Journal:Transferring exome sequencing data from clinical laboratories to healthcare providers: Lessons learned at a pediatric hospital
| Full article title | Transferring exome sequencing data from clinical laboratories to healthcare providers: Lessons learned at a pediatric hospital |
|---|---|
| Journal | Frontiers in Genetics |
| Author(s) |
Swaminathan, Rajeswari; Huang, Yungui; Miller, Katherine; Pastore, Matthew; Hashimoto, Sayaka; Jacobson, Theodora; Mouhlas, Danielle; Lin, Simon |
| Author affiliation(s) | Nationwide Children's Hospital |
| Primary contact | Email: simon dot lin at nationwidechildrens dot org |
| Editors | Patrinos, George P. |
| Year published | 2018 |
| Volume and issue | 9 |
| Page(s) | 54 |
| DOI | 10.3389/fgene.2018.00054 |
| ISSN | 1664-8021 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://www.frontiersin.org/articles/10.3389/fgene.2018.00054/full |
| Download | https://www.frontiersin.org/articles/10.3389/fgene.2018.00054/pdf (PDF) |
Abstract
The adoption rate of genome sequencing for clinical diagnostics has been steadily increasing, leading to the possibility of improvement in diagnostic yields. Although laboratories generate a summary clinical report, sharing raw genomic data with healthcare providers is equally important, both for secondary research studies as well as for a deeper analysis of the data itself, as seen by the efforts from organizations such as American College of Medical Genetics and Genomics, as well as Global Alliance for Genomics and Health. Here, we aim to describe the existing protocol of genomic data sharing between a certified clinical laboratory and a healthcare provider and highlight some of the lessons learned. This study tracked and subsequently evaluated the data transfer workflow for 19 patients, all of whom consented to be part of this research study and visited the genetics clinic at a tertiary pediatric hospital between April 2016 and December 2016. Two of the most noticeable elements observed through this study are the manual validation steps and the discrepancies in patient identifiers used by a clinical lab vs. healthcare provider. Both of these add complexity to the transfer process as well as make it more susceptible to errors. The results from this study highlight some of the critical changes that need to be made in order to improve genomic data sharing workflows between healthcare providers and clinical sequencing laboratories.
Keywords: genomic data sharing, genomic data transfer, whole exome sequencing, clinical genomics, interoperability, laboratory workflows
Introduction
The rate of genome sequencing is rising sharply, leading to the generation of substantial volumes of data. Despite the surge in data generation, utilizing the wealth of knowledge embedded in that data for the improvement of clinical outcomes is still lagging behind.[1]Additional research is still required in order to better associate genes/variants with diseases. Currently, clinical laboratories return a summary report back to the ordering physician. However, depending on the complexity of the disease—as well as the availability of information within knowledge bases—not every report ends up with a diagnosis. In many cases, when a sequencing rest is unable to detect the underlying genetic cause, clinicians may choose to obtain the raw sequencing data (available as FASTQ, VCF, or BAM files) and perform a more detailed research study/analysis on it, in hopes of untangling some of the complex details associated with the case. However, the underlying decision to share data ultimately rests in the hands of the patient/participant. Sharing sequencing data directly with the patient itself can also be beneficial, especially when a researcher does not have adequate resources to return any clinically actionable information back to the patient.[2] Sharing data directly with individuals makes them feel empowered and better controls the further flow of their confidential information.[3] There are currently several initiatives, such as GenomeConnect, My Research Legacy by the American Heart Association, etc. that are involved in sharing biomedical information for research and health purposes.[4] Although there are several challenges associated with patient-controlled sharing of genomic data, it is not within the scope of the current study.
At present, clinical laboratories either load the data onto hard drives or Universal Serial Bus (USB) drives and ship them to the providers or directly transfer data over a secure network. There is currently no standard protocol for transferring sequencing data from laboratories to healthcare providers. Through this study, we aim to describe the current state of the genomic data transfer process, specifically, data obtained from whole-exome sequencing (WES) studies between sequencing laboratories and healthcare providers and highlight some of the key lessons learned.
References
- ↑ Ginsburg, G. (2014). "Medical genomics: Gather and use genetic data in health care". Nature 508 (7497): 451–3. doi:10.1038/508451a. PMID 24765668.
- ↑ Middleton, A.; Wright, C.F.; Morley, K.I. et al. (2015). "Potential research participants support the return of raw sequence data". Journal of Medical Genetics 52 (8): 571–4. doi:10.1136/jmedgenet-2015-103119. PMC PMC4518751. PMID 25995218. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518751.
- ↑ Shabani, M.; Vears, D.; Borry, P. (2018). "Raw Genomic Data: Storage, Access, and Sharing". Trends in Genetics 34 (1): 8–10. doi:10.1016/j.tig.2017.10.004. PMID 29132689.
- ↑ Miller. K.E.; Lin, S.M. (2017). "Addressing a patient-controlled approach for genomic data sharing". Genetics in Medicine 19 (11): 1280–1. doi:10.1038/gim.2017.36. PMID 28425983.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. The original paper listed references alphabetically; this wiki lists them by order of appearance, by design.
