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Fusion Protein:HMGCS2-PSMA2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: HMGCS2-PSMA2
	FusionPDB ID: 36926
	FusionGDB2.0 ID: 36926
		Hgene	Tgene
	Gene symbol	HMGCS2	PSMA2
	Gene ID	3158	5683
	Gene name	3-hydroxy-3-methylglutaryl-CoA synthase 2	proteasome 20S subunit alpha 2
	Synonyms	-	HC3\|MU\|PMSA2\|PSC2
	Cytomap	1p12	7p14.1
	Type of gene	protein-coding	protein-coding
	Description	hydroxymethylglutaryl-CoA synthase, mitochondrial3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)HMG-CoA synthasetesticular tissue protein Li 88	proteasome subunit alpha type-2macropain subunit C3multicatalytic endopeptidase complex subunit C3proteasome (prosome, macropain) subunit, alpha type, 2proteasome component C3proteasome subunit HC3proteasome subunit alpha 2
	Modification date	20200313	20200327
	UniProtAcc	P54868 Main function of 5'-partner protein: FUNCTION: Catalyzes the first irreversible step in ketogenesis, condensing acetyl-CoA to acetoacetyl-CoA to form HMG-CoA, which is converted by HMG-CoA reductase (HMGCR) into mevalonate. {ECO:0000269\|PubMed:11228257, ECO:0000269\|PubMed:23751782, ECO:0000269\|PubMed:29597274}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000369406, ENST00000544913, ENST00000476640,	ENST00000223321, ENST00000442788, ENST00000445517, ENST00000538645,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 1 X 2=4	3 X 3 X 2=18
	# samples	2	3
	** MAII score	log2(2/4*10)=2.32192809488736	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: HMGCS2 [Title/Abstract] AND PSMA2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: HMGCS2 [Title/Abstract] AND PSMA2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	HMGCS2(120298049)-PSMA2(42964396), # samples:1
Anticipated loss of major functional domain due to fusion event.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:120298049/chr7:42964396)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.

Retention analysis results of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features, are available here.

Fusion gene breakpoints across HMGCS2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across PSMA2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000369406	HMGCS2	chr1	120298049	-	ENST00000442788	PSMA2	chr7	42964396	-	3400	1237	32	1690	552
ENST00000369406	HMGCS2	chr1	120298049	-	ENST00000223321	PSMA2	chr7	42964396	-	2404	1237	32	1690	552
ENST00000369406	HMGCS2	chr1	120298049	-	ENST00000445517	PSMA2	chr7	42964396	-	1852	1237	32	1690	552
ENST00000369406	HMGCS2	chr1	120298049	-	ENST00000538645	PSMA2	chr7	42964396	-	5284	1237	32	1519	495
ENST00000544913	HMGCS2	chr1	120298049	-	ENST00000442788	PSMA2	chr7	42964396	-	3285	1122	43	1575	510
ENST00000544913	HMGCS2	chr1	120298049	-	ENST00000223321	PSMA2	chr7	42964396	-	2289	1122	43	1575	510
ENST00000544913	HMGCS2	chr1	120298049	-	ENST00000445517	PSMA2	chr7	42964396	-	1737	1122	43	1575	510
ENST00000544913	HMGCS2	chr1	120298049	-	ENST00000538645	PSMA2	chr7	42964396	-	5169	1122	43	1404	453

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000369406	ENST00000442788	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.000895974	0.99910396
ENST00000369406	ENST00000223321	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.000347885	0.99965215
ENST00000369406	ENST00000445517	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.000542323	0.99945766
ENST00000369406	ENST00000538645	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.000193126	0.99980694
ENST00000544913	ENST00000442788	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.001225026	0.99877495
ENST00000544913	ENST00000223321	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.000430593	0.99956936
ENST00000544913	ENST00000445517	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.000729584	0.9992704
ENST00000544913	ENST00000538645	HMGCS2	chr1	120298049	-	PSMA2	chr7	42964396	-	0.000326475	0.9996735

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for HMGCS2-PSMA2

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
HMGCS2	chr1	120298049	PSMA2	chr7	42964396	1122	360	SSLYGCLASLLSQVLVHRARKLAQQY
HMGCS2	chr1	120298049	PSMA2	chr7	42964396	1237	402	SSLYGCLASLLSQVLVHRARKLAQQY

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Potential FusionNeoAntigen Information of HMGCS2-PSMA2 in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

HMGCS2-PSMA2_120298049_42964396.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B51:01	LASLLSQV	0.9997	0.8757	6	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:22	CLASLLSQV	0.9986	0.7132	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:13	CLASLLSQV	0.9974	0.8137	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:27	CLASLLSQV	0.9971	0.7617	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:16	CLASLLSQV	0.9957	0.6258	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:38	CLASLLSQV	0.9955	0.7824	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:11	CLASLLSQV	0.9952	0.72	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:67	CLASLLSQV	0.9948	0.6986	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:60	CLASLLSQV	0.9948	0.7091	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:21	CLASLLSQV	0.9948	0.7946	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:24	CLASLLSQV	0.9948	0.6986	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:30	CLASLLSQV	0.9948	0.6986	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:19	CLASLLSQV	0.9935	0.6836	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:29	CLASLLSQV	0.9931	0.6976	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:20	CLASLLSQV	0.992	0.7085	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B35:03	LASLLSQVL	0.9873	0.9083	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:35	CLASLLSQV	0.9837	0.7216	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B51:02	LASLLSQVL	0.9795	0.5123	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:04	CLASLLSQV	0.9774	0.8544	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:11	LLSQVLVHR	0.9648	0.5919	9	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:09	LLSQVLVHR	0.9648	0.5919	9	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:03	LLSQVLVHR	0.9648	0.5919	9	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B35:04	LASLLSQVL	0.9506	0.9592	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B35:02	LASLLSQVL	0.9506	0.9592	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A31:02	LLSQVLVHR	0.9085	0.5826	9	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:22	GCLASLLSQV	0.984	0.6681	4	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:16	GCLASLLSQV	0.9633	0.6248	4	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:13	GCLASLLSQV	0.9444	0.8065	4	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:27	GCLASLLSQV	0.9361	0.7219	4	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:38	GCLASLLSQV	0.9227	0.7605	4	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:22	YGCLASLLSQV	0.9598	0.6901	3	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:09	ASLLSQVLVHR	0.9407	0.5504	7	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:03	ASLLSQVLVHR	0.9407	0.5504	7	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:11	ASLLSQVLVHR	0.9407	0.5504	7	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:19	LASLLSQVL	0.9997	0.9878	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:08	LASLLSQVL	0.9996	0.9413	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:07	LASLLSQVL	0.9996	0.9389	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C15:06	LASLLSQVL	0.9989	0.8755	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:02	CLASLLSQV	0.9986	0.5782	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:05	CLASLLSQV	0.9983	0.6837	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C04:06	LASLLSQVL	0.9965	0.9327	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:01	CLASLLSQV	0.9948	0.6986	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C08:13	LASLLSQVL	0.994	0.9553	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C12:12	LASLLSQVL	0.994	0.9408	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C08:04	LASLLSQVL	0.994	0.9553	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C12:04	LASLLSQVL	0.9917	0.9902	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C06:03	LASLLSQVL	0.9906	0.9918	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:14	LASLLSQVL	0.975	0.956	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A31:01	LLSQVLVHR	0.9557	0.5677	9	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C08:03	LASLLSQVL	0.9539	0.992	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B35:12	LASLLSQVL	0.9506	0.9592	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C02:06	LASLLSQVL	0.9139	0.9478	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B39:10	LASLLSQVL	0.777	0.9449	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:02	GCLASLLSQV	0.9844	0.5494	4	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A31:01	ASLLSQVLVHR	0.9513	0.5163	7	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B51:14	LASLLSQV	0.9997	0.8594	6	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B51:13	LASLLSQV	0.9996	0.7463	6	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:04	LASLLSQVL	0.9998	0.9887	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:03	LASLLSQVL	0.9998	0.9887	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:67	LASLLSQVL	0.9996	0.985	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:17	LASLLSQVL	0.9995	0.9676	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:05	LASLLSQVL	0.9995	0.9306	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:02	LASLLSQVL	0.9994	0.9606	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C15:02	ASLLSQVLV	0.9989	0.8303	7	16
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:03	CLASLLSQV	0.9988	0.8121	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C16:04	LASLLSQVL	0.9965	0.979	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:06	CLASLLSQV	0.9948	0.7946	5	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C12:02	LASLLSQVL	0.9944	0.9727	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C12:03	LASLLSQVL	0.9925	0.9756	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C03:06	LASLLSQVL	0.9876	0.9884	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B35:13	LASLLSQVL	0.9833	0.914	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C16:02	LASLLSQVL	0.983	0.9852	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C16:01	LASLLSQVL	0.977	0.9772	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B51:06	LASLLSQVL	0.9762	0.675	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A30:01	QVLVHRARK	0.9696	0.8244	12	21
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:01	LLSQVLVHR	0.9648	0.5919	9	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C08:01	LASLLSQVL	0.9539	0.992	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B35:09	LASLLSQVL	0.9506	0.9592	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-C17:01	LASLLSQVL	0.8681	0.9247	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-B07:13	LASLLSQVL	0.6667	0.8214	6	15
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:03	GCLASLLSQV	0.9755	0.8043	4	14
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A74:01	ASLLSQVLVHR	0.9407	0.5504	7	18
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	HLA-A02:03	YGCLASLLSQV	0.9371	0.8245	3	14

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Potential FusionNeoAntigen Information of HMGCS2-PSMA2 in HLA II

HMGCS2-PSMA2_120298049_42964396.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-0103	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-0103	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-0103	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-0820	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-0828	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1102	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1102	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1103	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1103	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1103	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1104	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1106	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1111	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1111	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1114	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1116	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1116	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1120	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1121	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1121	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1121	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1125	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1135	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1136	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1136	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1138	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1141	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1141	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1143	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1144	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1146	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1147	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1148	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1148	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1154	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1155	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1155	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1155	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1157	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1158	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1159	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1159	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1160	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1163	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1163	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1163	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1165	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1165	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1167	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1170	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1170	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1170	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1176	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1176	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1176	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1177	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1178	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1184	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1185	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1185	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1185	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1186	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1186	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1192	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1301	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1301	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1302	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1304	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1304	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1308	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1308	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1311	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1315	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1315	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1315	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1316	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1316	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1317	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1317	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1318	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1319	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1319	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1320	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1320	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1322	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1322	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1323	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1324	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1324	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1324	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1327	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1327	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1331	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1332	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1332	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1334	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1335	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1335	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1339	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1342	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1343	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1343	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1348	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1348	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1351	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1351	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1352	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1352	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1353	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1353	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1354	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1354	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1354	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1357	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1357	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1357	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1359	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1359	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1361	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1361	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1363	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1363	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1364	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1364	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1368	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1368	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1369	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1369	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1370	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1370	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1371	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1371	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1372	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1372	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1373	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1374	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1375	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1375	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1376	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1376	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1378	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1378	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1379	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1379	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1380	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1380	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1383	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1383	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1384	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1384	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1387	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1387	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1391	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1391	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1392	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1392	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1393	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1393	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1397	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1398	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1398	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1399	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1412	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1416	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1416	SQVLVHRARKLAQQY	11	26
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1510	LSQVLVHRARKLAQQ	10	25
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1510	LLSQVLVHRARKLAQ	9	24
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	1237	DRB1-1510	SQVLVHRARKLAQQY	11	26

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Fusion breakpoint peptide structures of HMGCS2-PSMA2

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
4791	LASLLSQVLVHRAR	HMGCS2	PSMA2	chr1	120298049	chr7	42964396	1237

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of HMGCS2-PSMA2

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	4791	LASLLSQVLVHRAR	-7.15543	-7.26883
HLA-B14:02	3BVN	4791	LASLLSQVLVHRAR	-4.77435	-5.80965
HLA-B52:01	3W39	4791	LASLLSQVLVHRAR	-6.80875	-6.92215
HLA-B52:01	3W39	4791	LASLLSQVLVHRAR	-4.20386	-5.23916
HLA-A11:01	4UQ2	4791	LASLLSQVLVHRAR	-7.5194	-8.5547
HLA-A11:01	4UQ2	4791	LASLLSQVLVHRAR	-6.9601	-7.0735
HLA-A24:02	5HGA	4791	LASLLSQVLVHRAR	-7.52403	-7.63743
HLA-A24:02	5HGA	4791	LASLLSQVLVHRAR	-5.82433	-6.85963
HLA-B27:05	6PYJ	4791	LASLLSQVLVHRAR	-3.28285	-4.31815
HLA-B44:05	3DX8	4791	LASLLSQVLVHRAR	-5.91172	-6.94702
HLA-B44:05	3DX8	4791	LASLLSQVLVHRAR	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of HMGCS2-PSMA2

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	12	21	QVLVHRARK	CCAAGTGCTTGTGCACAGAGCTCGAAA
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	3	14	YGCLASLLSQV	GTACGGGTGCCTGGCCTCGCTTCTGTCCCAAGT
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	4	14	GCLASLLSQV	CGGGTGCCTGGCCTCGCTTCTGTCCCAAGT
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	5	14	CLASLLSQV	GTGCCTGGCCTCGCTTCTGTCCCAAGT
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	6	14	LASLLSQV	CCTGGCCTCGCTTCTGTCCCAAGT
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	6	15	LASLLSQVL	CCTGGCCTCGCTTCTGTCCCAAGTGCT
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	7	16	ASLLSQVLV	GGCCTCGCTTCTGTCCCAAGTGCTTGT
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	7	18	ASLLSQVLVHR	GGCCTCGCTTCTGTCCCAAGTGCTTGTGCACAG
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	9	18	LLSQVLVHR	GCTTCTGTCCCAAGTGCTTGTGCACAG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	10	25	LSQVLVHRARKLAQQ	TCTGTCCCAAGTGCTTGTGCACAGAGCTCGAAAACTAGCTCAACA
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	11	26	SQVLVHRARKLAQQY	GTCCCAAGTGCTTGTGCACAGAGCTCGAAAACTAGCTCAACAATA
HMGCS2-PSMA2	chr1	120298049	chr7	42964396	9	24	LLSQVLVHRARKLAQ	GCTTCTGTCCCAAGTGCTTGTGCACAGAGCTCGAAAACTAGCTCA

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Information of the samples that have these potential fusion neoantigens of HMGCS2-PSMA2

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
Non-Cancer	HMGCS2-PSMA2	chr1	120298049	ENST00000369406	chr7	42964396	ENST00000223321	135N

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Potential target of CAR-T therapy development for HMGCS2-PSMA2

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to HMGCS2-PSMA2

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to HMGCS2-PSMA2

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)