Genomics en Genetics

datE: 14-08-2024 Status: Under DEVELOPMENT

 

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 genomics 

• Targeted Sequencing 

  • Whole Exome Sequencing (WES)

  • Panel sequencing  

• Long read sequencing 

  • methylation profiling (nanopore) 

• GWAS – DNA genotyping arrays + Imputation 

• CHipSeq 

• Immunosequencing (AIRR) 

• Epigenomics

  • MEDseq

  • bisulfite sequencing

  • methylation arrays 

• Toxicogenomics 

• Nutrigenomics / Nutrigenetics 

• Pharmacogenomics 

• Genome Diagnostics

• Gene Therapies

• Metagenomics 

File formats

• BIM - GWAS

• FAM - GWAS

• BED - 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: About FAIR genomes ; https://github.com/fairgenomes/fairgenomes-semantic-model; https://decor.nictiz.nl/art-decor/decor-project--fairgenomes-