private static string GetHgvsFrameshiftNotation(ISequence refSequence, int cdsBegin, int cdsEnd,
string transcriptAltAllele, ITranscript transcript, bool isMitochondrial, string proteinId, int start,
int end)
{
var peptideSeq = transcript.Translation.PeptideSeq;
var altPeptideSeq = HgvsUtilities.GetAltPeptideSequence(refSequence, cdsBegin, cdsEnd, transcriptAltAllele, transcript, isMitochondrial);
if (start > end)
{
Swap.Int(ref start, ref end);
}
var frameshiftedParameters = HgvsUtilities.GetChangesAfterFrameshift(start, peptideSeq, altPeptideSeq);
start = frameshiftedParameters.Item1;
var refAminoAcid = frameshiftedParameters.Item2;
var altAminoAcid = frameshiftedParameters.Item3;
var refAbbreviation = AminoAcids.ConvertAminoAcidToAbbreviation(refAminoAcid);
if (altAminoAcid == AminoAcids.StopCodonChar)
{
return(HgvspNotation.GetSubstitutionNotation(proteinId, start, refAbbreviation, "Ter"));
}
var altAbbreviation = AminoAcids.ConvertAminoAcidToAbbreviation(altAminoAcid);
var countToStop = HgvsUtilities.GetNumAminoAcidsUntilStopCodon(altPeptideSeq, peptideSeq, start - 1, true);
return(HgvspNotation.GetFrameshiftNotation(proteinId, start, refAbbreviation, altAbbreviation, countToStop));
}
public static string GetHgvscAnnotation(ITranscript transcript, ISimpleVariant variant, ISequence refSequence,
int regionStart, int regionEnd)
{
// sanity check: don't try to handle odd characters, make sure this is not a reference allele,
// and make sure that we have protein coordinates
if (variant.Type == VariantType.reference || SequenceUtilities.HasNonCanonicalBase(variant.AltAllele))
{
return(null);
}
var onReverseStrand = transcript.Gene.OnReverseStrand;
var refAllele = onReverseStrand ? SequenceUtilities.GetReverseComplement(variant.RefAllele) : variant.RefAllele;
var altAllele = onReverseStrand ? SequenceUtilities.GetReverseComplement(variant.AltAllele) : variant.AltAllele;
// decide event type from HGVS nomenclature
var genomicChange = GetGenomicChange(transcript, onReverseStrand, refSequence, variant);
var variantStart = variant.Start;
var variantEnd = variant.End;
if (genomicChange == GenomicChange.Duplication)
{
(variantStart, variantEnd, refAllele, regionStart, regionEnd) = transcript.TranscriptRegions.ShiftDuplication(variantStart, altAllele, onReverseStrand);
}
var startPositionOffset = HgvsUtilities.GetCdnaPositionOffset(transcript, variantStart, regionStart);
var endPositionOffset = variantStart == variantEnd
? startPositionOffset
: HgvsUtilities.GetCdnaPositionOffset(transcript, variantEnd, regionEnd);
if (onReverseStrand)
{
var tmp = startPositionOffset;
startPositionOffset = endPositionOffset;
endPositionOffset = tmp;
}
// sanity check: make sure we have coordinates
if (startPositionOffset == null || endPositionOffset == null)
{
return(null);
}
var transcriptLen = transcript.End - transcript.Start + 1;
//_hgvs notation past the transcript
if (startPositionOffset.Position > transcriptLen || endPositionOffset.Position > transcriptLen)
{
return(null);
}
var hgvsNotation = new HgvscNotation(refAllele, altAllele, transcript.Id.WithVersion, genomicChange,
startPositionOffset, endPositionOffset, transcript.Translation != null);
// generic formatting
return(hgvsNotation.ToString());
}
internal static ProteinChange GetProteinChange(int start, string refAminoAcids, string altAminoAcids,
string peptideSeq, IVariantEffect variantEffect)
{
if (refAminoAcids == altAminoAcids ||
variantEffect.IsStopRetained())
{
return(ProteinChange.None);
}
//insertion before the transcript
if (refAminoAcids.Length == 0 && start == 1)
{
return(ProteinChange.None);
}
if (variantEffect.IsStartLost())
{
return(ProteinChange.StartLost);
}
// todo: add start gained
// according to var nom, only if the Stop codon is effected, we call it an extension
if (variantEffect.IsStopLost() && refAminoAcids.StartsWith(AminoAcids.StopCodon))
{
return(ProteinChange.Extension);
}
if (variantEffect.IsFrameshiftVariant())
{
return(ProteinChange.Frameshift);
}
if (altAminoAcids.Length > refAminoAcids.Length && HgvsUtilities.IsAminoAcidDuplicate(start, altAminoAcids, peptideSeq))
{
return(ProteinChange.Duplication);
}
if (refAminoAcids.Length == 0 && altAminoAcids.Length != 0)
{
return(ProteinChange.Insertion);
}
if (refAminoAcids.Length != 0 && altAminoAcids.Length == 0)
{
return(ProteinChange.Deletion);
}
if (refAminoAcids.Length == 1 && altAminoAcids.Length == 1)
{
return(ProteinChange.Substitution);
}
// the only remaining possibility is deletions/insertions
return(ProteinChange.DelIns);
}
public static GenomicChange GetGenomicChange(IInterval interval, bool onReverseStrand, ISequence refSequence, ISimpleVariant variant)
{
// length of the reference allele. Negative lengths make no sense
int refLength = variant.End - variant.Start + 1;
if (refLength < 0)
{
refLength = 0;
}
// length of alternative allele
int altLength = variant.AltAllele.Length;
// sanity check: make sure that the alleles are different
if (variant.RefAllele == variant.AltAllele)
{
return(GenomicChange.Unknown);
}
// deletion
if (altLength == 0)
{
return(GenomicChange.Deletion);
}
if (refLength == altLength)
{
// substitution
if (refLength == 1)
{
return(GenomicChange.Substitution);
}
// inversion
string rcRefAllele = SequenceUtilities.GetReverseComplement(variant.RefAllele);
return(variant.AltAllele == rcRefAllele ? GenomicChange.Inversion : GenomicChange.DelIns);
}
// deletion/insertion
if (refLength != 0)
{
return(GenomicChange.DelIns);
}
// If this is an insertion, we should check if the preceding reference nucleotides
// match the insertion. In that case it should be annotated as a multiplication.
bool isGenomicDuplicate = HgvsUtilities.IsDuplicateWithinInterval(refSequence, variant, interval, onReverseStrand);
return(isGenomicDuplicate ? GenomicChange.Duplication : GenomicChange.Insertion);
}
public static string GetNotation(string refseqAccession, ISimpleVariant variant, ISequence refSequence,
IInterval referenceInterval)
{
var rotatedVariant = VariantRotator.Right(variant, referenceInterval, refSequence, false);
var start = Math.Min(rotatedVariant.Start, rotatedVariant.End);
var end = Math.Max(rotatedVariant.Start, rotatedVariant.End);
var referenceBases = rotatedVariant.RefAllele;
var alternateBases = rotatedVariant.AltAllele;
var type = HgvsCodingNomenclature.GetGenomicChange(referenceInterval, false, refSequence, rotatedVariant);
if (type == GenomicChange.Duplication && variant.Type == VariantType.insertion)
{
referenceBases = alternateBases;
end = start;
start = end - referenceBases.Length + 1;
}
return(HgvsUtilities.FormatDnaNotation(start.ToString(), end.ToString(), refseqAccession, referenceBases, alternateBases, type, NotationType));
}
public static string GetHgvsProteinAnnotation(
ITranscript transcript,
string refAminoAcids,
string altAminoAcids,
string transcriptAltAllele,
IMappedPosition position,
VariantEffect variantEffect,
ISimpleVariant variant,
ISequence refSequence,
string hgvscNotation,
bool isMitochondrial)
{
if (IsHgvspNull(transcriptAltAllele, position.CdsStart, position.CdsEnd, variant, hgvscNotation))
{
return(null);
}
var peptideSeq = transcript.Translation.PeptideSeq;
// Amino acid seq should never go past the stop codon
refAminoAcids = !refAminoAcids.EndsWith(AminoAcids.StopCodon) && refAminoAcids.Contains(AminoAcids.StopCodon)
? refAminoAcids.OptimizedSplit(AminoAcids.StopCodon[0])[0] + AminoAcids.StopCodon
: refAminoAcids;
int proteinStart = position.ProteinStart;
HgvsUtilities.ShiftAndRotateAlleles(ref proteinStart, ref refAminoAcids, ref altAminoAcids, peptideSeq);
var end = proteinStart + refAminoAcids.Length - 1;
var refAbbreviation = AminoAcids.GetAbbreviations(refAminoAcids);
var altAbbreviation = AminoAcids.GetAbbreviations(altAminoAcids);
var proteinId = transcript.Translation.ProteinId.WithVersion;
var proteinChange = GetProteinChange(proteinStart, refAminoAcids, altAminoAcids, peptideSeq, variantEffect);
// ReSharper disable once SwitchStatementMissingSomeCases
switch (proteinChange)
{
case ProteinChange.Substitution:
return(HgvspNotation.GetSubstitutionNotation(proteinId, proteinStart, refAbbreviation, altAbbreviation));
case ProteinChange.Unknown:
return(HgvspNotation.GetUnknownNotation(proteinId, proteinStart, end, refAbbreviation, altAbbreviation));
case ProteinChange.Deletion:
return(HgvspNotation.GetDeletionNotation(proteinId, proteinStart, end, refAbbreviation, variantEffect.IsStopGained()));
case ProteinChange.Duplication:
proteinStart -= altAminoAcids.Length;
return(HgvspNotation.GetDuplicationNotation(proteinId, proteinStart, end, altAbbreviation));
case ProteinChange.Frameshift:
return(GetHgvsFrameshiftNotation(refSequence, position.CdsStart, position.CdsEnd, transcriptAltAllele,
transcript, isMitochondrial, proteinId, proteinStart, end));
case ProteinChange.None:
return(HgvspNotation.GetSilentNotation(hgvscNotation, proteinStart, refAbbreviation, variantEffect.IsStopRetained()));
case ProteinChange.DelIns:
return(HgvspNotation.GetDelInsNotation(proteinId, proteinStart, end, refAbbreviation, altAbbreviation));
case ProteinChange.Insertion:
Swap.Int(ref proteinStart, ref end);
return(HgvspNotation.GetInsertionNotation(proteinId, proteinStart, end, altAbbreviation, peptideSeq));
case ProteinChange.Extension:
var altPeptideSequence = HgvsUtilities.GetAltPeptideSequence(refSequence, position.CdsStart, position.CdsEnd,
transcriptAltAllele, transcript, isMitochondrial);
altAbbreviation = proteinStart <= altPeptideSequence.Length ? AminoAcids.ConvertAminoAcidToAbbreviation(altPeptideSequence[proteinStart - 1]): "Ter";
var countToStop = HgvsUtilities.GetNumAminoAcidsUntilStopCodon(altPeptideSequence, peptideSeq, proteinStart - 1, false);
return(HgvspNotation.GetExtensionNotation(proteinId, proteinStart, refAbbreviation, altAbbreviation, countToStop));
case ProteinChange.StartLost:
return(HgvspNotation.GetStartLostNotation(proteinId, proteinStart, end, refAbbreviation));
}
return(null);
}
public static string GetHgvscAnnotation(ITranscript transcript, ISimpleVariant variant, ISequence refSequence,
int regionStart, int regionEnd, string transcriptRef, string transcriptAlt)
{
// sanity check: don't try to handle odd characters, make sure this is not a reference allele,
// and make sure that we have protein coordinates
if (variant.Type == VariantType.reference || SequenceUtilities.HasNonCanonicalBase(variant.AltAllele))
{
return(null);
}
// do not report HGVSc notation when variant lands inside gap region
if (regionStart > -1 && regionEnd > -1)
{
var startRegion = transcript.TranscriptRegions[regionStart];
var endRegion = transcript.TranscriptRegions[regionEnd];
if (startRegion.Id == endRegion.Id && startRegion.Type == TranscriptRegionType.Gap &&
endRegion.Type == TranscriptRegionType.Gap)
{
return(null);
}
}
bool onReverseStrand = transcript.Gene.OnReverseStrand;
string refAllele = string.IsNullOrEmpty(transcriptRef)? onReverseStrand ? SequenceUtilities.GetReverseComplement(variant.RefAllele) : variant.RefAllele
: transcriptRef;
string altAllele = string.IsNullOrEmpty(transcriptAlt)
? onReverseStrand ? SequenceUtilities.GetReverseComplement(variant.AltAllele) : variant.AltAllele
: transcriptAlt;
// decide event type from HGVS nomenclature
var genomicChange = GetGenomicChange(transcript, onReverseStrand, refSequence, variant);
int variantStart = variant.Start;
int variantEnd = variant.End;
if (genomicChange == GenomicChange.Duplication)
{
(variantStart, variantEnd, refAllele, regionStart, regionEnd) = transcript.TranscriptRegions.ShiftDuplication(variantStart, altAllele, onReverseStrand);
}
var startPositionOffset = HgvsUtilities.GetCdnaPositionOffset(transcript, variantStart, regionStart, true);
var endPositionOffset = variantStart == variantEnd
? startPositionOffset
: HgvsUtilities.GetCdnaPositionOffset(transcript, variantEnd, regionEnd, false);
if (onReverseStrand)
{
var tmp = startPositionOffset;
startPositionOffset = endPositionOffset;
endPositionOffset = tmp;
}
if (startPositionOffset == null && variant.Type == VariantType.insertion)
{
startPositionOffset = new PositionOffset(endPositionOffset.Position + 1, endPositionOffset.Offset, $"{endPositionOffset.Position + 1}", endPositionOffset.HasStopCodonNotation);
}
// sanity check: make sure we have coordinates
if (startPositionOffset == null || endPositionOffset == null)
{
return(null);
}
var hgvsNotation = new HgvscNotation(refAllele, altAllele, transcript.Id.WithVersion, genomicChange,
startPositionOffset, endPositionOffset, transcript.Translation != null);
// generic formatting
return(hgvsNotation.ToString());
}
