public void GetCdnaPosition_Snv_AfterOutframeRnaEditInsertion()
{
// NM_033517.1
var variant = new Interval(51135986, 51135986);
var observed = MappedPositionUtilities.GetCdnaPositions(_regionsNm33517[20], _regionsNm33517[20], variant, false, false);
Assert.Equal(1343, observed.CdnaStart);
}
public void GetCdnaPosition_Snv_AfterOutFrameRnaEditDeletion()
{
// NM_001317107.1
var variant = new Interval(22138550, 22138550);
var observed = MappedPositionUtilities.GetCdnaPositions(_regionsNm1317107[0], _regionsNm1317107[0], variant, true, false);
Assert.Equal(681, observed.CdnaStart);
}
public void GetCdnaPosition_Snv_AfterInframeRnaEditInsertion()
{
// NM_000682.6
var variant = new Interval(96780984, 96780984);
var observed = MappedPositionUtilities.GetCdnaPositions(_regionsNm682[0], _regionsNm682[0], variant, true, false);
Assert.Equal(1010, observed.CdnaStart);
}
public void GetProteinPosition_Forward_Insertion()
{
int proteinStart = MappedPositionUtilities.GetProteinPosition(225);
int proteinEnd = MappedPositionUtilities.GetProteinPosition(224);
Assert.Equal(75, proteinStart);
Assert.Equal(75, proteinEnd);
}
public void GetCdnaPositions_Reverse_Deletion()
{
var variant = new Interval(ReverseVariantStart, ReverseVariantEnd);
var observed = MappedPositionUtilities.GetCdnaPositions(_reverseTranscriptRegions[6], _reverseTranscriptRegions[7], variant, true, false);
Assert.Equal(123, observed.CdnaStart);
Assert.Equal(-1, observed.CdnaEnd);
}
public void GetProteinPosition_Reverse_Deletion()
{
int proteinStart = MappedPositionUtilities.GetProteinPosition(-1);
int proteinEnd = MappedPositionUtilities.GetProteinPosition(-1);
Assert.Equal(-1, proteinStart);
Assert.Equal(-1, proteinEnd);
}
public void GetCdnaPositions_Forward_Insertion()
{
var variant = new Interval(ForwardVariantStart, ForwardVariantEnd);
var observed = MappedPositionUtilities.GetCdnaPositions(_forwardTranscriptRegions[4],
_forwardTranscriptRegions[4], variant, false, true);
Assert.Equal(486, observed.CdnaStart);
Assert.Equal(485, observed.CdnaEnd);
}
public void GetCdsPosition_Reverse_NoCodingRegion_Deletion()
{
const byte startExonPhase = 0;
var(cdsStart, cdsEnd) = MappedPositionUtilities.GetCdsPositions(null, -1, 123, startExonPhase, false);
Assert.Equal(-1, cdsStart);
Assert.Equal(-1, cdsEnd);
}
public void GetCdsPosition_Snv_AfterOutframeRnaEditInsertion()
{
// NM_033517.1
var codingRegion = new CodingRegion(51113070, 51169740, 1, 5196, 5157);
const byte startExonPhase = 0;
(int cdsStart, _) = MappedPositionUtilities.GetCdsPositions(codingRegion, 1343, 1343, startExonPhase, false);
Assert.Equal(1343, cdsStart);
}
public void GetCdsPosition_Forward_Insertion()
{
var codingRegion = new CodingRegion(78001559, 78024355, 262, 495, 234);
const byte startExonPhase = 0;
var(cdsStart, cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, 486, 485, startExonPhase, true);
Assert.Equal(225, cdsStart);
Assert.Equal(224, cdsEnd);
}
public void FindRegion_Reverse_Deletion()
{
var observedStart = MappedPositionUtilities.FindRegion(_reverseTranscriptRegions, ReverseVariantStart);
var observedEnd = MappedPositionUtilities.FindRegion(_reverseTranscriptRegions, ReverseVariantEnd);
Assert.Equal(6, observedStart.Index);
Assert.Equal(7, observedEnd.Index);
Assert.NotNull(observedStart.Region);
Assert.NotNull(observedEnd.Region);
}
public void FindRegion_Forward_Insertion()
{
var observedStart = MappedPositionUtilities.FindRegion(_forwardTranscriptRegions, ForwardVariantStart);
var observedEnd = MappedPositionUtilities.FindRegion(_forwardTranscriptRegions, ForwardVariantEnd);
Assert.Equal(4, observedStart.Index);
Assert.Equal(4, observedEnd.Index);
Assert.NotNull(observedStart.Region);
Assert.NotNull(observedEnd.Region);
}
private static IMappedPosition GetMappedPosition(ITranscriptRegion[] regions, IInterval variant)
{
(int startIndex, _) = MappedPositionUtilities.FindRegion(regions, variant.Start);
(int endIndex, _) = MappedPositionUtilities.FindRegion(regions, variant.End);
(int exonStart, int exonEnd, int intronStart, int intronEnd) = regions.GetExonsAndIntrons(startIndex, endIndex);
return(new MappedPosition(-1, -1, -1, -1, -1, -1, exonStart, exonEnd, intronStart, intronEnd, startIndex,
endIndex));
}
public void GetCdsPosition_Forward_Insertion_WithStartExonPhase()
{
var codingRegion = new CodingRegion(6413107, 6415837, 1, 953, 953);
const byte startExonPhase = 1;
var(cdsStart, cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, 29, 28, startExonPhase, true);
Assert.Equal(30, cdsStart);
Assert.Equal(29, cdsEnd);
}
public void GetCdsPosition_Snv_AfterInframeRnaEditInsertion()
{
// NM_000682.6
var codingRegion = new CodingRegion(96780545, 96781888, 97, 1449, 1344);
const byte startExonPhase = 0;
(int cdsStart, _) = MappedPositionUtilities.GetCdsPositions(codingRegion, 1010, 1010, startExonPhase, false);
Assert.Equal(914, cdsStart);
}
public void GetCdsPosition_Snv_AfterOutFrameRnaEditDeletion()
{
// NM_001317107.1
var codingRegion = new CodingRegion(22138201, 22139150, 83, 1030, 948);
const byte startExonPhase = 0;
(int cdsStart, _) = MappedPositionUtilities.GetCdsPositions(codingRegion, 681, 681, startExonPhase, false);
Assert.Equal(599, cdsStart);
}
public void FixExonEndpointInsertion_VariantStart_ExonStart_Forward()
{
var startRegion = new TranscriptRegion(TranscriptRegionType.Exon, 2, 99459243, 99459360, 108, 225);
var endRegion = new TranscriptRegion(TranscriptRegionType.Intron, 1, 99456512, 99459242, 107, 108);
var result = MappedPositionUtilities.FixExonEndpointInsertion(108, -1, false, startRegion, endRegion,
new Interval(99459243, 99459242));
Assert.Equal(108, result.CdnaStart);
Assert.Equal(107, result.CdnaEnd);
}
public void FixExonEndpointInsertion_VariantEnd_ExonEnd_Forward()
{
var startRegion = new TranscriptRegion(TranscriptRegionType.Intron, 16, 89521770, 89528546, 3071, 3072);
var endRegion = new TranscriptRegion(TranscriptRegionType.Exon, 16, 89521614, 89521769, 2916, 3071);
var result = MappedPositionUtilities.FixExonEndpointInsertion(-1, 3071, false, startRegion, endRegion,
new Interval(89521770, 89521769));
Assert.Equal(3072, result.CdnaStart);
Assert.Equal(3071, result.CdnaEnd);
}
public void FixExonEndpointInsertion_VariantEnd_ExonEnd_Reverse()
{
var startRegion = new TranscriptRegion(TranscriptRegionType.Intron, 7, 243736351, 243776972, 762, 763);
var endRegion = new TranscriptRegion(TranscriptRegionType.Exon, 8, 243736228, 243736350, 763, 885);
var result = MappedPositionUtilities.FixExonEndpointInsertion(-1, 763, true, startRegion, endRegion,
new Interval(243736351, 243736350));
Assert.Equal(762, result.CdnaStart);
Assert.Equal(763, result.CdnaEnd);
}
public void GetCdsPosition_SilenceOutput_InsertionBeforeCodingRegion_Reverse()
{
// variant: [37480320, 37480319] insertion after coding region
var codingRegion = new CodingRegion(37480320, 37543667, 556, 3228, 2673);
const byte startExonPhase = 0;
var(cdsStart, cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, 3229, 3228, startExonPhase, true);
Assert.Equal(-1, cdsStart);
Assert.Equal(-1, cdsEnd);
}
public void GetCdsPosition_DoNotSilenceOutput_Reverse()
{
// variant: [179315139, 179315692]
var codingRegion = new CodingRegion(179308070, 179315170, 617, 942, 326);
const byte startExonPhase = 0;
var(cdsStart, cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, 95, 648, startExonPhase, false);
Assert.Equal(-1, cdsStart);
Assert.Equal(32, cdsEnd);
}
public void GetCdsPosition_SilenceOutput_InsertionAfterCodingRegion_Reverse()
{
// variant: [103629803, 103629804] insertion after coding region
var codingRegion = new CodingRegion(103113259, 103629803, 161, 10543, 10383);
const byte startExonPhase = 0;
var(cdsStart, cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, 161, 160, startExonPhase, true);
Assert.Equal(-1, cdsStart);
Assert.Equal(-1, cdsEnd);
}
public void GetCdsPosition_SilenceOutput_InsertionAfterCodingRegion_Forward()
{
// variant: [6647337, 6647336] insertion after coding region
var codingRegion = new CodingRegion(6643999, 6647336, 667, 1674, 1008);
const byte startExonPhase = 0;
var(cdsStart, cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, 1675, 1674, startExonPhase, true);
Assert.Equal(-1, cdsStart);
Assert.Equal(-1, cdsEnd);
}
public void FixExonEndpointInsertion_VariantStart_ExonStart_Reverse()
{
// N.B. this configuration has never been spotted in the wild
var startRegion = new TranscriptRegion(TranscriptRegionType.Exon, 2, 2000, 2199, 1, 200);
var endRegion = new TranscriptRegion(TranscriptRegionType.Intron, 2, 1999, 1000, 200, 201);
var result = MappedPositionUtilities.FixExonEndpointInsertion(200, -1, true, startRegion, endRegion,
new Interval(2000, 1999));
Assert.Equal(200, result.CdnaStart);
Assert.Equal(201, result.CdnaEnd);
}
/// <summary>
/// Adjust positions by alt allele length
/// </summary>
internal static (int Start, int End, string RefAllele, int RegionStart, int RegionEnd) ShiftDuplication(
this ITranscriptRegion[] regions, int start, string altAllele, bool onReverseStrand)
{
int incrementLength = altAllele.Length;
int dupStart = onReverseStrand ? start + incrementLength - 1 : start - incrementLength;
int dupEnd = onReverseStrand ? dupStart - incrementLength + 1 : dupStart + incrementLength - 1;
(int regionStart, _) = MappedPositionUtilities.FindRegion(regions, dupStart);
(int regionEnd, _) = MappedPositionUtilities.FindRegion(regions, dupEnd);
return(dupStart, dupEnd, altAllele, regionStart, regionEnd);
}
public void GetHgvscAnnotation_in_intron_gap_substitution(int variantStart, int variantEnd, string reference, string alt,
string transcriptRef, VariantType variantType, string expectedHgvsc)
{
var(startIndex, _) =
MappedPositionUtilities.FindRegion(_gapTranscript.TranscriptRegions, variantStart);
var(endIndex, _) =
MappedPositionUtilities.FindRegion(_gapTranscript.TranscriptRegions, variantEnd);
var variant = new SimpleVariant(ChromosomeUtilities.Chr10, variantStart, variantEnd, reference, alt, variantType);
var observedHgvsc =
HgvsCodingNomenclature.GetHgvscAnnotation(_gapTranscript, variant, null, startIndex, endIndex, transcriptRef, null);
Assert.Equal(expectedHgvsc, observedHgvsc);
}
internal static void GetGeneFusionsByTranscript(this Dictionary <string, IAnnotatedGeneFusion> transcriptIdToGeneFusions,
BreakEndAdjacency adjacency, ITranscript[] originTranscripts, ITranscript[] partnerTranscripts)
{
var geneFusions = new List <IGeneFusion>();
foreach (var originTranscript in originTranscripts)
{
geneFusions.Clear();
bool originOnReverseStrand = originTranscript.Gene.OnReverseStrand ^ adjacency.Origin.OnReverseStrand;
(int originIndex, ITranscriptRegion originRegion) = MappedPositionUtilities.FindRegion(originTranscript.TranscriptRegions, adjacency.Origin.Position);
int?originExon = originRegion.Type == TranscriptRegionType.Exon ? (int?)originRegion.Id : null;
int?originIntron = originRegion.Type == TranscriptRegionType.Intron ? (int?)originRegion.Id : null;
foreach (var partnerTranscript in partnerTranscripts)
{
bool partnerOnReverseStrand = partnerTranscript.Gene.OnReverseStrand ^ adjacency.Partner.OnReverseStrand;
bool differentStrand = originOnReverseStrand != partnerOnReverseStrand;
bool differentTranscriptSource = originTranscript.Source != partnerTranscript.Source;
bool sameGeneSymbol = originTranscript.Gene.Symbol == partnerTranscript.Gene.Symbol;
bool codingRegionAlreadyOverlaps = originTranscript.Translation.CodingRegion.Overlaps(partnerTranscript.Translation.CodingRegion);
if (differentStrand || differentTranscriptSource || sameGeneSymbol || codingRegionAlreadyOverlaps)
{
continue;
}
(int partnerIndex, ITranscriptRegion partnerRegion) = MappedPositionUtilities.FindRegion(partnerTranscript.TranscriptRegions, adjacency.Partner.Position);
int?partnerExon = partnerRegion.Type == TranscriptRegionType.Exon ? (int?)partnerRegion.Id : null;
int?partnerIntron = partnerRegion.Type == TranscriptRegionType.Intron ? (int?)partnerRegion.Id : null;
BreakPointTranscript origin = new BreakPointTranscript(originTranscript, adjacency.Origin.Position, originIndex);
BreakPointTranscript partner = new BreakPointTranscript(partnerTranscript, adjacency.Partner.Position, partnerIndex);
(BreakPointTranscript first, BreakPointTranscript second) = originOnReverseStrand ? (partner, origin) : (origin, partner);
string hgvsCoding = GetHgvsCoding(first, second);
geneFusions.Add(new GeneFusion(partnerExon, partnerIntron, hgvsCoding));
}
if (geneFusions.Count == 0)
{
continue;
}
var annotatedGeneFusion = new AnnotatedGeneFusion(originExon, originIntron, geneFusions.ToArray());
transcriptIdToGeneFusions[originTranscript.Id.WithVersion] = annotatedGeneFusion;
}
}
AltAminoAcids, string RefCodons, string AltCodons, string TranscriptAltAllele, string TranscriptRefAllele) AnnotateTranscript(ITranscript transcript, ISimpleVariant variant, AminoAcids aminoAcids, ISequence refSequence)
{
bool onReverseStrand = transcript.Gene.OnReverseStrand;
var start = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.Start);
var end = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.End);
var position = GetMappedPosition(transcript.TranscriptRegions, start.Region, start.Index, end.Region,
end.Index, variant, onReverseStrand, transcript.Translation?.CodingRegion, transcript.StartExonPhase,
variant.Type == VariantType.insertion);
var codingSequence = GetCodingSequence(transcript, refSequence);
var cdnaSequence = GetCdnaSequence(transcript, refSequence);
string transcriptAltAllele = HgvsUtilities.GetTranscriptAllele(variant.AltAllele, onReverseStrand);
var codons = Codons.GetCodons(transcriptAltAllele, position.CdsStart, position.CdsEnd, position.ProteinStart, position.ProteinEnd, codingSequence);
var aa = aminoAcids.Translate(codons.Reference, codons.Alternate);
(aa, position.ProteinStart, position.ProteinEnd) = TryTrimAminoAcidsAndUpdateProteinPositions(aa, position.ProteinStart, position.ProteinEnd);
(position.CoveredCdnaStart, position.CoveredCdnaEnd) = transcript.TranscriptRegions.GetCoveredCdnaPositions(position.CdnaStart, start.Index, position.CdnaEnd, end.Index, onReverseStrand);
(position.CoveredCdsStart, position.CoveredCdsEnd, position.CoveredProteinStart, position.CoveredProteinEnd) = MappedPositionUtilities.GetCoveredCdsAndProteinPositions(position.CoveredCdnaStart, position.CoveredCdnaEnd, transcript.StartExonPhase, transcript.Translation?.CodingRegion);
var transcriptRefAllele = GetTranscriptRefAllele(position, cdnaSequence, variant, onReverseStrand);
SequenceChange coveredAa;
// only generate the covered version of ref & alt alleles when CDS start/end is -1
if (position.CdsStart == -1 || position.CdsEnd == -1)
{
coveredAa = GetCoveredAa(aminoAcids, transcriptAltAllele, position.CoveredCdsStart, position.CoveredCdsEnd, position.CoveredProteinStart, position.CoveredProteinEnd, codingSequence);
(coveredAa, position.CoveredProteinStart, position.CoveredProteinEnd) = TryTrimAminoAcidsAndUpdateProteinPositions(coveredAa, position.CoveredProteinStart, position.CoveredProteinEnd);
}
else
{
coveredAa = aa;
position.CoveredProteinStart = position.ProteinStart;
position.CoveredProteinEnd = position.ProteinEnd;
}
var positionalEffect = GetPositionalEffect(transcript, variant, position, aa.Reference, aa.Alternate,
position.CoveredCdnaStart, position.CoveredCdnaEnd, position.CoveredCdsStart, position.CoveredCdsEnd);
var variantEffect = new VariantEffect(positionalEffect, variant, transcript, aa.Reference, aa.Alternate,
codons.Reference, codons.Alternate, position.ProteinStart, coveredAa.Reference, coveredAa.Alternate);
return(variantEffect, position, aa.Reference, aa.Alternate, codons.Reference, codons.Alternate, transcriptAltAllele, transcriptRefAllele);
}
private static IMappedPosition GetMappedPosition(ITranscriptRegion[] regions, ITranscriptRegion startRegion,
int startIndex, ITranscriptRegion endRegion, int endIndex, IInterval variant, bool onReverseStrand,
ICodingRegion codingRegion, byte startExonPhase, bool isInsertion)
{
(int cdnaStart, int cdnaEnd) = MappedPositionUtilities.GetCdnaPositions(startRegion, endRegion, variant, onReverseStrand, isInsertion);
if (onReverseStrand)
{
Swap.Int(ref cdnaStart, ref cdnaEnd);
}
(int cdsStart, int cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, cdnaStart, cdnaEnd,
startExonPhase, isInsertion);
int proteinStart = MappedPositionUtilities.GetProteinPosition(cdsStart);
int proteinEnd = MappedPositionUtilities.GetProteinPosition(cdsEnd);
(int exonStart, int exonEnd, int intronStart, int intronEnd) = regions.GetExonsAndIntrons(startIndex, endIndex);
return(new MappedPosition(cdnaStart, cdnaEnd, cdsStart, cdsEnd, proteinStart, proteinEnd, exonStart,
exonEnd, intronStart, intronEnd, startIndex, endIndex));
}
AltAminoAcids, string RefCodons, string AltCodons, string TranscriptAltAllele) AnnotateTranscript(ITranscript transcript, ISimpleVariant variant, AminoAcids aminoAcids,
ISequence refSequence)
{
var onReverseStrand = transcript.Gene.OnReverseStrand;
var start = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.Start);
var end = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.End);
var position = GetMappedPosition(transcript.TranscriptRegions, start.Region, start.Index, end.Region,
end.Index, variant, onReverseStrand, transcript.Translation?.CodingRegion, transcript.StartExonPhase,
variant.Type == VariantType.insertion);
var transcriptRefAllele = HgvsUtilities.GetTranscriptAllele(variant.RefAllele, onReverseStrand);
var transcriptAltAllele = HgvsUtilities.GetTranscriptAllele(variant.AltAllele, onReverseStrand);
var codingSequence = transcript.Translation == null
? null
: new CodingSequence(refSequence, transcript.Translation.CodingRegion, transcript.TranscriptRegions,
transcript.Gene.OnReverseStrand, transcript.StartExonPhase);
var codons = Codons.GetCodons(transcriptRefAllele, transcriptAltAllele, position.CdsStart, position.CdsEnd,
position.ProteinStart, position.ProteinEnd, codingSequence);
var coveredCdna = transcript.TranscriptRegions.GetCoveredCdnaPositions(position.CdnaStart, start.Index,
position.CdnaEnd, end.Index, onReverseStrand);
var coveredCds = MappedPositionUtilities.GetCoveredCdsPositions(coveredCdna.Start, coveredCdna.End,
transcript.StartExonPhase, transcript.Translation?.CodingRegion);
var aa = aminoAcids.Translate(codons.Reference, codons.Alternate);
var positionalEffect = GetPositionalEffect(transcript, variant, position, aa.Reference, aa.Alternate,
coveredCdna.Start, coveredCdna.End, coveredCds.Start, coveredCds.End);
var variantEffect = new VariantEffect(positionalEffect, variant, transcript, aa.Reference, aa.Alternate,
codons.Reference, codons.Alternate, position.ProteinStart);
return(variantEffect, position, aa.Reference, aa.Alternate, codons.Reference, codons.Alternate,
transcriptAltAllele);
}
