Health-RI wiki v4.0 -> consultatie (open tot 03-12-2024)
Genomics en Genetics
Data from Genomics and genetics are data measured on DNA, often but not always specifically the DNA of the 23 chromosomes in the nucleus of a human cell. There is also DNA in the mitochondria, relevant to certain diseases. Determinations can be made on healthy cells (germline) and on cells that deviate from them in the body (somatic; for example relevant to cancer). Genomics and genetics relevant to human health can also be done on model organisms or on pathogenic organisms. There is a sliding scale distinction between genetics that concerns selective data (for example of 1 gene) and genomics that collects information about a large part of the DNA in an entire organism. Metagenomics determines the DNA of a diverse population of organisms in a specific biotope in one go.
Epigenetics are data measured on DNA that record something other than the order of the DNA building blocks. An important example is methylation of DNA.
Experiments
Whole genome sequencing (WGS)
Cancer genomicsÂ
Targeted SequencingÂ
Whole Exome Sequencing (WES)
Panel sequencing Â
Long read sequencingÂ
methylation profiling (nanopore)Â
GWAS – DNA genotyping arrays + ImputationÂ
CHipSeqÂ
Immunosequencing (AIRR)Â
Epigenomics
MEDseq
bisulfite sequencing
methylation arraysÂ
ToxicogenomicsÂ
Nutrigenomics / NutrigeneticsÂ
PharmacogenomicsÂ
Genome Diagnostics
Gene Therapies
MetagenomicsÂ
File formats
BIM - GWAS
FAM - GWAS
BEDÂ - GWAS
FASTQ - WGS; Raw, machine-independent data
SAM - WGS; Mapped data
BAM - WGS; Mapped data with generic data compression
CRAM-WGS; Mapped data with specific (reference-based) data compression
VCF - WGS; Variant Call Format
gVCF
AFA
GTF
GFF
BED
AIRR
Metadataschemes
FairGenomes: https://fairgenomes.org/ ; https://github.com/fairgenomes/fairgenomes-semantic-model; https://decor.nictiz.nl/art-decor/decor-project--fairgenomes-Â
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