Dataset Information
Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.
Ontology highlight
ABSTRACT: Background
While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community.Methods
A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally. Additionally, respondents were asked as to provide the primary intent of their initiative (clinical diagnostic, research or combination).Results
Of 107 initiatives invited to participate, 59 responded (response rate?=?55%). Whole exome sequencing (P?=?0.03) and whole genome sequencing (P?=?0.01) were utilized less frequently in clinical diagnostic than in research initiatives. Procedures to identify cancer-specific variants were heterogeneous, with bioinformatics pipelines employing different mutation calling/variant annotation algorithms. Measurement of treatment efficacy varied amongst initiatives, with time on treatment (57%) and RECIST (53%) being the most common; however, other parameters were also employed. Whilst 72% of initiatives indicated data sharing, its scope varied, with a number of restrictions in place (e.g. transfer of raw data). The largest perceived barriers to data harmonization were the lack of financial support (P?ConclusionsThese results identify the main barriers, as perceived by the cancer sequencing community, to effective sharing of cancer genomic and clinical data. They highlight the need for greater harmonization of technical, ethical and data capture processes in cancer sample sequencing worldwide, in order to support effective and responsible data sharing for the benefit of patients.
SUBMITTER: Vis DJ
PROVIDER: S-EPMC5406763 | biostudies-literature | 2017 May
REPOSITORIES: biostudies-literature
Publications
Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.
Annals of oncology : official journal of the European Society for Medical Oncology 20170501 5
<h4>Background</h4>While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community.<h4>Methods</h4>A multi-item survey was conducted assessi ...[more]