Update 03.methods.md

- rearrange table order - add S2 title
AlexsLemonade · Sep 24, 2020 · 77e9f00 · 77e9f00
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commit 77e9f00
Showing 1 changed file with 17 additions and 13 deletions.
diff --git 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].