A

##########
Patient 1:
#########

Tum:

    
1	RP11-208G20.2--PSPHP1	INTRACHROMOSOMAL[chr7:96.59Mb]		
3	RP11-384F7.2--LSAMP	INTRACHROMOSOMAL[chr3:0.53Mb]		
5	RP1-34H18.1--NAV3	INTRACHROMOSOMAL[chr12:0.26Mb]		
8	CTD-2008L17.1--RP11-456O19.2	INTRACHROMOSOMAL[chr18:0.02Mb];NEIGHBORS[18613]		
10	RP11-444D3.1--SOX5	[SOX5:Oncogene];INTRACHROMOSOMAL[chr12:0.26Mb]


# min 5 cells
1	RP11-208G20.2--PSPHP1	INTRACHROMOSOMAL[chr7:96.59Mb]		
3	RP11-384F7.2--LSAMP	INTRACHROMOSOMAL[chr3:0.53Mb]		
5	RP1-34H18.1--NAV3	INTRACHROMOSOMAL[chr12:0.26Mb]    *** reported in normals: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9402576/


Om:

RP11-208G20.2--PSPHP1	Mesothelial.cells	121	0.8231293	
RP11-384F7.2--LSAMP	Mesothelial.cells	30	0.8823529	
YAF2--RYBP	Mesothelial.cells	9	0.6428571	INTERCHROMOSOMAL[chr12--chr3]
RP11-96H19.1--RP11-446N19.1	Mesothelial.cells	8	1.0000000	
SAMD5--RP11-307P5.1	Mesothelial.cells	8	1.0000000	INTRACHROMOSOMAL[chr6:0.09Mb];NEIGHBORS[90682]
RP11-444D3.1--SOX5	Fibroblasts	6	0.7500000	
RP1-34H18.1--NAV3	Mesothelial.cells	5	0.7142857	
YWHAE--CRK	Mesothelial.cells	5	1.0000000   # [YWHAE:Oncogene];[CRK:Oncogene];[DEEPEST2019];INTRACHROMOSOMAL[chr17:0.02Mb];LOCAL_REARRANGEMENT:-:[20311]



    

###########
Patient 3:
###########

    
1	ZCCHC8--RSRC2       [YOSHIHARA_TCGA,DEEPEST2019,TumorFusionsNAR2018,ChimerSeq,TCGA_StarF2019,CCLE_StarF2019];INTRACHROMOSOMAL[chr12:0.00Mb];LOCAL_REARRANGEMENT:-:[2863]	
3	RP11-208G20.2--PSPHP1	****** both   INTRACHROMOSOMAL[chr7:96.59Mb]
9	RP11-384F7.2--LSAMP	 ******* both     INTRACHROMOSOMAL[chr3:0.53Mb]
10	RP11-444D3.1--SOX5	  ****** both     [SOX5:Oncogene];INTRACHROMOSOMAL[chr12:0.26Mb]
14	RP11-420N3.2--RBFOX1	INTRACHROMOSOMAL[chr16:0.42Mb]
15	DSCR3--TTC3	[ChimerSeq];INTRACHROMOSOMAL[chr21:0.02Mb];LOCAL_INVERSION:-:+:[20308]
16	RP11-96H19.1--RP11-446N19.1   INTRACHROMOSOMAL[chr12:0.12Mb]



# min 4 cells
ZCCHC8--RSRC2	105	
RP11-208G20.2--PSPHP1	36  **** both	
RP11-384F7.2--LSAMP	5	    **** both
RP11-444D3.1--SOX5	5	



#########
Melanoma:
#########

NUTM2A-AS1--RP11-203L2.4	4	221	0.684210526	TRUE	
RP11-444D3.1--SOX5	4	7	0.021671827	TRUE	
BACH2--PNRC1	0	6	0.018575851	FALSE	
RP11-14D22.2--PRICKLE2	4	5	0.015479876	TRUE	
ZNF292--PNRC1	0	5	0.015479876	FALSE	
RP1-34H18.1--NAV3	4	4	0.012383901	TRUE	
DPH6-AS1--RP11-684B21.1	4	3	0.009287926	TRUE	
SRSF7--CXCR4	0	2	0.006191950	FALSE	




#################
Curious findings:
#################

    


RP11-444D3.1--SOX5 :  melanoma: 10 cells with RP11-444D3.1--SOX5 fusion, 70% are in tumor, 30% are in normal clusters.

                      HGSOC P1:  Om: 6 fibroblasts and 2 mesothelial cells
                      HGSOC P1: Tum: 7 HGSOC, 5 across other cell types.

                      HGSOC P2: Tum: 1 HGSOC and 1 T.NK.cells

    				  HGSOC P3: Om: 4 fibroblasts, 1 mesothelial
					  HGSOC P3: Tum: 5 fibroblasts, 1 HGSOC, 1 mesothelial, 1 uncertain


           paper reporting this fusion related to cancer: PMID:30888986, 31039818
           also found in normals: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9402576/
    

RP11-208G20.2--PSPHP1: not finding it in melanoma

                       HGSOC P1: Om: 25% of all cells and 82% of mesothelial cells
                       HGSOC P1: Tum: 24% of all cells, and mostly HGSOC, mesothelial, and T.NK

                       HGSOC P2: Tum: not finding it.

                       HGSOC P3: roughly 20% of Om and Tum cells, wide distribution of expression.

    	the above is interesting because it would involve an ~100 mb deletion or other SV. 

        *** actually not sure what this is... it's gnarly - probably some sequence not in the reference. Could check T2T or pangenome for it.



###########
Fusions found with oncogenes in normal cells:

P1 normals:  YWHAE--CRK in 5 mesothelial cells in the Om sample, only one HGSOC cell in the tumor sample.


P3 normals: ZCCHC8--RSRC2


    
