Related Experiment Video
Updated: Sep 4, 2025
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
33.9K
Applying FHIR Genomics for Research - From Sequencing to Database
Sean Hernandez1, Karen Fairchild2,3, Mark Pemberton4
1Wake Forest School of Medicine, Winston-Salem, NC.
Summary
Harmonizing next-generation sequencing (NGS) genomic data to FHIR standards enables its integration into large databases. This facilitates clinical trial recruitment and advances genomic research.
Area of Science:
- Genomics
- Bioinformatics
- Health Informatics
Background:
- Next-generation sequencing (NGS) generates vast genomic datasets, but data lacks standardization.
- Current data formats (PDF, XML, JSON) hinder interoperability and analysis.
- Profiling external vendor testing platforms lacks uniformity.
Purpose of the Study:
- To harmonize and map genomic data to FHIR Genomic standards.
- To import harmonized genomic data into the TriNetX database.
- To establish a translatable process for other institutions and platforms.
Main Methods:
- Genomic data from Atrium Health Wake Forest Baptist was mapped to FHIR Genomic standards.
- A data pipeline was utilized to import the harmonized data into the TriNetX database.
- The process was designed for broad applicability to various sequencing platforms and institutions.
Main Results:
- Successfully harmonized and imported genomic data into the TriNetX database.
- Established a standardized data pipeline for genomic data integration.
- Demonstrated the translatability of the process for broader adoption.
Conclusions:
- Integrating standardized genomic data enhances phenotypic data reservoirs.
- Facilitates improved clinical trial recruitment and genomic benchmarking.
- Enables advanced inter-institutional genomic research and treatment paradigm shifts.
More Related Videos
09:06High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
Published on: October 5, 2018
10.4K
10:19Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
Published on: April 8, 2017
17.5K
Related Concept Videos
02:02Genomics
37.3K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
37.3K
03:00Next-generation Sequencing
92.4K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
92.4K
01:57Sanger Sequencing
756.7K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
756.7K
01:05Maxam-Gilbert Sequencing
11.4K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
11.4K
03:21RNA-seq
10.4K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.4K
03:36Genome Annotation and Assembly
19.3K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.3K