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Chr2 (115,918,613) exon3 Typical DNA read and direction Chr2 Deletion (multiple exons of DPP10 lost) Chr2 (116,314,797) 29 transcriptome read map to this.

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Presentation on theme: "Chr2 (115,918,613) exon3 Typical DNA read and direction Chr2 Deletion (multiple exons of DPP10 lost) Chr2 (116,314,797) 29 transcriptome read map to this."— Presentation transcript:

1 Chr2 (115,918,613) exon3 Typical DNA read and direction Chr2 Deletion (multiple exons of DPP10 lost) Chr2 (116,314,797) 29 transcriptome read map to this gene (before and after exon 3, before and after exon25). exon2aexon26exon25 DPP10 (NM_020868): 26 exons, 2a-26 coding 633..728516..632 F1: from 693 2640..2713 2714..4863 R1: from 2952 Primer and its starting location in mRNA F2: from 2969 R2: from 3082 cDNA PCR result: patient4 tumor: F1+R1: clear band of ~300bp, no other band. F2+R2: clear band of ~100bp S18 control: clear band patient4 normal and patient 6 normal: F1+R1: no band F2+R2: no band S18 control: clear band exon1 Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 DPP1029765900

2 Chr3 (98,917,287) Exon16exon17exon18 EPHA6 (23 exons, 1-23 coding) NM_001080448 Typical DNA read and direction Chr3 deletion ( 90,095bp including gene ARL6) Chr3 (99,007,383) 41 reads map to exon 10 to exon 19 Exon1Exon2Exon3 DKFZp667G2110 (19 exons, 1-19 coding) NM_153605 2 transcriptome read map to exon 1. Gene Symbol SID55 9SID524SID557SID558SID816 SID127 6 EPHA6200002 DKFZp667G21104122613610643

3 Chr6 (64,615,701)Chr6 (57,319,605) Typical DNA read and direction PRIM2 (14 exons, 2-14 coding) NM_000947 exon8exon7exon6 EYS (44 exons, 4-44 coding) NM_001142800 exon37exon38exon39 Chr6 chimera changing two genes’ structure Gene SymbolSID559SID524SID557SID558SID816 SID127 6 EYS000000 PRIM2752837653817 4 transcriptome reads map exon 2 to 5, 71 transcriptome read map exon 6 to 14 0 transcriptome read maps to this gene

4 Chr8 (6,749,979) Typical DNA read and direction Chr8 deletion (28127285bp deleted) Chr8 (34,877,265) DEFB1 (2 exons, 1-2 coding) NM_005218 3 transcriptome read map to exon 2 of this gene UNC5D (17 exons, 1-17 coding) NM_080872 no transcriptome read map to this gene exon2exon1exon3exon2exon1 Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 DEFB131420010 UNC5D010000

5 Chr8 (6,786,552) Chr8 Chimera Chr8 (34,863,640) Typical DNA read and direction Exon 3Exon 2Exon 1 DUSP26 (4 exons, 2-4 coding) NM_024025 exon1exon2exon3 DEFA4 (3 exons, 2-3 coding) NM_001925 no transcriptome read maps to this gene Gene SymbolSID559SID524SID557SID558SID816 SID127 6 DEFA4000000 DUSP26000006

6 Chr8 ( 21,254,202) Typical DNA read and direction Chr8 Chimera Chr8 ( 72,593,210 ) exon2 MSC (2 exons, 1-2 coding) NM_005098 exon9exon8exon7 GFRA2 (9 exons, 1-9 coding) NM_001495 exon1 no transcriptome read maps to this gene12 transcriptome read map to this gene Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 GFRA20006013 MSC12561048115

7 Chr8 (72,573,255) Chr8 Chimera: breakpoint in intergenic region Chr8 (34,816,557) Typical DNA read and direction DUSP26 (4 exons, 2-3 coding) NM_024025 exon1exon2exon3 EYA1 (18 exons, 3-18 coding) NM_000503 exon2exon1exon3 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 DUSP26000006 EYA10001315 0 transcriptome read maps to this gene

8 Chr8 (34,816,593)Chr8 (72,577,581) Typical DNA read and direction EYA1 (18 exons, 3-18 coding) NM_000503 exon2exon3exon1 UNC5D (17 exons, 1-17 coding) NM_080872 exon2Exon 1Exon 3 Gene Symbol SID55 9 SID52 4 SID55 7 SID55 8 SID81 6 SID12 76 UNC5D010000 EYA10001315 Chr8 chimera, fusion points in intergenic region. no transcriptome read maps to this gene

9 Chr8 (36,550,070) Chr8 Chimera Chr8 (72,552,661) Typical DNA read and direction Exon 15Exon 16Exon 17 EYA1 (18 exons, 2-18 coding) NM_172058 exon1exon2exon3 UNC5D (17 exons, 1-17 coding) NM_080872 no transcriptome read maps to this gene Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 UNC5D010000 EYA10001315

10 Chr9 (21,957,500) Typical DNA read and direction Chr9 Chimera (117534bp deletion) Chr9 (22,075,035) MTAP (8 exons, 1-8 coding) NM_002451 DMRTA1 (2 exons, 1-2 coding) NM_022160 149 transcriptome reads map to exon 1 to 8 of this gene Exon 2Exon 1Exon 7Exon 8Exon 6 8 transcriptome reads map to this gene Gene SymbolSID559SID524SID557SID558SID816 SID127 6 MTAP14948127399193 DMRTA1800243

11 Chr10 (84,083,200) exon1 NRG3 (9 exons, 1-9 coding) NM_001010848 Typical DNA read and direction Chr10 deletion (73,978 bp including exon 2 of gene NRG3) Chr10 (84,157,179) Exon 3Exon 4 No transcriptome read map to this gene. NRG3 (9 exons, 1-9 coding) NM_001010848 Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 NRG3000020

12 Chr11 (55,762,996) Chr11 (55,765,854) Typical DNA read and direction Chr11 deletion in intergenic region. OR5T3 (1 exon, 1 coding) NM_001004747 OR5T2 (1 exon, 1 coding) NM_001004746 Exon 1 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 OR5T2000000 OR5T3000000 0 transcriptome read maps to this gene

13 Chr11 (59,018,943) Chr11 (59,023,522) Typical DNA read and direction exon1 OR4D10 (1 exon, 1 coding) NM_001004705 OR4D11 (1 exon, 1 coding) NM_001004706 exon1 Chr11 chimera, fusion points in intergenic region. Gene SymbolSID559SID524SID557SID558SID816 SID127 6 OR4D10000000 OR4D11000000 no transcriptome read maps to this gene

14 Chr12 (126,530,113)Chr12 (127,300,384) Typical DNA read and direction TMEM132B (9 exons, 1-9 coding) NM_052907 exon9exon8exon7 TMEM132B (9 exons, 1-9 coding) NM_052907 exon7exon8exon9 Chr12 chimera, break points in intergenic region. Gene SymbolSID559SID524SID557SID558SID816 SID127 6 TMEM132B121670 1 transcriptome read maps to this gene

15 Chr17 (65,721,910) exon25 NOS2A(27 exons, 2-27 coding) NM_000625 Typical DNA read and direction Chr17 Chimera Chr17 (23,113,949) 1 transcriptome read map to exon 27 of this gene exon24exon23 KCNJ2(2 exons, exon 2 coding) NM_000891 14 transcriptome read map to exon 2 of this gene exon2 exon1 Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 NOS2A101204 KCNJ21411131851

16 Chr17 (26,853,914) exon3 RAB11FIP4(15 exons, 1-15 coding) NM_032932 Typical DNA read and direction Chr17 Chimera (not deletion) Chr17 (47,815,374) 89 transcriptome read map to exon 7 to 15 of this gene exon2exon1 CA10(11 exons, 3-11 coding) NM_001082534 exon2exon1exon3 No transcriptome read map to this gene. Gene SymbolSID559SID524SID557SID558SID816 SID127 6 RAB11FIP489 10411087162 CA10000001

17 Chr17 ( 47,110,011) CA10 (10 exons, 3-10 coding) NM_001082534 Typical DNA read and direction Chr17 Chimera Chr17 ( 68,044,222 ) no transcriptome read map to this gene Exon 4 Exon 3 SLC39A11 (10 exons, 2-10 coding) NM_139177 44 transcriptome reads map to exon 1 to 10 of this gene Exon 9Exon 8Exon 10 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 CA10000001 SLC39A114455356513727 Exon 5

18 Chr17 (65,036,914) Exon8exon9exon10 CA10 (11 exons, 3-11 coding) NM_020178 Typical DNA read and direction Chr17 chimera Chr17 (47,505,787) MAP2K6 (12 exons 1-12 coding) NM_002758 Exon2 No transcriptome read map to this gene.3 transcriptome reads map to exon 12 and one read maps to exon 11 Exon1 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 MAP2K6461505 CA10000001

19 Chr17 (63,830,958) ARSG(11 exons, 1-11 coding) NM_014960 Typical DNA read and direction Chr17 Chimera Chr17 (47,696,961) 4 transcriptome read map to exon 1, 5 and 11 of this gene Exon 4 exon1 No transcriptome read map to this gene. KIF2B (1 exon) NM_032559 Exon 5Exon 3 Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 KIF2B000000 ARSG4516100

20 Chr19 ( 38,085,640 ) Chr19 deletion, part of intron 14 of gene CCDC123 lost. Chr19 ( 38,091,701 ) Typical DNA read and direction CCDC123 (19 exons, 1-19 coding) NM_032816 CCDC123 (19 exons, 1-19 coding) NM_032816 Exon 17Exon 16Exon 15 exon14exon13exon12 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 FLJ14640262421171820 12 transcriptome read map to exon 1 to 14, 11 transcriptome reads map to exon 15 to 17 3 transcriptome reads map to exon14-15 junction

21 Ch21 (18,540,069) Exon 1 CHODL (6 exons, 1-6 coding) NM_024944 Typical DNA read and direction Mutation 3: Ch21 deletion (15,130,502bp was deleted ) Ch21 (33,670,572) 3 transcriptome reads map to exon 3, 4 and 6 of this gene. IFNGR2 (7 exons, 1-7 coding) NM_005534 314 reads map to exon 1 to exon 7 Exon 1Exon 2 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 CHODL332211 IFNGR2314318209241200174

22 Chr21 (20,864,799) Typical DNA read and direction Chr21 Chimera (not a deletion) Chr21 (18,281,613) exon1exon2exon3 exon1exon2exon3 PRSS7 (25 exons, 1-25 coding) NM_002772 No transcriptome reads map to this gene. CHODL (6 exons, 1-6 coding) NM_024944 3 transcriptome reads map to exon 3, 4 and 6 of this gene. Gene SymbolSID559SID524SID557SID558SID816 SID127 6 PRSS7000020 CHODL332211

23 Chr21 ( 19,693,189) Typical DNA read and direction Chr21 Chimera Chr21 ( 31,062,421 ) exon1 KRTAP8-1 (1 exon) NM_175857 exon1exon2exon3 NCAM2 (18 exons, 1-18 coding) NM_004540 no transcriptome read maps to this gene 2 transcriptome reads map to this gene Gene SymbolSID559SID524SID557SID558SID816 SID127 6 NCAM22100209 KRTAP8-1000000

24 Chr21 (21,167,077) Typical DNA read and direction Chr21 Chimera (6694268bp deletion) Chr21 (27,861,346) exon1exon2exon3 exon6exon5exon4 PRSS7 (25 exons, 1-25 coding) NM_002772 no transcriptome read maps to this gene. N6AMT1 (6 exons, 1-6 coding) NM_013240 16 transcriptome reads map to the gene Gene SymbolSID559SID524SID557SID558SID816 SID127 6 PRSS7000020 N6AMT1161115261210

25 Chr9 (31,759,669) Chr9-Chr11 Chimera: gene structure disrupted Chr11 (84,923,849) Typical DNA read and direction DLG2 (32 exons, 3-32 coding) NM_001142699 exon3exon2exon1 LINGO2 (7 exons, 7 coding) NM_152570 exon3exon2exon1 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 LRRN6C000000 DLG20190318 0 transcriptome read maps to this gene

26 Chr10 (117,768,069) Typical DNA read and direction Chr10-Chr17 Chimera (not deletion) Chr17 (48,272,943) ATRNL1 (29 exons, 1-29 coding) NM_207303 1 transcriptome read maps to this gene KIF2B (1 exons, exon 1 coding) NM_032559 No transcriptome read maps to this gene exon1exon28exon27exon29 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 ATRNL1154402 KIF2B000000

27 Chr10 ( 121,001,050 ) KCNJ12 (3 exons, 3 coding) NM_021012 Typical DNA read and direction Chr10-Chr17 Chimera Chr17( 21,238,006 ) no transcriptome read maps to this gene Exon 2Exon 3 GRK5 (16 exons, 1-16 coding) NM_005308 Exon 4Exon 3Exon2 1 transcriptome read map to exon 1 of this gene 27 reads map to other exons Gene SymbolSID559SID524SID557SID558SID816 SID127 6 GRK52833295930215 KCNJ12041415

28 Chr6 (67,079,455) Chr15-Chr6 Chimera, fusion points in intergenic region Chr15 (23,876,380) Typical DNA read and direction BAI3 (32 exons, 3-32 coding) NM_001704 exon3exon2exon1 ATP10A (21 exons, 1-21 coding) NM_024490 exon3exon2exon1 Gene SymbolSID559SID524SID557SID558SID816 SID127 6 ATP10A15752141223663 BAI3000005 0 transcriptome read maps to this gene 157 transcriptome reads map this gene

29 Chr17 ( 61,459,185) Typical DNA read and direction Chr17-Chr21 Chimera Chr21 ( 21,169,765 ) CCDC46 (28 exons, 2-28 coding) NM_145036 Exon 10Exon 11Exon 12 18 transcriptome reads map exons before the breakpoint 16 reads map to the exons after the breakpoint NCAM2 (18 exons, 1-18 coding) NM_004540 exon1exon2exon3 2 transcriptome reads map to this gene Gene SymbolSID559SID524SID557SID558SID816 SID127 6 CCDC463482672115 NCAM22100209

30 Chr21 (35,609,289) exon10 TANC2(25 exons, 1-25 coding) NM_025185 Typical DNA read and direction Chr21-Chr17 Chimera Chr17 (58,726,449) 63 transcriptome reads map to this gene (before and after exon 7). exon9exon8 RUNX1 (10 exons, 2-10 coding) NM_001754 268 transcriptome reads map to this gene (exon 2 to 10). Exon 1exon2exon3 Gene Symbo lSID559SID524SID557SID558SID816 SID127 6 TANC2636810645213139 RUNX1268226192229251265

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