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TASK-2103 #224

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Sep 27, 2022
Merged

TASK-2103 #224

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21 changes: 21 additions & 0 deletions .../main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariantEvidence.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ public class ClinicalVariantEvidence {
private boolean fullyExplainPhenotypes;
private List<String> compoundHeterozygousVariantIds;
private RoleInCancer roleInCancer;
@Deprecated
private boolean actionable;

private ClinicalEvidenceReview review;
Expand All @@ -52,6 +53,7 @@ public ClinicalVariantEvidence() {
review = new ClinicalEvidenceReview();
}

@Deprecated
public ClinicalVariantEvidence(String interpretationMethodName, List<Phenotype> phenotypes, GenomicFeature genomicFeature,
List<ModeOfInheritance> modeOfInheritances, String panelId, VariantClassification classification,
Penetrance penetrance, double score, boolean fullyExplainPhenotypes,
Expand All @@ -72,6 +74,25 @@ public ClinicalVariantEvidence(String interpretationMethodName, List<Phenotype>
this.review = review;
}

public ClinicalVariantEvidence(String interpretationMethodName, List<Phenotype> phenotypes, GenomicFeature genomicFeature,
List<ModeOfInheritance> modeOfInheritances, String panelId, VariantClassification classification,
Penetrance penetrance, double score, boolean fullyExplainPhenotypes,
List<String> compoundHeterozygousVariantIds, RoleInCancer roleInCancer,
ClinicalEvidenceReview review) {
this.interpretationMethodName = interpretationMethodName;
this.phenotypes = phenotypes;
this.genomicFeature = genomicFeature;
this.modeOfInheritances = modeOfInheritances;
this.panelId = panelId;
this.classification = classification;
this.penetrance = penetrance;
this.score = score;
this.fullyExplainPhenotypes = fullyExplainPhenotypes;
this.compoundHeterozygousVariantIds = compoundHeterozygousVariantIds;
this.roleInCancer = roleInCancer;
this.review = review;
}

@Override
public String toString() {
final StringBuilder sb = new StringBuilder("ClinicalVariantEvidence{");
Expand Down
56 changes: 8 additions & 48 deletions biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java
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Expand Up @@ -58,29 +58,24 @@ public abstract class ClinicalVariantCreator {
protected Penetrance penetrance;

protected Map<String, RoleInCancer> roleInCancer;
protected Map<String, List<String>> actionableVariants;

protected String assembly;

public ClinicalVariantCreator(List<DiseasePanel> diseasePanels, Disorder disorder,
List<ModeOfInheritance> modeOfInheritances, Penetrance penetrance,
Map<String, RoleInCancer> roleInCancer, Map<String, List<String>> actionableVariants,
String assembly) {
this(diseasePanels, disorder, modeOfInheritances, penetrance, roleInCancer, actionableVariants, assembly,
new ArrayList<>(proteinCoding), new ArrayList<>(extendedLof));
public ClinicalVariantCreator(List<DiseasePanel> diseasePanels, Disorder disorder, List<ModeOfInheritance> modeOfInheritances,
Penetrance penetrance, Map<String, RoleInCancer> roleInCancer, String assembly) {
this(diseasePanels, disorder, modeOfInheritances, penetrance, roleInCancer, assembly, new ArrayList<>(proteinCoding),
new ArrayList<>(extendedLof));
}

public ClinicalVariantCreator(List<DiseasePanel> diseasePanels, Disorder disorder,
List<ModeOfInheritance> modeOfInheritances, Penetrance penetrance,
Map<String, RoleInCancer> roleInCancer, Map<String, List<String>> actionableVariants,
String assembly, List<String> biotypes, List<String> soNames) {
public ClinicalVariantCreator(List<DiseasePanel> diseasePanels, Disorder disorder, List<ModeOfInheritance> modeOfInheritances,
Penetrance penetrance, Map<String, RoleInCancer> roleInCancer, String assembly, List<String> biotypes,
List<String> soNames) {

this.diseasePanels = diseasePanels;
this.disorder = disorder;
this.modeOfInheritances = modeOfInheritances;
this.penetrance = penetrance;
this.roleInCancer = roleInCancer;
this.actionableVariants = actionableVariants;
this.assembly = assembly;

this.biotypeSet = new HashSet<>();
Expand Down Expand Up @@ -113,20 +108,6 @@ public List<ClinicalVariant> createSecondaryFindings(List<Variant> variants) {
for (Variant variant : variants) {
List<ClinicalVariantEvidence> clinicalVariantEvidences = new ArrayList<>();

// Tier 3, actionable variants
if (MapUtils.isNotEmpty(actionableVariants)) {
if (variant.getAnnotation() != null && actionableVariants.containsKey(variant.toString())) {
if (CollectionUtils.isNotEmpty(variant.getAnnotation().getConsequenceTypes())) {
for (ConsequenceType ct : variant.getAnnotation().getConsequenceTypes()) {
clinicalVariantEvidences.addAll(createClinicalVariantEvidences("", null, ct, variant));
}
} else {
// We create the evidences anyway!
clinicalVariantEvidences.addAll(createClinicalVariantEvidences("", null, null, variant));
}
}
}

// If we have clinical variant evidences, then we have to create the clinical variant
if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
Expand Down Expand Up @@ -267,27 +248,6 @@ protected ClinicalVariantEvidence createClinicalVariantEvidence(GenomicFeature g
}
}

// Actionable management
if (MapUtils.isNotEmpty(actionableVariants) && actionableVariants.containsKey(variant.getId())) {
clinicalVariantEvidence.setActionable(true);
// Set tier 3 only if it is null or untiered
if (tier == null || UNTIERED.equals(tier)) {
clinicalVariantEvidence.getClassification().setTier(TIER_3);
} else {
clinicalVariantEvidence.getClassification().setTier(tier);
}
// Add 'actionable' phenotypes
if (CollectionUtils.isNotEmpty(actionableVariants.get(variant.getId()))) {
List<Phenotype> evidences = new ArrayList<>();
for (String phenotypeId : actionableVariants.get(variant.getId())) {
evidences.add(new Phenotype(phenotypeId, phenotypeId, ""));
}
if (CollectionUtils.isNotEmpty(evidences)) {
clinicalVariantEvidence.setPhenotypes(evidences);
}
}
}

return clinicalVariantEvidence;
}

Expand Down Expand Up @@ -347,7 +307,7 @@ protected List<ClinicalVariantEvidence> createClinicalVariantEvidences(String ti
}
}
} else {
// We report events without panels, e.g., actionable variants (tier 3)
// We report events without panels
if (CollectionUtils.isNotEmpty(soTerms)) {
ClinicalVariantEvidence clinicalVariantEvidence = createClinicalVariantEvidence(genomicFeature, null, modeOfInheritances,
penetrance, tier, variant);
Expand Down
6 changes: 2 additions & 4 deletions ...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java
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Expand Up @@ -41,13 +41,11 @@ public class DefaultClinicalVariantCreator extends ClinicalVariantCreator {

private boolean includeUntieredVariants;

public DefaultClinicalVariantCreator(Map<String, ClinicalProperty.RoleInCancer> roleInCancer,
Map<String, List<String>> actionableVariants, Disorder disorder,
public DefaultClinicalVariantCreator(Map<String, ClinicalProperty.RoleInCancer> roleInCancer, Disorder disorder,
List<ModeOfInheritance> modeOfInheritances, Penetrance penetrance,
List<DiseasePanel> diseasePanels, List<String> biotypes, List<String> soNames,
boolean includeUntieredVariants) {
super(diseasePanels, disorder, modeOfInheritances, penetrance, roleInCancer, actionableVariants, null,
biotypes, soNames);
super(diseasePanels, disorder, modeOfInheritances, penetrance, roleInCancer, null, biotypes, soNames);

this.includeUntieredVariants = includeUntieredVariants;
}
Expand Down
21 changes: 2 additions & 19 deletions ...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java
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Expand Up @@ -41,10 +41,9 @@

public class TeamClinicalVariantCreator extends ClinicalVariantCreator {

public TeamClinicalVariantCreator(List<DiseasePanel> diseasePanels, Map<String, RoleInCancer> roleInCancer,
Map<String, List<String>> actionableVariants, Disorder disorder,
public TeamClinicalVariantCreator(List<DiseasePanel> diseasePanels, Map<String, RoleInCancer> roleInCancer, Disorder disorder,
List<ModeOfInheritance> modeOfInheritances, Penetrance penetrance) {
super(diseasePanels, disorder, modeOfInheritances, penetrance, roleInCancer, actionableVariants, null);
super(diseasePanels, disorder, modeOfInheritances, penetrance, roleInCancer, null);
}

@Override
Expand Down Expand Up @@ -106,22 +105,6 @@ public List<ClinicalVariant> create(List<Variant> variants) throws Interpretatio
}
}

// Tier 3, actionable variants
if (!hasTier && MapUtils.isNotEmpty(actionableVariants)) {
if (variant.getAnnotation() != null && actionableVariants.containsKey(variant.getId())) {
if (CollectionUtils.isNotEmpty(variant.getAnnotation().getConsequenceTypes())) {
for (ConsequenceType ct : variant.getAnnotation().getConsequenceTypes()) {
if (ct.getBiotype() != null && proteinCoding.contains(ct.getBiotype())) {
clinicalVariantEvidences.addAll(createClinicalVariantEvidences(UNTIERED, null, ct, variant));
}
}
} else {
// We create the clinical variant evidences anyway!
clinicalVariantEvidences.addAll(createClinicalVariantEvidences(UNTIERED, null, null, variant));
}
}
}

// If we have clinical variant evidences, then we have to create the clinical variant
if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
Expand Down
6 changes: 2 additions & 4 deletions ...-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java
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Expand Up @@ -55,11 +55,9 @@ public class TieringClinicalVariantCreator extends ClinicalVariantCreator {
"SO:0001821", "inframe_insertion", "SO:0001822", "inframe_deletion", "SO:0001583", "missense_variant",
"SO:0001630", "splice_region_variant", "SO:0001626", "incomplete_terminal_codon_variant"));

public TieringClinicalVariantCreator(List<DiseasePanel> diseasePanels, Map<String, RoleInCancer> roleInCancer,
Map<String, List<String>> actionableVariants, Disorder disorder,
public TieringClinicalVariantCreator(List<DiseasePanel> diseasePanels, Map<String, RoleInCancer> roleInCancer, Disorder disorder,
ModeOfInheritance modeOfInheritance, Penetrance penetrance, String assembly) {
super(diseasePanels, disorder, Collections.singletonList(modeOfInheritance), penetrance, roleInCancer,
actionableVariants, assembly);
super(diseasePanels, disorder, Collections.singletonList(modeOfInheritance), penetrance, roleInCancer, assembly);
}

@Override
Expand Down