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JamesKaneJamesKane
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**feat(genomics): Add targeted sequencing support and services**
- Added database schema for `test_type_target_region` to define targeted test regions. - Introduced new test types (`BIG_Y_700`, `Y_ELITE`, `MT_FULL_SEQUENCE`, etc.) with attributes and successor relationships. - Created `TargetedSequencingService` to manage targeted test capabilities, coverage assessments, and upgrade paths. - Updated `TestType` enum and repository with new targeted test types and capabilities. - Implemented unit tests for `TargetedSequencingService` to validate functionality and coverage assessment tiers.
1 parent 84dc6ea commit c84f451

9 files changed

Lines changed: 642 additions & 1 deletion

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‎app/models/dal/DatabaseSchema.scala‎

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@@ -81,6 +81,7 @@ object DatabaseSchema {
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val specimenDonors = TableQuery[SpecimenDonorsTable]
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val validationServices = TableQuery[ValidationServicesTable]
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val testTypeDefinition = TableQuery[TestTypeTable]
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val testTypeTargetRegions = TableQuery[TestTypeTargetRegionTable]
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// Consolidated variant schema (replaces variant + variant_alias)
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val variantsV2 = TableQuery[VariantV2Table]

‎app/models/dal/domain/genomics/TestTypeTargetRegionTable.scala‎

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package models.dal.domain.genomics
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import models.dal.MyPostgresProfile
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import models.dal.MyPostgresProfile.api.*
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import models.domain.genomics.TestTypeTargetRegion
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import slick.lifted.{ProvenShape, Tag}
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class TestTypeTargetRegionTable(tag: Tag)
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extends MyPostgresProfile.api.Table[TestTypeTargetRegion](tag, "test_type_target_region") {
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def id = column[Int]("id", O.PrimaryKey, O.AutoInc)
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def testTypeId = column[Int]("test_type_id")
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def contigName = column[String]("contig_name")
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def startPosition = column[Option[Int]]("start_position")
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def endPosition = column[Option[Int]]("end_position")
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def regionName = column[String]("region_name")
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def regionType = column[String]("region_type")
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def expectedCoveragePct = column[Option[Double]]("expected_coverage_pct")
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def expectedMinDepth = column[Option[Double]]("expected_min_depth")
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override def * : ProvenShape[TestTypeTargetRegion] = (
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id.?,
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testTypeId,
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contigName,
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startPosition,
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endPosition,
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regionName,
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regionType,
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expectedCoveragePct,
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expectedMinDepth
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).mapTo[TestTypeTargetRegion]
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}

‎app/models/domain/genomics/TestType.scala‎

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@@ -7,7 +7,8 @@ import play.api.mvc.QueryStringBindable
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* This enum provides a structured way to classify genomic data based on how it was generated.
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*/
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enum TestType {
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case WGS, WES, TARGETED_Y, TARGETED_MT, SNP_ARRAY_23ANDME, SNP_ARRAY_ANCESTRY
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case WGS, WES, TARGETED_Y, TARGETED_MT, SNP_ARRAY_23ANDME, SNP_ARRAY_ANCESTRY,
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BIG_Y_700, BIG_Y_500, Y_ELITE, Y_PRIME, MT_FULL_SEQUENCE, MT_PLUS
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override def toString: String = this match {
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case WGS => "WGS"
@@ -16,6 +17,12 @@ enum TestType {
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case TARGETED_MT => "TARGETED_MT"
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case SNP_ARRAY_23ANDME => "SNP_ARRAY_23ANDME"
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case SNP_ARRAY_ANCESTRY => "SNP_ARRAY_ANCESTRY"
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case BIG_Y_700 => "BIG_Y_700"
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case BIG_Y_500 => "BIG_Y_500"
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case Y_ELITE => "Y_ELITE"
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case Y_PRIME => "Y_PRIME"
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case MT_FULL_SEQUENCE => "MT_FULL_SEQUENCE"
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case MT_PLUS => "MT_PLUS"
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}
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}
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@@ -36,6 +43,12 @@ object TestType {
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case "TARGETED_MT" => Some(TARGETED_MT)
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case "SNP_ARRAY_23ANDME" => Some(SNP_ARRAY_23ANDME)
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case "SNP_ARRAY_ANCESTRY" => Some(SNP_ARRAY_ANCESTRY)
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case "BIG_Y_700" => Some(BIG_Y_700)
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case "BIG_Y_500" => Some(BIG_Y_500)
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case "Y_ELITE" => Some(Y_ELITE)
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case "Y_PRIME" => Some(Y_PRIME)
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case "MT_FULL_SEQUENCE" => Some(MT_FULL_SEQUENCE)
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case "MT_PLUS" => Some(MT_PLUS)
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case _ => None
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}
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‎app/models/domain/genomics/TestTypeTargetRegion.scala‎

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package models.domain.genomics
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import play.api.libs.json.{Json, OFormat}
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case class TestTypeTargetRegion(
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id: Option[Int] = None,
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testTypeId: Int,
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contigName: String,
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startPosition: Option[Int] = None,
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endPosition: Option[Int] = None,
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regionName: String,
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regionType: String,
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expectedCoveragePct: Option[Double] = None,
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expectedMinDepth: Option[Double] = None
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) {
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def regionSize: Option[Int] = for {
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s <- startPosition
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e <- endPosition
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} yield e - s + 1
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}
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object TestTypeTargetRegion {
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implicit val format: OFormat[TestTypeTargetRegion] = Json.format[TestTypeTargetRegion]
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}
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case class RegionCoverageResult(
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regionName: String,
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contigName: String,
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startPosition: Option[Int],
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endPosition: Option[Int],
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expectedCoveragePct: Option[Double],
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expectedMinDepth: Option[Double],
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actualMeanDepth: Option[Double],
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actualCoveragePct: Option[Double],
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meetsExpectation: Boolean
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)
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object RegionCoverageResult {
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implicit val format: OFormat[RegionCoverageResult] = Json.format[RegionCoverageResult]
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}
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case class TargetedCoverageAssessment(
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testTypeCode: String,
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testTypeDisplayName: String,
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targetRegions: Seq[RegionCoverageResult],
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overallCoveragePct: Double,
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overallMeetsExpectation: Boolean,
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qualityTier: String
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)
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object TargetedCoverageAssessment {
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implicit val format: OFormat[TargetedCoverageAssessment] = Json.format[TargetedCoverageAssessment]
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def qualityTierFromCoverage(coveragePct: Double): String = {
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if (coveragePct >= 0.95) "HIGH"
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else if (coveragePct >= 0.80) "MEDIUM"
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else if (coveragePct >= 0.50) "LOW"
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else "INSUFFICIENT"
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}
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}

‎app/modules/BaseModule.scala‎

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@@ -62,6 +62,10 @@ class BaseModule extends AbstractModule {
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.to(classOf[InstrumentProposalRepositoryImpl])
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.asEagerSingleton()
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bind(classOf[TestTypeTargetRegionRepository])
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.to(classOf[TestTypeTargetRegionRepositoryImpl])
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.asEagerSingleton()
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bind(classOf[SequenceFileRepository])
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.to(classOf[SequenceFileRepositoryImpl])
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.asEagerSingleton()

‎app/repositories/TestTypeTargetRegionRepository.scala‎

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package repositories
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import jakarta.inject.{Inject, Singleton}
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import models.dal.DatabaseSchema
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import models.domain.genomics.TestTypeTargetRegion
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import play.api.db.slick.DatabaseConfigProvider
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import scala.concurrent.{ExecutionContext, Future}
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trait TestTypeTargetRegionRepository {
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def findByTestTypeId(testTypeId: Int): Future[Seq[TestTypeTargetRegion]]
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def findByTestTypeCode(code: String): Future[Seq[TestTypeTargetRegion]]
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def findByContigName(contigName: String): Future[Seq[TestTypeTargetRegion]]
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def create(region: TestTypeTargetRegion): Future[TestTypeTargetRegion]
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def delete(id: Int): Future[Boolean]
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}
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@Singleton
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class TestTypeTargetRegionRepositoryImpl @Inject()(
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override protected val dbConfigProvider: DatabaseConfigProvider
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)(implicit override protected val ec: ExecutionContext)
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extends BaseRepository(dbConfigProvider)
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with TestTypeTargetRegionRepository {
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import models.dal.MyPostgresProfile.api.*
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private val regions = DatabaseSchema.domain.genomics.testTypeTargetRegions
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private val testTypes = DatabaseSchema.domain.genomics.testTypeDefinition
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override def findByTestTypeId(testTypeId: Int): Future[Seq[TestTypeTargetRegion]] = {
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db.run(regions.filter(_.testTypeId === testTypeId).result)
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}
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override def findByTestTypeCode(code: String): Future[Seq[TestTypeTargetRegion]] = {
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val query = regions
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.join(testTypes).on(_.testTypeId === _.id)
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.filter(_._2.code === code)
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.map(_._1)
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db.run(query.result)
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}
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override def findByContigName(contigName: String): Future[Seq[TestTypeTargetRegion]] = {
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db.run(regions.filter(_.contigName === contigName).result)
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}
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override def create(region: TestTypeTargetRegion): Future[TestTypeTargetRegion] = {
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db.run(
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(regions returning regions.map(_.id)
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into ((r, id) => r.copy(id = Some(id)))) += region
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)
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}
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override def delete(id: Int): Future[Boolean] = {
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db.run(regions.filter(_.id === id).delete.map(_ > 0))
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}
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}

‎app/services/TargetedSequencingService.scala‎

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package services
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import jakarta.inject.{Inject, Singleton}
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import models.domain.genomics.*
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import play.api.Logging
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import repositories.{TestTypeRepository, TestTypeTargetRegionRepository}
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import scala.concurrent.{ExecutionContext, Future}
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case class TargetedTestCapabilities(
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testType: TestTypeRow,
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targetRegions: Seq[TestTypeTargetRegion],
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supportsYDna: Boolean,
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supportsMtDna: Boolean,
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primaryContig: Option[String],
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totalTargetedBases: Option[Long]
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)
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@Singleton
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class TargetedSequencingService @Inject()(
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testTypeRepo: TestTypeRepository,
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targetRegionRepo: TestTypeTargetRegionRepository
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)(implicit ec: ExecutionContext) extends Logging {
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def getTargetedTestCapabilities(testTypeCode: String): Future[Option[TargetedTestCapabilities]] = {
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testTypeRepo.findByCode(testTypeCode).flatMap {
27+
case None => Future.successful(None)
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case Some(testType) =>
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testType.id match {
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case None => Future.successful(None)
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case Some(ttId) =>
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targetRegionRepo.findByTestTypeId(ttId).map { regions =>
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val primaryContig = regions.headOption.map(_.contigName)
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val totalBases = regions.flatMap(_.regionSize).sum
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Some(TargetedTestCapabilities(
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testType = testType,
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targetRegions = regions,
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supportsYDna = testType.supportsHaplogroupY,
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supportsMtDna = testType.supportsHaplogroupMt,
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primaryContig = primaryContig,
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totalTargetedBases = if (totalBases > 0) Some(totalBases.toLong) else None
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))
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}
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}
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}
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}
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def assessCoverage(
49+
testTypeCode: String,
50+
actualMeanDepth: Option[Double],
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actualCoveragePct: Option[Double]
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): Future[Option[TargetedCoverageAssessment]] = {
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testTypeRepo.findByCode(testTypeCode).flatMap {
54+
case None => Future.successful(None)
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case Some(testType) =>
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testType.id match {
57+
case None => Future.successful(None)
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case Some(ttId) =>
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targetRegionRepo.findByTestTypeId(ttId).map { regions =>
60+
if (regions.isEmpty) None
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else Some(buildAssessment(testType, regions, actualMeanDepth, actualCoveragePct))
62+
}
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}
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}
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}
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private[services] def buildAssessment(
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testType: TestTypeRow,
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regions: Seq[TestTypeTargetRegion],
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actualMeanDepth: Option[Double],
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actualCoveragePct: Option[Double]
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): TargetedCoverageAssessment = {
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val regionResults = regions.map { region =>
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val meetsDepth = (actualMeanDepth, region.expectedMinDepth) match {
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case (Some(actual), Some(expected)) => actual >= expected
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case _ => true
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}
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val meetsCoverage = (actualCoveragePct, region.expectedCoveragePct) match {
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case (Some(actual), Some(expected)) => actual >= expected
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case _ => true
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}
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RegionCoverageResult(
84+
regionName = region.regionName,
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contigName = region.contigName,
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startPosition = region.startPosition,
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endPosition = region.endPosition,
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expectedCoveragePct = region.expectedCoveragePct,
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expectedMinDepth = region.expectedMinDepth,
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actualMeanDepth = actualMeanDepth,
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actualCoveragePct = actualCoveragePct,
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meetsExpectation = meetsDepth && meetsCoverage
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)
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}
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val overallCoverage = actualCoveragePct.getOrElse(0.0)
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val allMeet = regionResults.forall(_.meetsExpectation)
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TargetedCoverageAssessment(
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testTypeCode = testType.code,
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testTypeDisplayName = testType.displayName,
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targetRegions = regionResults,
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overallCoveragePct = overallCoverage,
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overallMeetsExpectation = allMeet,
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qualityTier = TargetedCoverageAssessment.qualityTierFromCoverage(overallCoverage)
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)
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}
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def getTargetedYTests: Future[Seq[TestTypeRow]] = {
110+
testTypeRepo.findByCapability(supportsY = Some(true)).map { tests =>
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tests.filter(_.targetType == TargetType.YChromosome)
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}
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}
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def getTargetedMtTests: Future[Seq[TestTypeRow]] = {
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testTypeRepo.findByCapability(supportsMt = Some(true)).map { tests =>
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tests.filter(_.targetType == TargetType.MtDna)
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}
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}
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def findUpgradePath(currentTestTypeCode: String): Future[Option[TestTypeRow]] = {
122+
testTypeRepo.findByCode(currentTestTypeCode).flatMap {
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case Some(current) if current.successorTestTypeId.isDefined =>
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testTypeRepo.getTestTypeRowsByIds(Seq(current.successorTestTypeId.get)).map(_.headOption)
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case _ => Future.successful(None)
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}
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}
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def isTargetedTest(testTypeCode: String): Future[Boolean] = {
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testTypeRepo.findByCode(testTypeCode).map {
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case Some(tt) => tt.targetType == TargetType.YChromosome || tt.targetType == TargetType.MtDna
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case None => false
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}
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}
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}

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