92822-6

LOINC 2.82

Genomic coordinate system [Type]

Genomic coord system

Definition

  • A genomic coordinate is a position along a sequence. Coordinate systems can start counting from: 0-based interval counting - Used by: GA4GH API, ClinGen data model, BED & BAM files, UCSC files, HLM 1.0 and NCBI's SPDI conversion format - Akin to cursor positioning in modern text editors with cursor between characters - A bit unnatural for humans, easier for computers - Sequences have an inclusive start and exclusive end - Insertions always go in the interval between characters 0-based character counting - Used by: Genbank database & ASN files - Sequences have an inclusive start, exclusive end - Length = end - start - A bit unnatural for human reading, easier for computers - Sequences have an inclusive start and inclusive end - Insertions not defined because GenBank and ASN do not model insertions to records they contain (historically ASN did internal to NCBI). SPDI was developed in part because of this inability to model insertions. 1-based character counting - Used by: HGVS, VCF, NCBI's ClinVar (uses HGVS), Genbank files, IPD-IMGT/HLA, UCSC genome browser (note different from UCSC file, which uses 0-based interval counting) - Akin to approach used in the earliest text processors - Length = (end - start) + 1 - Sequences have inclusive start and inclusive end - More natural for humans - Insertions. Be careful in theory for 1-base, the insertion location could be defined in three ways: a) before position, b) after position, c) specify the di-nucleotide which where the insertion goes; but in practice there is only one way to do it per coordinate type. Distinctions for describing sub sequences with the three approaches with examples Consider ACGTAGTC as an example string and what nucleotides would be in the range 2-4 - 0-based interval counting (e.g..SPDI): GT - 0-based character counting (i.e. GenBank): GTA - 1-based character counting (i.e. VCF): CGT Distinctions regarding insertions with examples. Insertions can be tricky with character counting. Now consider that you want to describe an insertion between T&A (4th and 5th characters in the example string): - 0-based interval counting (i.e. SPDI) insert at position 4. - 0-based character counting. Insert between 3&4. Note: insertions are not supported in GenBank's model. - 1-based character counting. Insert between 4&5. Note: HGVS requires specification of the dinucleotide between which the insertion goes. For VCF, this would be represented as insert after 4 and does not require other information but the result is the same.

Component

  • Genomic coordinate system

Specimen / system

  • XXX

Class

  • MOLPATH

Property

  • Type

Scale

  • Nom

Method

  • Molgen

Related names

  • Genetic; Genetics; Genomic coord system; Misc; Miscellaneous; Molecular genetics; Molecular pathology; MOLPATH; Nominal; Other; PCR; Point in time; Random; Spec; To be specified in another part of the message; Typ; Unspecified

Index terms

  • Genetic
  • Genetics
  • Genomic coord system
  • Misc
  • Miscellaneous
  • Molecular genetics
  • Molecular pathology
  • MOLPATH
  • Nominal
  • Other
  • PCR
  • Point in time
  • Random
  • Spec
  • To be specified in another part of the message
  • Typ
  • Unspecified