Callable cancer loci - test

The coverage report is generated with cacao version 0.3.1, using the following key settings:

• Genome assembly: grch37

• Mode: Hereditary cancer AND actionable somatic loci AND somatic hotspots

• Data sources - cancer loci:

  • ClinVar - release 20201128
  • CIViC - December 9th 2020
  • cancerhotspots.org - version 2 (2017)

• Alignment quality threshold (MAPQ): 0

• Alignment filename: 143B.filtered_alignments.bam

• Target regions filename: NA

• Callability levels (somatic):

  • NO_COVERAGE: No coverage (zero sequencing depth)

  • LOW_COVERAGE: Sequencing depth from 1 to 29

  • CALLABLE: Sequencing depth from 30 to 199

  • HIGH_COVERAGE: Sequencing depth above 200

• Callability levels (germline):

  • NO_COVERAGE: No coverage (zero sequencing depth)

  • LOW_COVERAGE: Sequencing depth from 1 to 9

  • CALLABLE: Sequencing depth from 10 to 99

  • HIGH_COVERAGE: Sequencing depth above 100

Hereditary cancer - pathogenic loci

Global distribution

Gene distribution

Coverage per variant locus

High coverage

Gene

Locus name

ClinVar phenotype(s)

Type of locus

Callable

Gene

Locus name

ClinVar phenotype(s)

Type of locus

Low coverage

Gene

Locus name

ClinVar phenotype(s)

Type of locus

No coverage

Gene

Locus name

ClinVar phenotype(s)

Type of locus

Sporadic cancers - actionable somatic mutations

Global distribution

Coverage per variant locus

Predictive

Callability

Gene

Locus name

Cancer type

Clinical significance

Level of evidence

Therapeutic context

Diagnostic

Callability

Gene

Locus name

Cancer type

Clinical significance

Level of evidence

Prognostic

Callability

Gene

Locus name

Cancer type

Clinical significance

Level of evidence

Somatic cancer hotspots

Global distribution

Coverage per locus

Callability

Gene

Locus name

Cancer type

Hotspot p-value