| Title |
Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care
|
|---|---|
| Published in |
npj Genomic Medicine, July 2016
|
| DOI | 10.1038/npjgenmed.2016.19 |
| Pubmed ID | |
| Authors |
Hanna Rennert, Kenneth Eng, Tuo Zhang, Adrian Tan, Jenny Xiang, Alessandro Romanel, Robert Kim, Wayne Tam, Yen-Chun Liu, Bhavneet Bhinder, Joanna Cyrta, Himisha Beltran, Brian Robinson, Juan Miguel Mosquera, Helen Fernandes, Francesca Demichelis, Andrea Sboner, Michael Kluk, Mark A Rubin, Olivier Elemento |
| Abstract |
We describe Exome Cancer Test v1.0 (EXaCT-1), the first New York State-Department of Health-approved whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation sequencing (Illumina) of tumour and matched constitutional control DNA. We present a detailed clinical development and validation pipeline suitable for simultaneous detection of somatic point/indel mutations and copy-number alterations (CNAs). A computational framework for data analysis, reporting and sign-out is also presented. For the validation, we tested EXaCT-1 on 57 tumours covering five distinct clinically relevant mutations. Results demonstrated elevated and uniform coverage compatible with clinical testing as well as complete concordance in variant quality metrics between formalin-fixed paraffin embedded and fresh-frozen tumours. Extensive sensitivity studies identified limits of detection threshold for point/indel mutations and CNAs. Prospective analysis of 337 cancer cases revealed mutations in clinically relevant genes in 82% of tumours, demonstrating that EXaCT-1 is an accurate and sensitive method for identifying actionable mutations, with reasonable costs and time, greatly expanding its utility for advanced cancer care. |
X Demographics
The data shown below were collected from the profiles of 52 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 | 18 | 35% |
| Australia | 4 | 8% |
| United Kingdom | 4 | 8% |
| France | 2 | 4% |
| Canada | 2 | 4% |
| Spain | 1 | 2% |
| Belgium | 1 | 2% |
| Germany | 1 | 2% |
| Netherlands | 1 | 2% |
| Other | 1 | 2% |
| Unknown | 17 | 33% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 27 | 52% |
| Members of the public | 24 | 46% |
| Practitioners (doctors, other healthcare professionals) | 1 | 2% |
Mendeley readers
The data shown below were compiled from readership statistics for 139 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Spain | 1 | <1% |
| United States | 1 | <1% |
| Denmark | 1 | <1% |
| Canada | 1 | <1% |
| Unknown | 135 | 97% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 32 | 23% |
| Student > Ph. D. Student | 20 | 14% |
| Other | 16 | 12% |
| Student > Master | 12 | 9% |
| Student > Doctoral Student | 8 | 6% |
| Other | 21 | 15% |
| Unknown | 30 | 22% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 54 | 39% |
| Agricultural and Biological Sciences | 27 | 19% |
| Medicine and Dentistry | 14 | 10% |
| Engineering | 4 | 3% |
| Computer Science | 2 | 1% |
| Other | 6 | 4% |
| Unknown | 32 | 23% |
Attention Score in Context
This research output has an Altmetric Attention Score of 52. 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 14 November 2016.
All research outputs
#825,170
of 25,736,439 outputs
Outputs from npj Genomic Medicine
#33
of 411 outputs
Outputs of similar age
#16,033
of 379,254 outputs
Outputs of similar age from npj Genomic Medicine
#2
of 8 outputs
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