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add alphaMissense Annotation #284

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dac8965
Add alphaMissense pipeline
JunheZoooo Aug 24, 2024
1e34174
Add alphaMissense pipeline
JunheZoooo Aug 24, 2024
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153 changes: 77 additions & 76 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -86,82 +86,83 @@ docker run -e GENOMENEXUS_BASE=https://grch38.genomenexus.org -v ${PWD}:/wd geno
```

### Annotation fields
| Field | Source | Note |
| --| -- | -- |
| Hugo_Symbol |||
|Entrez_Gene_Id|||
|Center|||
|NCBI_Build|||
|Chromosome|GN response / Input||
|Start_Position|GN response / Input||
|End_Position|GN response / Input||
|Strand|||
|Consequence|||
|Variant_Classification|||
|Variant_Type|||
|Reference_Allele|GN response / Input||
|Tumor_Seq_Allele1|||
|Tumor_Seq_Allele2|GN response / Input||
|dbSNP_RS|||
|dbSNP_Val_Status|||
|Tumor_Sample_Barcode|||
|Matched_Norm_Sample_Barcode|||
|Match_Norm_Seq_Allele1|||
|Match_Norm_Seq_Allele2|||
|Tumor_Validation_Allele1|||
|Tumor_Validation_Allele2|||
|Match_Norm_Validation_Allele1|||
|Match_Norm_Validation_Allele2|||
|Verification_Status|||
|Validation_Status|||
|Mutation_Status|||
|Sequencing_Phase|||
|Sequence_Source|||
|Validation_Method|||
|Score|||
|BAM_File|||
|Sequencer|||
|t_ref_count|||
|t_alt_count|||
|n_ref_count|||
|n_alt_count|||
|HGVSc|||
|HGVSp|||
|HGVSp_Short|||
|Transcript_ID|||
|RefSeq|VEP||
|Protein_position|VEP||
|Codons|VEP||
|Exon_Number|VEP||
|gnomAD_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_AFR_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_AMR_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_ASJ_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_EAS_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_FIN_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_NFE_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_OTH_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_SAS_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|MA:FIS|Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
|MA:FImpact|Mutation Assessor|Need to add "mutation_assessor" in genomenexus.enrichment_fields"|
|MA:link.MSA|Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
|MA:link.PDB|Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
|Polyphen_Prediction|Polyphen|Need to add "polyphen" in "genomenexus.enrichment_fields"|
|Polyphen_Score|Polyphen|Need to add "polyphen" in "genomenexus.enrichment_fields"|
|SIFT_Prediction|SIFT|Need to add "sift" in "genomenexus.enrichment_fields"|
|SIFT_Score|SIFT|Need to add "sift" in "genomenexus.enrichment_fields"|
|Ref_Tri||Need to add "nucleotide_context" in "genomenexus.enrichment_field"|
|Var_Tri||Need to add "nucleotide_context" in "genomenexus.enrichment_field"|
|oncokb_geneExist|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
|oncokb_highestDXLevel|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
|oncokb_highestPXLevel|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
|oncokb_highestResistanceLevel|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_highestSensitiveLevel |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_mutationEffect|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
|oncokb_mutationEffectCitations|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_oncogenic|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_variantExist |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
|Annotation_Status||FAILED / SUCCESS|
| Field | Source | Note |
|--------------------------------| -- | -- |
| Hugo_Symbol |||
| Entrez_Gene_Id |||
| Center |||
| NCBI_Build |||
| Chromosome |GN response / Input||
| Start_Position |GN response / Input||
| End_Position |GN response / Input||
| Strand |||
| Consequence |||
| Variant_Classification |||
| Variant_Type |||
| Reference_Allele |GN response / Input||
| Tumor_Seq_Allele1 |||
| Tumor_Seq_Allele2 |GN response / Input||
| dbSNP_RS |||
| dbSNP_Val_Status |||
| Tumor_Sample_Barcode |||
| Matched_Norm_Sample_Barcode |||
| Match_Norm_Seq_Allele1 |||
| Match_Norm_Seq_Allele2 |||
| Tumor_Validation_Allele1 |||
| Tumor_Validation_Allele2 |||
| Match_Norm_Validation_Allele1 |||
| Match_Norm_Validation_Allele2 |||
| Verification_Status |||
| Validation_Status |||
| Mutation_Status |||
| Sequencing_Phase |||
| Sequence_Source |||
| Validation_Method |||
| Score |||
| BAM_File |||
| Sequencer |||
| t_ref_count |||
| t_alt_count |||
| n_ref_count |||
| n_alt_count |||
| HGVSc |||
| HGVSp |||
| HGVSp_Short |||
| Transcript_ID |||
| RefSeq |VEP||
| Protein_position |VEP||
| Codons |VEP||
| Exon_Number |VEP||
| AlphaMissense |VEP||
| gnomAD_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_AFR_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_AMR_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_ASJ_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_EAS_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_FIN_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_NFE_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_OTH_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| gnomAD_SAS_AF |myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
| MA:FIS |Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
| MA:FImpact |Mutation Assessor|Need to add "mutation_assessor" in genomenexus.enrichment_fields"|
| MA:link.MSA |Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
| MA:link.PDB |Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
| Polyphen_Prediction |Polyphen|Need to add "polyphen" in "genomenexus.enrichment_fields"|
| Polyphen_Score |Polyphen|Need to add "polyphen" in "genomenexus.enrichment_fields"|
| SIFT_Prediction |SIFT|Need to add "sift" in "genomenexus.enrichment_fields"|
| SIFT_Score |SIFT|Need to add "sift" in "genomenexus.enrichment_fields"|
| Ref_Tri ||Need to add "nucleotide_context" in "genomenexus.enrichment_field"|
| Var_Tri ||Need to add "nucleotide_context" in "genomenexus.enrichment_field"|
| oncokb_geneExist |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_highestDXLevel |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_highestPXLevel |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_highestResistanceLevel |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_highestSensitiveLevel |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_mutationEffect |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_mutationEffectCitations |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_oncogenic |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| oncokb_variantExist |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
| Annotation_Status ||FAILED / SUCCESS|


### Add additional annotation columns
Expand Down
3 changes: 2 additions & 1 deletion annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java
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Expand Up @@ -34,7 +34,6 @@

import java.time.Duration;
import java.time.Instant;
import java.time.temporal.Temporal;
import java.util.*;
import org.mskcc.cbio.maf.MafUtil;

Expand Down Expand Up @@ -409,13 +408,15 @@ else if (stripMatchingBases.equals("first")) {
annotationUtil.resolveConsequence(canonicalTranscript),
annotationUtil.resolveProteinPosition(canonicalTranscript, mRecord),
annotationUtil.resolveExon(canonicalTranscript),
annotationUtil.resolveAlphaMissense(canonicalTranscript),
mRecord.getAdditionalProperties());
if (addOriginalGenomicLocation) {
annotatedRecord.setOriginalGenomicLocation(genomeNexusOriginalChromosome, genomeNexusOriginalStartPosition, genomeNexusOriginalEndPosition, genomeNexusOriginalReferenceAllele, genomeNexusOriginalTumorSeqAllele1, genomeNexusOriginalTumorSeqAllele2);
}
if (noteColumn) {
annotatedRecord.setGenomicLocationExplanation(gnResponse.getGenomicLocationExplanation() != null ? gnResponse.getGenomicLocationExplanation() : "");
}
annotatedRecord.setAlphaMissenseFields(annotationUtil.resolveAlphaMissense(canonicalTranscript));

if (enrichmentFields.contains("my_variant_info")) {
// get the gnomad allele frequency
Expand Down
18 changes: 18 additions & 0 deletions annotator/src/main/java/org/cbioportal/annotator/util/AnnotationUtil.java
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Expand Up @@ -376,6 +376,24 @@ public String resolveSiftScore(TranscriptConsequenceSummary canonicalTranscript)
return parseDoubleAsString(toReturn);
}

public String resolveAlphaMissense(TranscriptConsequenceSummary canonicalTranscript) {
String pathogenicity = null;
String score = null;
String res = "N/A";
if (canonicalTranscript != null && canonicalTranscript.getAlphaMissense() != null){
AlphaMissense alphaMissense = canonicalTranscript.getAlphaMissense();
if (alphaMissense.getPathogenicity() != null){
pathogenicity = alphaMissense.getPathogenicity();
}
if (alphaMissense.getScore() != null){
score = " (" + alphaMissense.getScore() + ")";
}
res = pathogenicity + score;
}
return res;

}

public String resolvePolyphenPrediction(TranscriptConsequenceSummary canonicalTranscript) {
String polyphenPrediction = "";
if (canonicalTranscript != null && canonicalTranscript.getPolyphenPrediction() != null) {
Expand Down
10 changes: 9 additions & 1 deletion annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@ public class AnnotatedRecord extends MutationRecord {
protected String consequence;
protected String proteinPosition;
protected String exon;
protected String alphaMissense;
protected String gnomadAlleleFrequency;
protected String gnomadAlleleFrequencyAFR;
protected String gnomadAlleleFrequencyAMR;
Expand Down Expand Up @@ -120,6 +121,7 @@ public AnnotatedRecord(String hugoSymbol,
String consequence,
String proteinPosition,
String exon,
String alphaMissense,
Map<String, String> additionalProperties
) {
super(hugoSymbol,
Expand Down Expand Up @@ -228,6 +230,7 @@ public AnnotatedRecord(MutationRecord mRecord) {
this.consequence = additionalProperties.get("Consequence") != null ? additionalProperties.get("Consequence") : "";
this.proteinPosition = additionalProperties.get("Protein_position") != null ? additionalProperties.get("Protein_position") : "";
this.exon = additionalProperties.get("exon") != null ? additionalProperties.get("exon") : "";
this.alphaMissense = additionalProperties.get("alphaMissense") != null ? additionalProperties.get("alphaMissense") : "";
this.additionalProperties = additionalProperties;
}

Expand Down Expand Up @@ -297,7 +300,11 @@ public void setSiftFields(String siftPrediction,
addAdditionalProperty("SIFT_Prediction", siftPrediction);
addAdditionalProperty("SIFT_Score", siftScore);
}


public void setAlphaMissenseFields(String alphaMissense){
addAdditionalProperty("AlphaMissense", alphaMissense);
}

public void setMutationAssessorFields(String maFunctionalImpact,
String maFunctionalImpactScore,
String maLinkMSA,
Expand Down Expand Up @@ -506,6 +513,7 @@ private void addAnnotatedFieldsToHeader() {
header.add("RefSeq");
header.add("Protein_position");
header.add("Codons");
header.add("AlphaMissense");
header.add("Exon_Number");
header.add(header.indexOf("Variant_Classification"), "Consequence");
}
Expand Down
8 changes: 7 additions & 1 deletion ...tator/src/test/java/org/cbioportal/annotator/mixin/TranscriptConsequenceSummaryMixin.java
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Expand Up @@ -43,4 +43,10 @@ public class TranscriptConsequenceSummaryMixin {

@JsonProperty("exon")
private String exon;
}

@JsonProperty("pathogencity")
private String pathogencity;

@JsonProperty("score")
private String pathogencityScore;;
}
4 changes: 2 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -100,12 +100,12 @@
<dependency>
<groupId>com.github.genome-nexus.genome-nexus-java-api-client</groupId>
<artifactId>genomeNexusPublicApiClient</artifactId>
<version>7128635f2704eb9ebe9c3062770f748ab4127003</version>
<version>8cf8851bd2d041db9ebef8710e6d019e6f0b9208</version>
</dependency>
<dependency>
<groupId>com.github.genome-nexus.genome-nexus-java-api-client</groupId>
<artifactId>genomeNexusInternalApiClient</artifactId>
<version>7128635f2704eb9ebe9c3062770f748ab4127003</version>
<version>8cf8851bd2d041db9ebef8710e6d019e6f0b9208</version>
</dependency>
<dependency>
<groupId>net.bytebuddy</groupId>
Expand Down