From 092773efacf87035d566f0541de1394dda2d1172 Mon Sep 17 00:00:00 2001 From: "Zhaoyuan (Ryan) Fu" Date: Thu, 12 Sep 2024 13:02:28 -0400 Subject: [PATCH] Demo rfc80 poc mutation data count unit tests (#10981) * Fix CNA table definition --- .../web/parameter/GenomicDataFilter.java | 7 ++ .../db-scripts/clickhouse/clickhouse.sql | 6 +- .../StudyViewFilterMapper.xml | 1 + .../mybatisclickhouse/StudyViewMapper.xml | 1 + .../GenomicDataFilterTest.java | 111 ++++++++++++++++++ .../StudyViewMapperTest.java | 4 +- src/test/resources/clickhouse_data.sql | 83 +++++++------ 7 files changed, 169 insertions(+), 44 deletions(-) create mode 100644 src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataFilterTest.java diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java b/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java index 5938595e5e7..edf95943436 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java +++ b/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java @@ -6,6 +6,13 @@ public class GenomicDataFilter extends DataFilter implements Serializable { private String hugoGeneSymbol; private String profileType; + public GenomicDataFilter() {} + + public GenomicDataFilter(String hugoGeneSymbol, String profileType) { + this.hugoGeneSymbol = hugoGeneSymbol; + this.profileType = profileType; + } + public String getHugoGeneSymbol() { return hugoGeneSymbol; } diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql index ffb18b1979d..b3b570c325c 100644 --- a/src/main/resources/db-scripts/clickhouse/clickhouse.sql +++ b/src/main/resources/db-scripts/clickhouse/clickhouse.sql @@ -298,18 +298,18 @@ SELECT sample_unique_id, cancer_study_identifier, hugo_gene_symbol, - profile_type, + replaceOne(stable_id, concat(sd.cancer_study_identifier, '_'), '') as profile_type, alteration_value FROM (SELECT sample_id, hugo_gene_symbol, - profile_type, + stable_id, alteration_value FROM (SELECT g.hugo_gene_symbol AS hugo_gene_symbol, - arrayElement(splitByString('_', assumeNotNull(gp.stable_id)), -1) AS profile_type, + gp.stable_id as stable_id, arrayMap(x -> (x = '' ? NULL : x), splitByString(',', assumeNotNull(trim(trailing ',' from ga.values)))) AS alteration_value, arrayMap(x -> (x = '' ? NULL : toInt32(x)), splitByString(',', assumeNotNull(trim(trailing ',' from gps.ordered_sample_list)))) AS sample_id FROM diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml index 7c78f4db52e..26e129d8c84 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml @@ -530,6 +530,7 @@ #{studyId} AND gpg.gene = #{mutationDataFilter.hugoGeneSymbol} + AND sgp.alteration_type = 'MUTATION_EXTENDED' ), mutated_samples AS ( SELECT DISTINCT sample_unique_id diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml index 4fad2f3b14c..e500707c8b5 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml @@ -282,6 +282,7 @@ JOIN gene_panel_to_gene_derived gpg ON sgp.gene_panel_id = gpg.gene_panel_id WHERE sample_unique_id IN () AND gpg.gene = #{genomicDataFilter.hugoGeneSymbol} + AND sgp.alteration_type = 'MUTATION_EXTENDED' ), mutated_count as ( SELECT count(distinct sample_unique_id) diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataFilterTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataFilterTest.java new file mode 100644 index 00000000000..87b6c101800 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataFilterTest.java @@ -0,0 +1,111 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static org.assertj.core.api.Assertions.assertThat; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class GenomicDataFilterTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + private static final String STUDY_ACC_TCGA = "acc_tcga"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getCNACounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + GenomicDataFilter genomicDataFilterCNA = new GenomicDataFilter("AKT1", "cna"); + List actualCountsCNA = studyViewMapper.getCNACounts(StudyViewFilterHelper.build(studyViewFilter, null), List.of(genomicDataFilterCNA)); + List expectedCountsCNA = List.of( + new GenomicDataCountItem("AKT1", "cna", List.of( + new GenomicDataCount("Homozygously deleted", "-2", 2), + new GenomicDataCount("Heterozygously deleted", "-1", 2), + new GenomicDataCount("Diploid", "0", 2), + new GenomicDataCount("Gained", "1", 2), + new GenomicDataCount("Amplified", "2", 2), + new GenomicDataCount("NA", "NA", 5) + ))); + assertThat(actualCountsCNA) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedCountsCNA); + + GenomicDataFilter genomicDataFilterGISTIC = new GenomicDataFilter("AKT1", "gistic"); + List actualCountsGISTIC = studyViewMapper.getCNACounts(StudyViewFilterHelper.build(studyViewFilter, null), List.of(genomicDataFilterGISTIC)); + List expectedCountsGISTIC = List.of( + new GenomicDataCountItem("AKT1", "gistic", List.of( + new GenomicDataCount("Homozygously deleted", "-2", 2), + new GenomicDataCount("Heterozygously deleted", "-1", 3), + new GenomicDataCount("Diploid", "0", 3), + new GenomicDataCount("Gained", "1", 3), + new GenomicDataCount("Amplified", "2", 3), + new GenomicDataCount("NA", "NA", 1) + ))); + assertThat(actualCountsGISTIC) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedCountsGISTIC); + } + + @Test + public void getMutationCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "cna"); + Map actualMutationCounts = studyViewMapper.getMutationCounts(StudyViewFilterHelper.build(studyViewFilter, null), genomicDataFilterMutation); + Map expectedMutationCounts = new HashMap<>(); + expectedMutationCounts.put("mutatedCount", 2); + expectedMutationCounts.put("notMutatedCount", 2); + expectedMutationCounts.put("notProfiledCount", 11); + assertThat(actualMutationCounts) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedMutationCounts); + } + + @Test + public void getMutationCountsByType() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "mutation"); + List actualMutationCountsByType = studyViewMapper.getMutationCountsByType(StudyViewFilterHelper.build(studyViewFilter, null), List.of(genomicDataFilterMutation)); + List expectedMutationCountsByType = List.of( + new GenomicDataCountItem("AKT1", "mutations", List.of( + new GenomicDataCount("nonsense mutation", "nonsense_mutation", 1, 1), + new GenomicDataCount("missense mutation", "missense_mutation", 1, 1) + ))); + assertThat(actualMutationCountsByType) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedMutationCountsByType); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java index b0c54597f3f..2225738959d 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java @@ -65,7 +65,7 @@ public void getMutatedGenes() { AlterationFilterHelper.build(studyViewFilter.getAlterationFilter())); assertEquals(3, alterationCountByGenes.size()); - var testBrca1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "brca1")).findFirst(); + var testBrca1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "BRCA1")).findFirst(); assert (testBrca1AlterationCount.isPresent()); assertEquals(Integer.valueOf(5), testBrca1AlterationCount.get().getTotalCount()); } @@ -118,7 +118,7 @@ public void getTotalProfiledCountsByGene() { assertEquals(3, totalProfiledCountsMap.size()); - var akt2TotalProfiledCounts = totalProfiledCountsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("akt2")).findFirst(); + var akt2TotalProfiledCounts = totalProfiledCountsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2")).findFirst(); assertTrue(akt2TotalProfiledCounts.isPresent()); assertEquals(4, akt2TotalProfiledCounts.get().getNumberOfProfiledCases().intValue()); } diff --git a/src/test/resources/clickhouse_data.sql b/src/test/resources/clickhouse_data.sql index 5dd3d7ab135..94cc12d32f4 100644 --- a/src/test/resources/clickhouse_data.sql +++ b/src/test/resources/clickhouse_data.sql @@ -34,32 +34,33 @@ insert into genetic_entity (id,entity_type,stable_id) values (20,'generic_assay' insert into genetic_entity (id,entity_type,stable_id) values (28,'generic_assay','mean_1'); insert into genetic_entity (id,entity_type,stable_id) values (29,'generic_assay','mean_2'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(207,'akt1',1,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(208,'akt2',2,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(10000,'akt3',3,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(369,'araf',4,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(472,'atm',5,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(673,'braf',6,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(672,'brca1',7,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(675,'brca2',8,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(3265,'hras',9,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(3845,'kras',10,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(4893,'nras',11,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(79501,'or4f5',12,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(148398,'samd11',13,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(26155,'noc2l',14,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2064,'erbb2',15,'protein-coding'); -insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2886,'grb7',16,'protein-coding'); -insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(3677745,'d45a',79501,1,'or4f5 d45 missense'); -insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(426644,'g145c',79501,1,'or4f5 g145 missense'); -insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(460103,'p23p',148398,1,'samd11 p23 silent'); -insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(4010395,'s146s',26155,1,'noc2l s146 silent'); -insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(1290240,'m1t',26155,1,'noc2l truncating'); -insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(4010425,'q197*',26155,1,'noc2l truncating'); +-- hugo_gene_symbol should be UPPERCASE +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(207,'AKT1',1,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(208,'AKT2',2,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(10000,'AKT3',3,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(369,'ARAF',4,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(472,'ATM',5,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(673,'BRAF',6,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(672,'BRCA1',7,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(675,'BRCA2',8,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(3265,'HRAS',9,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(3845,'KRAS',10,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(4893,'NRAS',11,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(79501,'OR4F5',12,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(148398,'SAMD11',13,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(26155,'NOC2L',14,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2064,'ERBB2',15,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2886,'GRB7',16,'protein-coding'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(3677745,'d45a',79501,1,'OR4F5 d45 missense'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(426644,'g145c',79501,1,'OR4F5 g145 missense'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(460103,'p23p',148398,1,'SAMD11 p23 silent'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(4010395,'s146s',26155,1,'NOC2L s146 silent'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(1290240,'m1t',26155,1,'NOC2L truncating'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(4010425,'q197*',26155,1,'NOC2L truncating'); insert into gene_alias (entrez_gene_id,gene_alias) values (207,'akt alias'); insert into gene_alias (entrez_gene_id,gene_alias) values (207,'akt alias2'); -insert into gene_alias (entrez_gene_id,gene_alias) values (675,'brca1 alias'); +insert into gene_alias (entrez_gene_id,gene_alias) values (675,'BRCA1 alias'); insert into reference_genome_gene (entrez_gene_id,cytoband,start,end,chr,reference_genome_id) values(207,'14q32.33',105235686,105262088,14,1); insert into reference_genome_gene (entrez_gene_id,cytoband,start,end,chr,reference_genome_id) values(207,'14q32.33',104769349,104795751,14,2); @@ -78,12 +79,14 @@ insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,geneti insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (9,'study_tcga_pub_gsva_scores',1,'geneset_score','gsva-score','gsva scores','gsva scores for oncogenic signature gene sets from msigdb calculated with gsva version 1.22.4, r version 3.3.2.',1); insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab,generic_assay_type) values (11,'study_tcga_pub_treatment_ic50',1,'generic_assay','ic50','treatment ic50 values','treatment response ic50 values',1,'treatment_response'); insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab,generic_assay_type) values (12,'study_tcga_pub_mutational_signature',1,'generic_assay','limit-value','mutational_signature values','mutational_signature values',1,'mutational_signature'); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (14,'study_tcga_pub_cna',1,'COPY_NUMBER_ALTERATION','discrete','Copy-number alterations','Copy number alterations (amplifications and deletions) from targeted sequencing.',1); insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (2,'1,2,3,4,5,6,7,8,9,10,11,12,13,14,'); insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (3,'2,3,6,8,9,10,12,13,'); insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (4,'1,2,3,4,5,6,7,8,9,10,11,12,13,14,'); insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (5,'2,'); insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (11,'1,2,3,4,5,6,7,8,9,10,11,12,13,14,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (14,'1,2,3,4,5,6,7,8,9,10,11,12,'); insert into patient (internal_id,stable_id,cancer_study_id) values (1,'tcga-a1-a0sb',1); insert into patient (internal_id,stable_id,cancer_study_id) values (2,'tcga-a1-a0sd',1); @@ -173,12 +176,12 @@ insert into sample (internal_id,stable_id,sample_type,patient_id) values (322,'G insert into sample (internal_id,stable_id,sample_type,patient_id) values (323,'GENIE-TEST-323-01','primary solid tumor',323); -insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2038,672,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'brca1 truncating'); -insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (22604,672,'17',41258504,41258504,'a','c','c61g','missense_mutation','37','+','snp','rs28897672','bycluster','nm_007294','c.(181-183)tgt>ggt','p38398',61,61,1,'brca1 c61 missense'); -insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2039,672,'17',41276033,41276033,'c','t','c27_splice','splice_site','37','+','snp','rs80358010','bycluster','nm_007294','c.e2+1','na',-1,-1,1,'brca1 truncating'); -insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2040,207,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'brca1 truncating'); -insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2041,207,'17',41258504,41258504,'a','c','c61g','missense_mutation','37','+','snp','rs28897672','bycluster','nm_007294','c.(181-183)tgt>ggt','p38398',61,61,1,'brca1 c61 missense'); -insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2042,208,'17',41276033,41276033,'c','t','c27_splice','splice_site','37','+','snp','rs80358010','bycluster','nm_007294','c.e2+1','na',-1,-1,1,'brca1 truncating'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2038,672,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'BRCA1 truncating'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (22604,672,'17',41258504,41258504,'a','c','c61g','missense_mutation','37','+','snp','rs28897672','bycluster','nm_007294','c.(181-183)tgt>ggt','p38398',61,61,1,'BRCA1 c61 missense'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2039,672,'17',41276033,41276033,'c','t','c27_splice','splice_site','37','+','snp','rs80358010','bycluster','nm_007294','c.e2+1','na',-1,-1,1,'BRCA1 truncating'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2040,207,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'BRCA1 truncating'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2041,207,'17',41258504,41258504,'a','c','c61g','missense_mutation','37','+','snp','rs28897672','bycluster','nm_007294','c.(181-183)tgt>ggt','p38398',61,61,1,'BRCA1 c61 missense'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2042,208,'17',41276033,41276033,'c','t','c27_splice','splice_site','37','+','snp','rs80358010','bycluster','nm_007294','c.e2+1','na',-1,-1,1,'BRCA1 truncating'); insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2038,6,6, 'putative_driver', 'pathogenic', 'tier 1', 'highly actionable'); insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (22604,6,6, 'putative_passenger', 'pathogenic', 'tier 2', 'potentially actionable'); @@ -506,9 +509,9 @@ insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2078,'erg',27,'protein-coding'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) -values(7,1,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-braf.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-braf.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-braf.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); +values(7,1,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) -values(7,2,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-braf.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-braf.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-braf.k16b10.cosf509','fusion','gain-of-function','GERMLINE'); +values(7,2,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','GERMLINE'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) values(7,1,8031,'enst00000344348','10','exon',-1,'q13.4',51582939,'ncoa4-ret.n7r12_1',5979,'enst00000340058','10','exon',-1,'p13.1',43612031,'ncoa4-ret.n7r12_2','grch37','no','yes',100001,80000,'ncoa4-ret.n7r1','fusion','gain-of-function','SOMATIC'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) @@ -518,9 +521,9 @@ values(7,2,27436,'enst00000318522','2','exon',-1,'q13.4',42492091,'eml4-alk.e6ba insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) values(7,1,7113,'enst00000332149','21','exon',-1,'q13.4',42880007,'tmprss2-erg.t1e2.cosf23.1_1',2078,'enst00000442448','21','exon',-1,'p13.1',39956869,'tmprss2-erg.t1e2.cosf23.1_2','grch37','no','yes',100003,60000,'tmprss2-erg.t1e2.cosf23.1','fusion','gain-of-function','SOMATIC'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) -values(7,2,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-braf.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-braf.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-braf.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); +values(7,2,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) -values(13,15,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-braf.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-braf.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-braf.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); +values(13,15,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) values(13,15,8031,'enst00000344348','10','exon',-1,'q13.4',51582939,'ncoa4-ret.n7r12_1',5979,'enst00000340058','10','exon',-1,'p13.1',43612031,'ncoa4-ret.n7r12_2','grch37','no','yes',100001,80000,'ncoa4-ret.n7r1-2','fusion','gain-of-function','SOMATIC'); insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) @@ -539,8 +542,9 @@ values (5,7,2, 'putative_driver', 'pathogenic', 'class 3', 'highly actionable'); insert into mut_sig (cancer_study_id,entrez_gene_id,rank,numbasescovered,nummutations,p_value,q_value) values (1,207,1,998421,17,0.00000315,0.00233); insert into mut_sig (cancer_study_id,entrez_gene_id,rank,numbasescovered,nummutations,p_value,q_value) values (1,208,2,3200341,351,0.000000012,0.00000000000212); -insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (2,1,'-0.4674,-0.6270,-1.2266,-1.2479,-1.2262,0.6962,-0.3338,-0.1264,0.7559,-1.1267,-0.5893,-1.1546,-1.0027,-1.3157,'); -insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (2,2,'1.4146,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1146,0.3498,0.0349,0.4927,-0.8665,-0.4754,-0.7221,'); +-- gistic values (genetic_profile_id = 2) should only be {-2, -1, 0, 1, 2} +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (2,1,'-1,2,0,1,-2,2,-1,0,1,-2,2,0,1,-1,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (4,2,'1.4146,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1146,0.3498,0.0349,0.4927,-0.8665,-0.4754,-0.7221,'); insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (3,2,'-0.8097,0.7360,-1.0225,-0.8922,0.7247,0.3537,1.2702,-0.1419,'); insert into cna_event (cna_event_id,entrez_gene_id,alteration) values (1,207,-2); @@ -605,11 +609,11 @@ insert into geneset_hierarchy_leaf (node_id,geneset_id) values (4,1); insert into geneset_hierarchy_leaf (node_id,geneset_id) values (4,2); insert into geneset_hierarchy_leaf (node_id,geneset_id) values (5,2); -insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'akt1 truncating', 207, 54, 64); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'AKT1 truncating', 207, 54, 64); insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, null, 207, 21, 22); -insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'araf g1513 missense', 369, 1, 2); -insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'araf g1514 missense', 369, 4, 7); -insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (8, 'noc2l truncating', 26155, 1, 3); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'ARAF g1513 missense', 369, 1, 2); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'ARAF g1514 missense', 369, 4, 7); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (8, 'NOC2L truncating', 26155, 1, 3); -- treatment test data @@ -634,3 +638,4 @@ insert into generic_entity_properties (id,genetic_entity_id,name,value) values ( insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (12,28,'-0.0670,-0.6270,-1.2266,-1.2079,-1.2262,0.6962,-0.3338,-0.1260,0.7559,-1.1267,-0.5893,-1.1506,-1.0027,-1.3157,'); insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (12,29,'1.0106,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1106,0.3098,0.0309,0.0927,-0.8665,-0.0750,-0.7221,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (14,1,'1,-1,NA,2,0,-2,1,NA,-1,0,2,-2,'); \ No newline at end of file