| Title |
Evaluation and comparison of two commercially available targeted next-generation sequencing platforms to assist oncology decision making
|
|---|---|
| Published in |
OncoTargets and therapy, April 2015
|
| DOI | 10.2147/ott.s81995 |
| Pubmed ID | |
| Authors |
Glen J Weiss, Brandi R Hoff, Robert P Whitehead, Ashish Sangal, Susan A Gingrich, Robert J Penny, David W Mallery, Scott M Morris, Eric J Thompson, David M Loesch, Vivek Khemka |
| Abstract |
It is widely acknowledged that there is value in examining cancers for genomic aberrations via next-generation sequencing (NGS). How commercially available NGS platforms compare with each other, and the clinical utility of the reported actionable results, are not well known. During the course of the current study, the Foundation One (F1) test generated data on a combination of somatic mutations, insertion and deletion polymorphisms, chromosomal abnormalities, and deoxyribonucleic acid (DNA) copy number changes at ~250× coverage, while the Paradigm Cancer Diagnostic (PCDx) test generated the same type of data at >5,000× coverage, plus provided messenger RNA (mRNA) expression levels. We sought to compare and evaluate paired formalin-fixed paraffin-embedded tumor tissue using these two platforms. Samples from patients with advanced solid tumors were submitted to both the F1 and PCDx vendors for NGS analysis. Turnaround time (TAT) was calculated. Biomarkers were considered clinically actionable if they had a published association with treatment response in humans and were assigned to the following categories: commercially available drug (CA), clinical trial drug (CT), or neither option (hereafter referred to as "None"). The demographics of the 21 unique patient tumor samples included ten men and eleven women, with a median age of 56 years. Due to insufficient archival tissue from the same collection period, in one case, we used samples from different collections. PCDx reported first results faster than F1 in 20 cases. When received at both vendors on the same day, PCDx reported first results for 14 of 15 cases, with a median TAT of 9 days earlier than F1 (P<0.0001). Categorization of CA compared to CT and none significantly favored PCDx (P=0.012). In the current analysis, commercially available NGS platforms provided clinically relevant actionable targets (CA or CT) in 47%-67% of diverse cancer types. In the samples analyzed, PCDx significantly outperformed F1 in TAT, and had statistically significant higher clinically relevant actionable targets categorized as CA. |
X Demographics
The data shown below were collected from the profiles of 36 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 11 | 31% |
| France | 2 | 6% |
| Spain | 2 | 6% |
| United Kingdom | 1 | 3% |
| Turkey | 1 | 3% |
| Australia | 1 | 3% |
| Mexico | 1 | 3% |
| India | 1 | 3% |
| Canada | 1 | 3% |
| Other | 1 | 3% |
| Unknown | 14 | 39% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 25 | 69% |
| Scientists | 9 | 25% |
| Science communicators (journalists, bloggers, editors) | 1 | 3% |
| Practitioners (doctors, other healthcare professionals) | 1 | 3% |
Mendeley readers
The data shown below were compiled from readership statistics for 49 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 2% |
| Unknown | 48 | 98% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 13 | 27% |
| Other | 6 | 12% |
| Student > Bachelor | 4 | 8% |
| Student > Ph. D. Student | 4 | 8% |
| Student > Master | 3 | 6% |
| Other | 6 | 12% |
| Unknown | 13 | 27% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 16 | 33% |
| Medicine and Dentistry | 9 | 18% |
| Agricultural and Biological Sciences | 4 | 8% |
| Engineering | 2 | 4% |
| Immunology and Microbiology | 1 | 2% |
| Other | 0 | 0% |
| Unknown | 17 | 35% |
Attention Score in Context
This research output has an Altmetric Attention Score of 22. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 04 May 2021.
All research outputs
#1,693,257
of 25,374,647 outputs
Outputs from OncoTargets and therapy
#35
of 3,016 outputs
Outputs of similar age
#21,446
of 279,170 outputs
Outputs of similar age from OncoTargets and therapy
#1
of 37 outputs
Altmetric has tracked 25,374,647 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,016 research outputs from this source. They receive a mean Attention Score of 2.9. This one has done particularly well, scoring higher than 98% of its peers.
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