABI-007, a novel nanoparticle formulation of paclitaxel in patients with advanced nonhematologic malignancies. J Clin Oncol (2005) 2.53

Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals. Hum Mol Genet (2010) 2.51

Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer. Nat Genet (2004) 2.44

Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. J Neural Transm (Vienna) (2008) 2.43

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Res (2010) 2.41

The cationic porphyrin TMPyP4 down-regulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo. Mol Cancer Ther (2002) 2.39

Preinvasive pancreatic neoplasia of ductal phenotype induced by acinar cell targeting of mutant Kras in transgenic mice. Cancer Res (2003) 2.28

HOXB13 is a susceptibility gene for prostate cancer: results from the International Consortium for Prostate Cancer Genetics (ICPCG). Hum Genet (2012) 2.18

Pharmacokinetics of hedgehog pathway inhibitor vismodegib (GDC-0449) in patients with locally advanced or metastatic solid tumors: the role of alpha-1-acid glycoprotein binding. Clin Cancer Res (2011) 2.12

A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly. Proc Natl Acad Sci U S A (2010) 2.12

Copy number alterations in pancreatic cancer identify recurrent PAK4 amplification. Cancer Biol Ther (2008) 2.09

Effects of RNase L mutations associated with prostate cancer on apoptosis induced by 2',5'-oligoadenylates. Cancer Res (2003) 1.95

Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. Neuroimage (2010) 1.94

SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. Bioinformatics (2006) 1.88

Tissue factor expression, angiogenesis, and thrombosis in pancreatic cancer. Clin Cancer Res (2007) 1.87

Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor. N Engl J Med (2015) 1.75

Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms. PLoS One (2008) 1.72

Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities. Mol Cancer Ther (2012) 1.72

Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc Natl Acad Sci U S A (2008) 1.70

Improved survival in resected biliary malignancies. Surgery (2002) 1.67

PRL phosphatases as potential molecular targets in cancer. Mol Cancer Ther (2005) 1.67

Increased fibroblast growth factor-inducible 14 expression levels promote glioma cell invasion via Rac1 and nuclear factor-kappaB and correlate with poor patient outcome. Cancer Res (2006) 1.66

The mitotic serine threonine kinase, Aurora-2, is a potential target for drug development in human pancreatic cancer. Mol Cancer Ther (2004) 1.65

Perineural invasion and associated pain in pancreatic cancer. Nat Rev Cancer (2011) 1.64

Neurological effects of high-dose idebenone in patients with Friedreich's ataxia: a randomised, placebo-controlled trial. Lancet Neurol (2007) 1.64

Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study. Diabetes (2007) 1.58

Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays. Cancer Res (2002) 1.58

Cumulative effect of five genetic variants on prostate cancer risk in multiple study populations. Prostate (2008) 1.53

Dlx1&2 and Mash1 transcription factors control striatal patterning and differentiation through parallel and overlapping pathways. J Comp Neurol (2009) 1.52

GRM7 variants confer susceptibility to age-related hearing impairment. Hum Mol Genet (2008) 1.49

RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinformatics (2010) 1.49

A novel prostate cancer susceptibility locus at 19q13. Cancer Res (2009) 1.49

Synthetic lethal RNAi screening identifies sensitizing targets for gemcitabine therapy in pancreatic cancer. J Transl Med (2009) 1.48

Genomic signatures of cancer: basis for individualized risk assessment, selective staging and therapy. J Surg Oncol (2011) 1.48

Advancing a clinically relevant perspective of the clonal nature of cancer. Proc Natl Acad Sci U S A (2011) 1.47

A successful social norms campaign to reduce alcohol misuse among college student-athletes. J Stud Alcohol (2006) 1.44

Combined genome-wide scan for prostate cancer susceptibility genes. J Natl Cancer Inst (2004) 1.44

Asparagine synthetase as a causal, predictive biomarker for L-asparaginase activity in ovarian cancer cells. Mol Cancer Ther (2006) 1.41

Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer. Cancer Res (2012) 1.41

DNA methylation analysis determines the high frequency of genic hypomethylation and low frequency of hypermethylation events in plasma cell tumors. Cancer Res (2010) 1.41

Drug targeting of the c-MYC promoter to repress gene expression via a G-quadruplex silencer element. Semin Oncol (2006) 1.39