From 2dcf50664b539b50117458cf739c6920b8b04962 Mon Sep 17 00:00:00 2001
From: Bo Li <li.bo@gene.com>
Date: Sun, 4 Dec 2022 12:15:47 -0800
Subject: [PATCH] Added Germinal Center B cell markers

---
 .../human_immune_cell_markers.json            | 52 +++++++++++++++++--
 1 file changed, 49 insertions(+), 3 deletions(-)

diff --git a/pegasus/annotate_cluster/human_immune_cell_markers.json b/pegasus/annotate_cluster/human_immune_cell_markers.json
index 3b49bb6e..60eaa54c 100644
--- a/pegasus/annotate_cluster/human_immune_cell_markers.json
+++ b/pegasus/annotate_cluster/human_immune_cell_markers.json
@@ -123,9 +123,9 @@
 						"name" : "Naive B cell",
 						"markers" : [
 							{
-								"genes" : ["TCL1A+", "FCER2+"],
+								"genes" : ["IGHD+", "TCL1A+", "FCER2+"],
 								"weight" : 1.0,
-								"comments" : "markers for naive B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data."
+								"comments" : "markers for naive B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data"
 							}
 						]
 					},
@@ -135,7 +135,53 @@
 							{
 								"genes" : ["CD27+", "TNFRSF13B+"],
 								"weight" : 1.0,
-								"comments" : "markers for memory B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data."
+								"comments" : "markers for memory B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data"
+							}
+						]
+					}
+				]
+			}
+		},
+
+		{
+			"name" : "Germinal Center B cell",
+			"markers" : [
+				{
+					"genes" : ["CD19+", "MS4A1+", "CD79A+", "CD79B+"],
+					"weight" : 0.3,
+					"comment" : "CD19, CD20 and CD79"
+				},
+				{
+					"genes" : ["CD38+", "BCL6+", "BCL2-", "RGS13+"],
+					"weight" : 0.6,
+					"comment" : "First 3 markers are from Klein et al. PNAS 2003 https://doi.org/10.1073/pnas.0437996100 (Fig. 1 & 2). The last marker is from XXX"
+				},
+				{
+					"genes" : ["PCNA+", "MKI67+"],
+					"weight" : 0.1,
+					"comment" : "From Klein et al. PNAS 2003 https://doi.org/10.1073/pnas.0437996100 (Fig. 2)"
+				}
+			],
+			"subtypes" : {
+				"title" : "GC B cell subtype markers",
+				"cell_types" : [
+					{
+						"name" : "Dark zone B cell",
+						"markers" : [
+							{
+								"genes" : ["CXCR4+", "AICDA+", "FOXP1+", "MME+"],
+								"weight" : 1.0,
+								"comment" : "Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper"
+							}
+						]
+					},
+					{
+						"name" : "Light zone B cell",
+						"markers" : [
+							{
+								"genes" : ["CD83+", "LMO2+"],
+								"weight" : 1.0,
+								"comment" : "Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper"
 							}
 						]
 					}