diff --git a/content/03.methods.md b/content/03.methods.md index 217ba6d3..ed609abb 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -289,18 +289,6 @@ The `short_histology` is an abbreviated version of either the `broad_histology` The `CNS_region` was subtyped into hemispheric, midline, mixed, or other based on specimen location (see table below). -| CNS_region | primary_site | -|-----------------|--------------------------------------------------------------------------------------------------------------------------------| -| Hemispheric | Frontal Lobe,Temporal Lobe,Parietal Lobe,Occipital Lobe | -| Midline | Pons/Brainstem,Brain Stem- Midbrain/Tectum,Brain Stem- Pons,Brain Stem-Medulla,Thalamus,Basal Ganglia,Hippocampus,Pineal Gland | -| Spine | Spinal Cord- Cervical,Spinal Cord- Thoracic,Spinal Cord- Lumbar/Thecal Sac,Spine NOS | -| Ventricles | Ventricles | -| Posterior fossa | Cerebellum/Posterior Fossa | -| Optic pathway | Optic Pathway | -| Suprasellar | Suprasellar/Hypothalamic/Pituitary | -| Other | Meninges/Dura,Other locations NOS,Skull,Cranial Nerves NOS,Brain | - - | Clinical and Histology Metadata | Definition | Possible values | |---------------------------|----------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | age_at_diagnosis_days | Patient age at diagnosis in days | numeric | @@ -316,7 +304,7 @@ The `CNS_region` was subtyped into hemispheric, midline, mixed, or other based o | experimental_strategy | Sequencing strategy | WGS;WXS;RNA-Seq;Panel | | germline_sex_estimate | Predicted sex of patient based on germline X and Y ratio calculation (described in methods) | Female;Male;Unknown | | CNS_region | Brain region based on `primary_site` | | -| `integrated_diagnosis` | 2016 WHO diagnosis integrated from pathology and molecular subtyping | text | +| integrated_diagnosis | 2016 WHO diagnosis integrated from pathology and molecular subtyping | text | | Kids_First_Biospecimen_ID | KidsFirst biospecimen identifier | BS_######## | | Kids_First_Participant_ID | KidsFirst patient identifier | PT_######## | | molecular_subtype | Molecular subtype defined by WHO 2016 guidelines | text | @@ -342,6 +330,22 @@ The `CNS_region` was subtyped into hemispheric, midline, mixed, or other based o Table S1. Clinical metadata collected for OpenPBTA. {#tbl:S1} + +| CNS_region | primary_site | +|-----------------|--------------------------------------------------------------------------------------------------------------------------------| +| Hemispheric | Frontal Lobe,Temporal Lobe,Parietal Lobe,Occipital Lobe | +| Midline | Pons/Brainstem,Brain Stem- Midbrain/Tectum,Brain Stem- Pons,Brain Stem-Medulla,Thalamus,Basal Ganglia,Hippocampus,Pineal Gland | +| Spine | Spinal Cord- Cervical,Spinal Cord- Thoracic,Spinal Cord- Lumbar/Thecal Sac,Spine NOS | +| Ventricles | Ventricles | +| Posterior fossa | Cerebellum/Posterior Fossa | +| Optic pathway | Optic Pathway | +| Suprasellar | Suprasellar/Hypothalamic/Pituitary | +| Other | Meninges/Dura,Other locations NOS,Skull,Cranial Nerves NOS,Brain | + + +Table S2. Harmonized CNS brain regions derived from primary site values. {#tbl:S2} + + #### Molecular Subtyping The `molecular_subtype` column in the `pbta-histologies.tsv` file contains molecular subtype information derived as described below, following World Health Organization 2016 classification criteria [@doi:10.1007/s00401-016-1545-1].