Skip to content

Commit

Permalink
add vicc classification result to NGSD table somatic_vicc_interpretation
Browse files Browse the repository at this point in the history
  • Loading branch information
@Ott-Alexander
Ott-Alexander committed Oct 23, 2023
1 parent 35c4640 commit b25d7fc
Show file tree
Hide file tree
Showing 4 changed files with 23 additions and 16 deletions.
13 changes: 9 additions & 4 deletions src/cppNGSD-TEST/NGSD_Test.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
#include "SomaticXmlReportGenerator.h"
#include "SomaticReportSettings.h"
#include "SomaticReportHelper.h"
#include "SomaticVariantInterpreter.h"
#include "GermlineReportGenerator.h"
#include "TumorOnlyReportWorker.h"
#include "StatisticsServiceLocal.h"
Expand Down Expand Up @@ -2264,9 +2265,6 @@ private slots:
IS_TRUE(res2.exclude_other_reason);
S_EQUAL(res2.comment, "This test somatic cnv shall be excluded.");




//Delete a somatic report configuration
I_EQUAL(db.getValue("SELECT count(*) FROM somatic_report_configuration").toInt(), 3);
I_EQUAL(db.getValue("SELECT count(*) FROM somatic_report_configuration_cnv").toInt(), 2); //one CNV is already inserted by NGSD init.
Expand Down Expand Up @@ -2346,8 +2344,10 @@ private slots:
IS_THROWN(DatabaseException, db.getSomaticViccData(Variant("chr1", 112175770, 112175770, "C", "A")) );



//somatic Variant Interpretation for Cancer Consortium
SomaticViccData vicc_data1 = db.getSomaticViccData(Variant("chr13", 32929387, 32929387, "T", "C"));

I_EQUAL(vicc_data1.null_mutation_in_tsg, SomaticViccData::State::VICC_TRUE);
I_EQUAL(vicc_data1.known_oncogenic_aa, SomaticViccData::State::VICC_FALSE);
I_EQUAL(vicc_data1.strong_cancerhotspot, SomaticViccData::State::VICC_FALSE);
Expand All @@ -2365,6 +2365,9 @@ private slots:
I_EQUAL(vicc_data1.benign_computational_evidence, SomaticViccData::State::VICC_FALSE);
I_EQUAL(vicc_data1.synonymous_mutation, SomaticViccData::State::NOT_APPLICABLE);
S_EQUAL(vicc_data1.comment, "this variant was evaluated as an oncogenic variant");
S_EQUAL(db.getValue("SELECT classification FROM somatic_vicc_interpretation WHERE id=" + QString::number(db.getSomaticViccId(Variant("chr13", 32929387, 32929387, "T", "C")))).toString(), "ONCOGENIC");
S_EQUAL(db.getValue("SELECT classification FROM somatic_vicc_interpretation WHERE id=" + QString::number(db.getSomaticViccId(Variant("chr13", 32929387, 32929387, "T", "C")))).toString(), SomaticVariantInterpreter::viccScoreAsString(vicc_data1));


S_EQUAL(vicc_data1.created_by, "ahmustm1");
S_EQUAL(vicc_data1.created_at.toString("yyyy-MM-dd hh:mm:ss"), "2020-11-05 13:06:13");
Expand All @@ -2375,6 +2378,8 @@ private slots:
S_EQUAL(vicc_data2.comment, "this variant was evaluated as variant of unclear significance");
S_EQUAL(vicc_data2.last_updated_by, "ahkerra1");
S_EQUAL(vicc_data2.last_updated_at.toString("yyyy-MM-dd hh:mm:ss"), "2020-12-08 13:45:11");
S_EQUAL(db.getValue("SELECT classification FROM somatic_vicc_interpretation WHERE id=" + QString::number(db.getSomaticViccId(Variant("chr15", 43707808, 43707808, "A", "T")))).toString(), "UNCERTAIN_SIGNIFICANCE");


//Update somatic VICC data in NGSD
SomaticViccData vicc_update = vicc_data2;
Expand Down Expand Up @@ -2412,9 +2417,9 @@ private slots:
I_EQUAL(vicc_data2.benign_computational_evidence, SomaticViccData::State::VICC_FALSE);
I_EQUAL(vicc_data2.synonymous_mutation, SomaticViccData::State::VICC_FALSE);
S_EQUAL(vicc_data2.comment, "This variant was reevaluated as oncogenic!");
S_EQUAL(db.getValue("SELECT classification FROM somatic_vicc_interpretation WHERE id=" + QString::number(db.getSomaticViccId(Variant("chr15", 43707808, 43707808, "A", "T")))).toString(), "ONCOGENIC");
S_EQUAL(vicc_data2.last_updated_by, "ahmustm1");
IS_TRUE(vicc_data2.last_updated_at.toString("yyyy-MM-dd hh:mm:ss") != "2020-12-08 13:45:11");

//Insert new somatic VICC interpretation
SomaticViccData new_vicc_data;
new_vicc_data.null_mutation_in_tsg = SomaticViccData::State::VICC_FALSE;
Expand Down
10 changes: 5 additions & 5 deletions src/cppNGSD-TEST/data_in/NGSD_in1.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -577,11 +577,11 @@ INSERT INTO `somatic_report_configuration_cnv` (`somatic_report_configuration_id
(3, 4, true, false, false, false, false, "");

-- somatic_vicc
INSERT INTO `somatic_vicc_interpretation` (`id`, `variant_id`, `null_mutation_in_tsg`, `known_oncogenic_aa`, `strong_cancerhotspot`, `located_in_canerhotspot`, `absent_from_controls`, `protein_length_change`, `other_aa_known_oncogenic`, `weak_cancerhotspot`, `computational_evidence`, `mutation_in_gene_with_etiology`, `very_weak_cancerhotspot`, `very_high_maf`, `benign_functional_studies`, `high_maf`, `benign_computational_evidence`, `synonymous_mutation`, `comment`, `created_by`, `created_date`, `last_edit_by`, `last_edit_date`) VALUES
(1, 210585, true, false, false, true, true, null, true, false, null, false, true, false, false, false, false, null, 'this variant was evaluated as an oncogenic variant', 99, '2020-11-05 13:06:13', 101, '2020-12-07 11:06:10'),
(2, 213346, false, true, false, true, true, null, true, false, null, false, true, true, true, true, true, true, 'this variant was evaluated as variant of unclear significance', 99, '2020-12-05 12:07:11', 101, '2020-12-08 13:45:11'),
(3, 2407600, true, false, false, true, true, null, true, false, null, false, true, false, false, false, false, null, 'this variant was evaluated as an oncogenic variant', 99, '2021-01-05 13:06:13', 101, '2021-02-07 11:06:10'),
(4, 2407601, false, false, false, false, true, null, true, false, null, false, true, true, true, false, false, null, 'this variant was evaluated as an oncogenic variant', 99, '2021-02-06 11:06:14', 101, '2021-02-08 13:06:10');
INSERT INTO `somatic_vicc_interpretation` (`id`, `variant_id`, `null_mutation_in_tsg`, `known_oncogenic_aa`, `strong_cancerhotspot`, `located_in_canerhotspot`, `absent_from_controls`, `protein_length_change`, `other_aa_known_oncogenic`, `weak_cancerhotspot`, `computational_evidence`, `mutation_in_gene_with_etiology`, `very_weak_cancerhotspot`, `very_high_maf`, `benign_functional_studies`, `high_maf`, `benign_computational_evidence`, `synonymous_mutation`, `classification`, `comment`, `created_by`, `created_date`, `last_edit_by`, `last_edit_date`) VALUES
(1, 210585, true, false, false, true, true, null, true, false, null, false, true, false, false, false, false, null, 'ONCOGENIC', 'this variant was evaluated as an oncogenic variant', 99, '2020-11-05 13:06:13', 101, '2020-12-07 11:06:10'),
(2, 213346, false, true, false, true, true, null, true, false, null, false, true, true, true, true, true, true, 'UNCERTAIN_SIGNIFICANCE', 'this variant was evaluated as variant of unclear significance', 99, '2020-12-05 12:07:11', 101, '2020-12-08 13:45:11'),
(3, 2407600, true, false, false, true, true, null, true, false, null, false, true, false, false, false, false, null, 'ONCOGENIC', 'this variant was evaluated as an oncogenic variant', 99, '2021-01-05 13:06:13', 101, '2021-02-07 11:06:10'),
(4, 2407601, false, false, false, false, true, null, true, false, null, false, true, true, true, false, false, null, 'BENIGN', 'this variant was evaluated as an benign variant', 99, '2021-02-06 11:06:14', 101, '2021-02-08 13:06:10');

-- somatic_pathway
INSERT INTO `somatic_pathway` (`id`, `name`) VALUES
Expand Down
15 changes: 8 additions & 7 deletions src/cppNGSD/NGSD.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4042,7 +4042,6 @@ void NGSD::setSomaticViccData(const Variant& variant, const SomaticViccData& vic
}

QString variant_id = variantId(variant);

SqlQuery query = getQuery();

//this lambda binds all values needed for both inserting and updating
Expand Down Expand Up @@ -4072,23 +4071,25 @@ void NGSD::setSomaticViccData(const Variant& variant, const SomaticViccData& vic
query.bindValue(14 , stateToVar( vicc_data.high_maf ) );
query.bindValue(15 , stateToVar( vicc_data.benign_computational_evidence ) );
query.bindValue(16 , stateToVar( vicc_data.synonymous_mutation ) );
query.bindValue(17 , vicc_data.comment );
query.bindValue(18 , userId(user_name) );
query.bindValue(17 , SomaticVariantInterpreter::viccScoreAsString(vicc_data)); //set classification by interpreter to make sure it fits with the states
query.bindValue(18 , vicc_data.comment );
query.bindValue(19 , userId(user_name) );

};

int vicc_id = getSomaticViccId(variant);
if(vicc_id != -1) //update data set
{
query.prepare("UPDATE `somatic_vicc_interpretation` SET `null_mutation_in_tsg`=:0, `known_oncogenic_aa`=:1, `oncogenic_funtional_studies`=:2, `strong_cancerhotspot`=:3, `located_in_canerhotspot`=:4, `absent_from_controls`=:5, `protein_length_change`=:6, `other_aa_known_oncogenic`=:7, `weak_cancerhotspot`=:8, `computational_evidence`=:9, `mutation_in_gene_with_etiology`=:10, `very_weak_cancerhotspot`=:11, `very_high_maf`=:12, `benign_functional_studies`=:13, `high_maf`=:14, `benign_computational_evidence`=:15, `synonymous_mutation`=:16, `comment`=:17, `last_edit_by`=:18, `last_edit_date`= CURRENT_TIMESTAMP WHERE `id`=" + QByteArray::number(vicc_id) );
query.prepare("UPDATE `somatic_vicc_interpretation` SET `null_mutation_in_tsg`=:0, `known_oncogenic_aa`=:1, `oncogenic_funtional_studies`=:2, `strong_cancerhotspot`=:3, `located_in_canerhotspot`=:4, `absent_from_controls`=:5, `protein_length_change`=:6, `other_aa_known_oncogenic`=:7, `weak_cancerhotspot`=:8, `computational_evidence`=:9, `mutation_in_gene_with_etiology`=:10, `very_weak_cancerhotspot`=:11, `very_high_maf`=:12, `benign_functional_studies`=:13, `high_maf`=:14, `benign_computational_evidence`=:15, `synonymous_mutation`=:16, `classification`=:17, `comment`=:18, `last_edit_by`=:19, `last_edit_date`= CURRENT_TIMESTAMP WHERE `id`=" + QByteArray::number(vicc_id));
bind();
query.exec();
}
else //insert new data set
{
query.prepare("INSERT INTO `somatic_vicc_interpretation` (`null_mutation_in_tsg`, `known_oncogenic_aa`, `oncogenic_funtional_studies`, `strong_cancerhotspot`, `located_in_canerhotspot`, `absent_from_controls`, `protein_length_change`, `other_aa_known_oncogenic`, `weak_cancerhotspot`, `computational_evidence`, `mutation_in_gene_with_etiology`, `very_weak_cancerhotspot`, `very_high_maf`, `benign_functional_studies`, `high_maf`, `benign_computational_evidence`, `synonymous_mutation`, `comment`, `last_edit_by`, `last_edit_date`, `created_by`, `created_date`, `variant_id`) VALUES (:0, :1, :2, :3, :4, :5, :6, :7, :8, :9, :10, :11, :12, :13, :14, :15, :16, :17, :18, CURRENT_TIMESTAMP, :19, CURRENT_TIMESTAMP, :20)");
query.prepare("INSERT INTO `somatic_vicc_interpretation` (`null_mutation_in_tsg`, `known_oncogenic_aa`, `oncogenic_funtional_studies`, `strong_cancerhotspot`, `located_in_canerhotspot`, `absent_from_controls`, `protein_length_change`, `other_aa_known_oncogenic`, `weak_cancerhotspot`, `computational_evidence`, `mutation_in_gene_with_etiology`, `very_weak_cancerhotspot`, `very_high_maf`, `benign_functional_studies`, `high_maf`, `benign_computational_evidence`, `synonymous_mutation`, `classification`, `comment`, `last_edit_by`, `last_edit_date`, `created_by`, `created_date`, `variant_id`) VALUES (:0, :1, :2, :3, :4, :5, :6, :7, :8, :9, :10, :11, :12, :13, :14, :15, :16, :17, :18, :19, CURRENT_TIMESTAMP, :20, CURRENT_TIMESTAMP, :21)");
bind();
query.bindValue(19, userId(user_name) );
query.bindValue(20, variant_id);
query.bindValue(20, userId(user_name) );
query.bindValue(21, variant_id);
query.exec();
}
}
Expand Down
1 change: 1 addition & 0 deletions src/cppNGSD/resources/NGSD_schema.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -720,6 +720,7 @@ CREATE TABLE IF NOT EXISTS `somatic_vicc_interpretation`
`high_maf` BOOLEAN NULL DEFAULT NULL,
`benign_computational_evidence` BOOLEAN NULL DEFAULT NULL,
`synonymous_mutation` BOOLEAN NULL DEFAULT NULL,
`classification` ENUM('ONCOGENIC', 'LIKELY_ONCOGENIC', 'BENIGN', 'LIKELY_BENIGN', 'UNCERTAIN_SIGNIFICANCE') NULL DEFAULT NULL,
`comment` TEXT NULL DEFAULT NULL,
`created_by` int(11) DEFAULT NULL,
`created_date` DATETIME NOT NULL,
Expand Down

0 comments on commit b25d7fc

Please sign in to comment.