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repeated sequences

Definition

Repeated sequence: a sequence where, compared to a reference sequence, a segment of one or more nucleotides (the repeat unit) is present several times, one after the other.

Description

*NOTE: a Community Consultation is prepared which will suggest to allow only one format* where the entire range of the repeated sequence must be indicated, e.g. g.123_191CAG[23] not g.123CAG[23]

Format (unique repeat): "prefix""position_first_nucleotide_first_repeat_unit""repeat_sequence"["copy_number"], e.g. g.123CAG[23]

  • "prefix" = reference sequence used = g.
  • "position_first_nucleotide_first_repeat_unit" = first nucleotide of first repeat unit = 123
  • "repeat_sequence" = sequence repeat unit = CAG
  • [ = opening symbol for copy number allele = [
  • "copy_number" = number of repeat units = 23
  • ] = closing symbol for copy number allele = ]

Format (mixed repeat): "prefix""range_repeated_sequence""repeat_sequence_unit1"["copy_number"]"repeat_sequence_unit2"["copy_number"]"...", e.g. g.123_191CAG[19]CAA[4]

  • "prefix" = reference sequence used = g.
  • "range_repeated_sequence" = position first to last nucleotide repeated sequence (range) = 123_191
  • "repeat_sequence_unit1" = sequence first repeat unit = CAG
  • [ = opening symbol for allele = [
  • "copy_number" = number of repeat units = 19
  • ] = closing symbol for allele = ]
  • "repeat_sequence_unit2" = sequence first repeat unit = CAA
  • [ = opening symbol for allele = [
  • "copy_number" = number of repeat units = 4
  • ] = closing symbol for allele = ]
  • ... = and so on for repeat_sequence_unit3, repeat_sequence_unit4, etc.

Notes

  • reference sequences accepted are g., o. m., c. and n. (genomic, mitochondrial, coding DNA and non-coding DNA)
  • for mixed repeats the range of the reapeat sequence is given followed by a listing of each repeat unit and the number of repeats in each unit; NC_000012.11:g.112036755_112036823CTG[9]TTG[1]CTG[13].
  • NM_000044.3:c.171GCA[23] describes a repeated sequence containing 23 GCA units (sequenced). NM_000044.3:c.(92_331)insN[33] describes an insertion of 3 nucleotides, in the amplified region from position c.92 to c.331 (not sequenced), of a repeated sequence containing 24 GCA units.
  • exception: using a coding DNA reference sequence ("c." description) a Repeated sequence variant description can be used only for repeat units with a length which is a multiple of 3, i.e. which can not affect the reading frame. Consequently, use NM_024312.4:c.2692_2693dup and not NM_024312.4:c.2686A[10], use NM_024312.4:c.1741_1742insTATATATA and not NM_024312.4:c.1738TA[6].

Examples

  • unique repeat

    • sequenced
      • NC_000014.8:g.101179660TG[14]: a repeated TG di-nucleotide sequence starting at position g.101179660 on human chromosome 14, with 14 TG copies
      • NC_000014.8:g.[101179660TG[14]];[101179660TG[18]]: a repeated TG di-nucleotide sequence starting at position g.101179660 on human chromosome 14, is present with 14 TG copies on one allele and 18 TG copies on the other allele
    • repeat expansion disorders
      • sequenced
        • NM_023035.2(CACNA1A):c.6955CAG[26] (or c.6955_6993dup): a repeated CAG tri-nucleotide sequence starting at position c.6955 in the CACNA1A gene with 26 CAG copies (p.(Gln2319[26] or p.(Gln2319_Gln2331dup))
        • NC_000003.12:g.63912687AGC[13] | c.89AGC[13]: a repeated AGC tri-nucleotide sequence in the ATXN7 gene on chromosome 3, starting at position g.63912687/c.89, with 13 AGC copies (the reference sequence has 10 copies): NOTE: in literature the tri-nucleotide repeat, encoding a poly-Gln repeat on protein level, is known as the CAG repeat. However, based on the ATXN7 coding DNA reference sequence (GenBank LRG_866t1 or NM_000333.3) and applying the 3'rule, the repeat has to be described as an AGC repeat
      • not sequenced
        • NC_000003.12:g.(63912602_63912844)insN[9] | NM_000333.3:c.(4_246)insN[9]: a fragment containing the AGC repeat in the ATXN7 gene was amplified (from nucleotide g.63912602/c.4 to g.63912844/c.246) and its size determined to be 9 nucleotides larger ( "insN[9]" ) then that of the reference sequence.: NOTE: since the fragment was not sequenced the variant can not be described as g.63912687AGC[13] / c.89AGC[13].
        • NC_000003.12:g.(63912602_63912844)delN[15] | NM_000333.3:c.(4_246)delN[15]: a fragment containing the AGC repeat in the ATXN7 gene was amplified (from nucleotide g.63912602/c.4 to g.63912844/c.246) and its size determined to be 15 nucleotides smaller ( "delN[15]" ) then that of the reference sequence.

  • mixed repeat reference sequence

    • repeat expansion disorders
      • FMR1 repeat (reference sequence GGC[9]GGA[1]GGC[10]): in literature the Fragile-X tri-nucleotide repeat is described as a CGG-repeat. However, based on a coding DNA reference sequence (GenBank NM_002024.5) and applying the 3'rule, the repeat has to be described as a mixed GGC-GGA-GGC repeat
        • NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]: a sequenced GGC tri-nucleotide repeat from position c.-128 to c.-69 contains 10 GGC, 1 GGA, 9 GGC, 1 GGA and 10 GGC units (31 repeat units)
        • NM_002024.5:c.-129CGG[79]: a repeated CGG tri-nucleotide sequence starting at position c.-129 with 79 CGG copies: NOTE: by definition, since the reference sequence contains a mixed repeat (CGG and AGG units), the variant description only covers the sequence up to the first AGG interruption (position c.-99). A better description, giving less confusion, is NM_002024.5:c.-128_-69GGC[78]GGA[1]GGC[10] (i.e. assuming only the length of the first CGG segment was meant and not the total length of the GGC-GGA-GGC repeat).
        • NM_002024.5:c.-128GGM[108]: a repeated mixed tri-nucleotide sequence starting at position c.-129 with 108 GGC/GGA copies
        • NM_002024.5:c.(-144_-16)insN[(1800_2400)]: the amplified region containing the FMR1 repeat region (between nucleotides c.-144 and c.-16) contains an insertion of 1800 to 2400 nucleotides (600 to 800 GGC/GGA units)
      • HTT repeat (reference sequence LRG_763t1:52_153CAG[21]CAA[1]CAG[1]CCG[1]CCA[1]CCG[7]CCT[2]): in literature the Huntington's Disease tri-nucleotide repeat, encoding a variable poly-Gln followed by a variable poly-Pro repeat on protein level, is known as the CAG repeat. Based on the HTT (huntingtin) coding DNA reference sequence (GenBank LRG_763t1 or NM_002111.8) and applying the 3'rule, the Poly-Gln encoding repeat has to be described as an AGC-AAC-AGC repeat.
        • LRG_763t1:c.53AGC[23]: a sequenced AGC tri-nucleotide repeat starting at position c.53 contains 23 units, on protein level described as NP_002102.4:p.(Gln18)[25]: NOTE: the AGC repeat is followed by AACAGC extending the encoded Gln-repeat by 2)
      • CFTR intron 9: NM_000492.3:c.1210-33_1210-6GT[11]T[6]: the mixed repeat sequence form position c.1210-33 to c.1210-6 contains 11 GT and 6 T copies: NOTE: when only the variable T-stretch is described the format is NM_000492.3:c.1210-12T[7] (see Q&A below)
    • NC_000012.11:g.112036755_112036823CTG[9]TTG[1]CTG[13]: a complex repeated sequence from position g.112036755 to g.112036823 on chromosome 12 with first a CTG unit present in 9 copies, then a TTG unit present in 1 copy and then a CTG unit present in 13 copies
  • differing genomic (g.) and coding DNA (c.) descriptions: NC_000001.10:g.57832719ATAAA[15] and NM_021080.3:c.-136-75952ATTTT[15] describe the same repeat allele in intron 3 of the DAB1 gene: NOTE: based on the 3' rule and the transcriptional orientation of the gene (minus strand) the description of the repeat units differs

Discussion

Intron 9 of the CFTR gene ends with the sequence ...tgtgtgtgtgtttttttaacag[exon_10]. Both the TG and T stretches are variable in length (from 9 to 13 and 5 to 9 resp.). The reference sequence has 11 TG copies and 7 T's. Is it correct to describe an allele as c.1210-14TG[13]T[5] or for the T stretch as c.1210-6T[5]?

A complex case. First note that by applying the 3'rule it is a variable GT and not TG stretch. When the coding DNA reference sequence has TG11 followed by T7, the reference allele is described as c.1210-33_1210-6GT[11]T[6]. When only variability of the T-stretch is reported, the reference allele is described as c.1210-12T[7].
To indicate the overall variability found in the population the description is c.1210-33_1210-6GT[9_13]T[4_8] for the combined repeat and c.1210-12T[5_9] for the T-stretch.