public void GetHgvsCoding_BothInUtr()
{
var first = new BreakPointTranscript(_enst00000427024, 131470304, 4);
var second = new BreakPointTranscript(_enst00000425361, 130190636, 3);
string observedResult = GeneFusionUtilities.GetHgvsCoding(first, second);
Assert.Equal("MZT2A{ENST00000427024.5}:c.?_-12_MZT2B{ENST00000425361.5}:c.378_?", observedResult);
}
public void GetHgvsCoding_FirstInCodingRegion_SecondIn5PrimeUtr()
{
var first = new BreakPointTranscript(_enst00000427024, 131488839, 5);
var second = new BreakPointTranscript(_enst00000425361, 130181730, 0);
string observedResult = GeneFusionUtilities.GetHgvsCoding(first, second);
Assert.Equal("MZT2A{ENST00000427024.5}:c.1_278+3037_MZT2B{ENST00000425361.5}:c.-7_?", observedResult);
}
public void GetHgvsCoding_FirstIn3PrimeUtr_SecondInCodingRegion()
{
var first = new BreakPointTranscript(_enst00000427024, 131492340, 6);
var second = new BreakPointTranscript(_enst00000425361, 130185834, 3);
string observedResult = GeneFusionUtilities.GetHgvsCoding(first, second);
Assert.Equal("MZT2A{ENST00000427024.5}:c.?_426_MZT2B{ENST00000425361.5}:c.210+3059_368", observedResult);
}
public void GetHgvsCoding_BothInCodingRegion()
{
var first = new BreakPointTranscript(_enst00000427024, 131488839, 5);
var second = new BreakPointTranscript(_enst00000425361, 130185834, 3);
string observedResult = GeneFusionUtilities.GetHgvsCoding(first, second);
Assert.Equal("MZT2A{ENST00000427024.5}:c.1_278+3037_MZT2B{ENST00000425361.5}:c.210+3059_368", observedResult);
}
public void ComputeGeneFusions_ReturnNull_NoFusions()
{
var chromosome = new Chromosome("chr1", "1", 0);
var chromosome2 = new Chromosome("chr6", "6", 5);
var transcriptId = CompactId.Convert("ENST00000491426", 2);
var transcriptId2 = CompactId.Convert("ENST00000313382", 9);
var breakEnds = new IBreakEnd[]
{
new BreakEnd(chromosome, chromosome2, 31410878, 42248252, true, false)
};
var transcriptRegions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 144890592, 144904679, 1, 670)
};
var transcriptRegions2 = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 144851424, 145040002, 1, 8150)
};
var transcript = new Mock <ITranscript>();
transcript.SetupGet(x => x.Chromosome).Returns(chromosome);
transcript.SetupGet(x => x.Gene.OnReverseStrand).Returns(true);
transcript.SetupGet(x => x.Gene.Symbol).Returns("PDE4DIP");
transcript.SetupGet(x => x.Translation.CodingRegion).Returns(new CodingRegion(144890975, 144904679, 1, 287, 287));
transcript.SetupGet(x => x.Start).Returns(144890592);
transcript.SetupGet(x => x.End).Returns(144904679);
transcript.SetupGet(x => x.Source).Returns(Source.Ensembl);
transcript.SetupGet(x => x.Id).Returns(transcriptId);
transcript.SetupGet(x => x.TranscriptRegions).Returns(transcriptRegions);
var transcript2 = new Mock <ITranscript>();
transcript2.SetupGet(x => x.Chromosome).Returns(chromosome2);
transcript2.SetupGet(x => x.Gene.OnReverseStrand).Returns(true);
transcript2.SetupGet(x => x.Gene.Symbol).Returns("PDE4DIP");
transcript2.SetupGet(x => x.Translation.CodingRegion).Returns(new CodingRegion(144852458, 145039609, 394, 7116, 6723));
transcript2.SetupGet(x => x.Start).Returns(144852458);
transcript2.SetupGet(x => x.End).Returns(145039609);
transcript2.SetupGet(x => x.Source).Returns(Source.Ensembl);
transcript2.SetupGet(x => x.Id).Returns(transcriptId2);
transcript2.SetupGet(x => x.TranscriptRegions).Returns(transcriptRegions2);
var fusedTranscriptCandidates = new[] { transcript2.Object };
var observedResult = GeneFusionUtilities.GetGeneFusionAnnotation(breakEnds, transcript.Object, fusedTranscriptCandidates);
Assert.Null(observedResult);
}
public void ComputeGeneFusions_ReturnOneGeneFusion()
{
var chromosome = new Chromosome("chr1", "1", 0);
var transcriptId = CompactId.Convert("ENST00000367819", 2);
var transcriptId2 = CompactId.Convert("ENST00000367818", 3);
var breakEnds = new IBreakEnd[]
{
new BreakEnd(chromosome, chromosome, 168512199, 168548478, false, false),
new BreakEnd(chromosome, chromosome, 168548478, 168512199, false, false)
};
var transcriptRegions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 3, 168510003, 168510358, 210, 565),
new TranscriptRegion(TranscriptRegionType.Intron, 2, 168510359, 168511230, 95, 210),
new TranscriptRegion(TranscriptRegionType.Exon, 2, 168511231, 168511345, 95, 209),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 168511346, 168513141, 94, 95),
new TranscriptRegion(TranscriptRegionType.Exon, 1, 168513142, 168513235, 1, 94)
};
var transcriptRegions2 = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 168545711, 168545936, 1, 226),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 168545937, 168549300, 226, 227),
new TranscriptRegion(TranscriptRegionType.Exon, 2, 168549301, 168549415, 227, 341),
new TranscriptRegion(TranscriptRegionType.Intron, 2, 168549416, 168550289, 341, 342),
new TranscriptRegion(TranscriptRegionType.Exon, 3, 168550290, 168551315, 342, 1367)
};
var transcript = new Mock <ITranscript>();
transcript.SetupGet(x => x.Chromosome).Returns(chromosome);
transcript.SetupGet(x => x.Gene.OnReverseStrand).Returns(true);
transcript.SetupGet(x => x.Gene.Symbol).Returns("XCL2");
transcript.SetupGet(x => x.Translation.CodingRegion).Returns(new CodingRegion(168510190, 168513202, 34, 378, 345));
transcript.SetupGet(x => x.Start).Returns(168510003);
transcript.SetupGet(x => x.End).Returns(168513235);
transcript.SetupGet(x => x.Source).Returns(Source.Ensembl);
transcript.SetupGet(x => x.Id).Returns(transcriptId);
transcript.SetupGet(x => x.TranscriptRegions).Returns(transcriptRegions);
var transcript2 = new Mock <ITranscript>();
transcript2.SetupGet(x => x.Chromosome).Returns(chromosome);
transcript2.SetupGet(x => x.Gene.OnReverseStrand).Returns(false);
transcript2.SetupGet(x => x.Gene.Symbol).Returns("XCL1");
transcript2.SetupGet(x => x.Translation.CodingRegion).Returns(new CodingRegion(168545876, 168550458, 166, 510, 345));
transcript2.SetupGet(x => x.Start).Returns(168545711);
transcript2.SetupGet(x => x.End).Returns(168551315);
transcript2.SetupGet(x => x.Source).Returns(Source.Ensembl);
transcript2.SetupGet(x => x.Id).Returns(transcriptId2);
transcript2.SetupGet(x => x.TranscriptRegions).Returns(transcriptRegions2);
var fusedTranscriptCandidates = new[] { transcript2.Object };
var expectedGeneFusions = new IGeneFusion[]
{
new GeneFusion(null, 1, "XCL1{ENST00000367818.3}:c.1_62-823_XCL2{ENST00000367819.2}:c.62-854_345")
};
var observedResult = GeneFusionUtilities.GetGeneFusionAnnotation(breakEnds, transcript.Object, fusedTranscriptCandidates);
Assert.Single(observedResult.GeneFusions);
Assert.Equal(expectedGeneFusions[0].Exon, observedResult.GeneFusions[0].Exon);
Assert.Equal(expectedGeneFusions[0].Intron, observedResult.GeneFusions[0].Intron);
Assert.Equal(expectedGeneFusions[0].HgvsCoding, observedResult.GeneFusions[0].HgvsCoding);
}
