StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	24055055	Li S, Shen D, Shao J, Crowder R, Liu W, Prat A, He X, Liu S, Hoog J, Lu C, Ding L, Griffith OL, Miller C, Larson D, Fulton RS, Harrison M, Mooney T, McMichael JF, Luo J, Tao Y, Goncalves R, Schlosberg C, Hiken JF, Saied L, Sanchez C, Giuntoli T, Bumb C, Cooper C, Kitchens RT, Lin A, Phommaly C, Davies SR, Zhang J, Kavuri MS, McEachern D, Dong YY, Ma C, Pluard T, Naughton M, Bose R, Suresh R, McDowell R, Michel L, Aft R, Gillanders W, DeSchryver K, Wilson RK, Wang S, Mills GB, Gonzalez-Angulo A, Edwards JR, Maher C, Perou CM, Mardis ER, Ellis MJ	Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts	Cell Reports	2013 Sep	1,2,3,4,6,7,9,10,11,12,13,14,15,16,17,18,19,20,21,X	Breast cancer	Next Generation Sequencing	Homo sapiens	WHIM8	Illumina	chr10:0-76919999:0;chr10:101490001-111219999:0;chr10:111220000-112660000:-1;chr10:112660001-135374737:0;chr10:76920000-80910000:1;chr10:76920000-80950000:1;chr10:80950001-80969999:0;chr10:80970000-81220000:1;chr10:81220001-81259999:0;chr10:81260000-81540000:1;chr10:81540001-81559999:0;chr10:81560000-82430000:1;chr10:82430001-82759999:0;chr10:82760000-83840000:-1;chr10:83840001-83849999:0;chr10:83850000-84890000:1;chr10:83860000-84890000:1;chr10:84890001-85149999:0;chr10:85150000-86220000:1;chr10:86220001-86239999:0;chr10:86240000-91130000:-1;chr10:91130001-91139999:0;chr10:91140000-93900000:1;chr10:91150000-94310000:1;chr10:94310001-94329999:0;chr10:94330000-101490000:-1;chr11:0-69999:0;chr11:14810000-16990000:-1;chr11:16990001-24279999:0;chr11:24280000-31320000:-1;chr11:270000-2010000:-1;chr11:31320001-36759999:0;chr11:3220001-3329999:0;chr11:3330000-4200000:-1;chr11:36760000-37290000:-1;chr11:37290001-37549999:0;chr11:37550000-42910000:-1;chr11:4200001-4299999:0;chr11:42910001-45329999:0;chr11:4300000-9660000:-1;chr11:45330000-47190000:-1;chr11:47190001-55219999:0;chr11:55220000-55550000:1;chr11:55550001-55569999:0;chr11:55570000-61310000:-1;chr11:61310001-134452384:0;chr11:70000-3220000:-1;chr11:9660001-14809999:0;chr12:0-64969999:0;chr12:120360000-121510000:-1;chr12:130830000-131990000:-1;chr12:132260001-132349534:0;chr12:64970000-74360000:-1;chr12:74360001-74369999:0;chr12:74370000-78630000:-1;chr12:74380000-78630000:-1;chr12:78630001-78649999:0;chr12:78650000-132260000:-1;chr13:0-17929999:0;chr13:17930000-55570000:-1;chr13:55570001-60399999:0;chr13:60400000-67060000:1;chr13:67060001-114142980:0;chr14:0-19499999:0;chr14:101400001-101799999:0;chr14:101800000-102780000:1;chr14:102780001-105609999:0;chr14:105610000-106340000:1;chr14:105640000-106340000:1;chr14:106340001-106368585:0;chr14:19500000-26220000:-1;chr14:26220001-26229999:0;chr14:26230000-32930000:1;chr14:26240000-32930000:1;chr14:32930001-32949999:0;chr14:32950000-36740000:-1;chr14:36740001-36749999:0;chr14:36750000-38780000:1;chr14:36760000-38790000:1;chr14:38790001-38809999:0;chr14:38810000-42880000:-1;chr14:42880001-42899999:0;chr14:42900000-43310000:-1;chr14:43310001-43329999:0;chr14:43330000-69720000:-1;chr14:69720001-70579999:0;chr14:70580000-78330000:-1;chr14:78330001-94499999:0;chr14:94500000-95010000:-1;chr14:95010001-97739999:0;chr14:97740000-101230000:1;chr14:97740000-101400000:1;chr15:0-18279999:0;chr15:100250001-100338915:0;chr15:18280000-18640000:-1;chr15:18640001-20219999:0;chr15:20220000-21060000:-1;chr15:21060001-21199999:0;chr15:21200000-26230000:-1;chr15:26230001-26619999:0;chr15:26620000-32470000:-1;chr15:32470001-32639999:0;chr15:32640000-41630000:-1;chr15:41630001-41779999:0;chr15:41780000-57200000:-1;chr15:57200001-57829999:0;chr15:57830000-62470000:-1;chr15:62470001-65219999:0;chr15:65220000-67050000:-1;chr15:67050001-74479999:0;chr15:74480000-80360000:-1;chr15:80360001-81019999:0;chr15:81020000-84910000:-1;chr15:84910001-84989999:0;chr15:84990000-86580000:-1;chr15:86580001-86729999:0;chr15:86730000-88020000:-1;chr15:88020001-88029999:0;chr15:88030000-88920000:1;chr15:88040000-88920000:1;chr15:88920001-90249999:0;chr15:90250000-91680000:1;chr15:90250000-91700000:1;chr15:91700001-92579999:0;chr15:92580000-94710000:1;chr15:94710001-95529999:0;chr15:95530000-97040000:1;chr15:97040001-98279999:0;chr15:98280000-100250000:1;chr15:98290000-100250000:1;chr16:0-3249999:0;chr16:3250000-3800000:-1;chr16:3800001-49069999:0;chr16:49070000-51800000:1;chr16:49080000-51700000:1;chr16:51800001-51819999:0;chr16:51820000-69390000:-1;chr16:69390001-69769999:0;chr16:69770000-72940000:-1;chr16:72940001-73029999:0;chr16:73030000-88800000:-1;chr16:86930000-88560000:-1;chr16:88800001-88827254:0;chr17:0-59999:0;chr17:16590001-16689999:0;chr17:16690000-18280000:-1;chr17:18280001-18419999:0;chr17:18420000-18860000:-1;chr17:18860001-19079999:0;chr17:19080000-21120000:-1;chr17:21120001-21139999:0;chr17:21140000-21290000:-1;chr17:21290001-21709999:0;chr17:2150000-2700000:-1;chr17:21710000-22150000:-1;chr17:21720000-22150000:-1;chr17:22150001-24659999:0;chr17:24660000-25940000:1;chr17:25940001-26079999:0;chr17:26080000-29200000:-1;chr17:29200001-29209999:0;chr17:29210000-30680000:1;chr17:29220000-30700000:1;chr17:30700001-30719999:0;chr17:30720000-31500000:-1;chr17:31500001-31899999:0;chr17:31900000-33350000:-1;chr17:33350001-33919999:0;chr17:33920000-35830000:1;chr17:34750000-35450000:1;chr17:35830001-35849999:0;chr17:35850000-36340000:-1;chr17:36340001-36549999:0;chr17:36550000-38590000:-1;chr17:38590001-38779999:0;chr17:38780000-40490000:-1;chr17:40490001-40499999:0;chr17:40500000-41150000:1;chr17:40510000-41150000:1;chr17:41150001-41169999:0;chr17:41170000-41510000:-1;chr17:41510001-41529999:0;chr17:41530000-41710000:-1;chr17:41710001-42149999:0;chr17:4190000-4920000:-1;chr17:42150000-44610000:-1;chr17:44610001-44719999:0;chr17:44720000-45050000:-1;chr17:45050001-45069999:0;chr17:45070000-46360000:1;chr17:46360001-48339999:0;chr17:48340000-48630000:1;chr17:48630001-49829999:0;chr17:49830000-50140000:1;chr17:50140001-52279999:0;chr17:52280000-57180000:1;chr17:52490000-56180000:1;chr17:57180001-57449999:0;chr17:57450000-58390000:-1;chr17:58390001-59199999:0;chr17:59200000-63420000:-1;chr17:60000-16590000:-1;chr17:63420001-64019999:0;chr17:640000-1900000:-1;chr17:64020000-64570000:-1;chr17:64030000-64570000:-1;chr17:64570001-64649999:0;chr17:64650000-65910000:-1;chr17:65910001-65929999:0;chr17:65930000-66390000:-1;chr17:66390001-66409999:0;chr17:66410000-68280000:-1;chr17:66420000-68280000:-1;chr17:68280001-69379999:0;chr17:69380000-74960000:-1;chr17:7000000-7690000:-1;chr17:70550000-71640000:-1;chr17:74960001-75239999:0;chr17:75240000-77300000:-1;chr17:76550000-77300000:-1;chr17:77300001-77539999:0;chr17:77540000-78620000:-1;chr17:78620001-78774742:0;chr18:0-18229999:0;chr18:18230000-24500000:-1;chr18:24500001-24519999:0;chr18:24520000-27170000:1;chr18:24540000-27170000:1;chr18:27170001-27189999:0;chr18:27190000-37320000:-1;chr18:37320001-37329999:0;chr18:37330000-38000000:1;chr18:37340000-38000000:1;chr18:38000001-38019999:0;chr18:38020000-38460000:-1;chr18:38460001-38479999:0;chr18:38480000-41890000:1;chr18:38480000-41960000:1;chr18:41960001-42279999:0;chr18:42280000-45170000:1;chr18:45170001-45189999:0;chr18:45190000-48610000:-1;chr18:48610001-48689999:0;chr18:48690000-51560000:-1;chr18:51560001-51569999:0;chr18:51570000-54220000:1;chr18:51580000-56330000:1;chr18:55310000-56330000:1;chr18:56330001-56839999:0;chr18:56840000-70260000:-1;chr18:70260001-72919999:0;chr18:72920000-76090000:1;chr18:72930000-75600000:1;chr18:75670000-76090000:1;chr18:76090001-76117153:0;chr19:0-439999:0;chr19:1230001-37639999:0;chr19:37640000-43850000:1;chr19:43850001-43869999:0;chr19:43870000-53090000:-1;chr19:43890000-44500000:-1;chr19:440000-1230000:-1;chr19:45340000-46000000:-1;chr19:49860000-51210000:-1;chr19:51490000-53090000:-1;chr19:53090001-53109999:0;chr19:53110000-53150000:-1;chr19:53150001-53169999:0;chr19:53170000-55980000:-1;chr19:53170000-63780000:-1;chr19:58730000-59410000:-1;chr19:59920000-60910000:-1;chr19:63780001-63811651:0;chr1:0-609999:0;chr1:1240001-1449999:0;chr1:144110000-144530000:1;chr1:144530001-144669999:0;chr1:144670000-145880000:1;chr1:144810000-145870000:1;chr1:1450000-3690000:-1;chr1:145880001-145969999:0;chr1:145970000-146290000:1;chr1:146290001-147309999:0;chr1:147310000-147460000:1;chr1:147460001-148029999:0;chr1:148030000-150100000:1;chr1:148030000-159710000:1;chr1:156470000-158100000:1;chr1:159710001-159769999:0;chr1:159770000-194900000:1;chr1:194900001-195089999:0;chr1:195090000-197900000:1;chr1:197900001-198039999:0;chr1:198040000-214280000:1;chr1:214280001-232309999:0;chr1:232310000-247170000:1;chr1:247170001-247249719:0;chr1:3690001-144109999:0;chr1:610000-1240000:-1;chr20:0-49009999:0;chr20:49010000-62410000:1;chr20:50280000-51500000:1;chr20:51910000-54340000:1;chr20:54970000-59500000:1;chr20:62410001-62435964:0;chr21:0-13379999:0;chr21:13380000-23200000:-1;chr21:23200001-34959999:0;chr21:34960000-46920000:1;chr21:34970000-36280000:1;chr21:37670000-39540000:1;chr21:39810000-41750000:1;chr21:42270000-42870000:1;chr21:46920001-46944323:0;chr22:0-49691432:0;chr2:0-121949999:0;chr2:121950000-130930000:-1;chr2:130930001-131029999:0;chr2:131030000-132470000:-1;chr2:132470001-132849999:0;chr2:132850000-231060000:-1;chr2:231060001-232129999:0;chr2:232130000-242160000:-1;chr2:242160001-242369999:0;chr2:242370000-242730000:-1;chr2:242730001-242951149:0;chr3:0-49999:0;chr3:101630001-102079999:0;chr3:102080000-102700000:-1;chr3:102700001-111079999:0;chr3:10300000-12550000:1;chr3:111080000-112730000:-1;chr3:112730001-117459999:0;chr3:117460000-121750000:-1;chr3:121750001-121909999:0;chr3:121910000-143150000:-1;chr3:12930000-17430000:1;chr3:143150001-143959999:0;chr3:143960000-147530000:-1;chr3:147530001-149039999:0;chr3:149040000-157470000:-1;chr3:157470001-160649999:0;chr3:160650000-163980000:-1;chr3:163980001-164119999:0;chr3:164120000-169700000:-1;chr3:169700001-169709999:0;chr3:169710000-170850000:1;chr3:169720000-171210000:1;chr3:171210001-171229999:0;chr3:171230000-180530000:-1;chr3:17430001-17449999:0;chr3:17450000-46320000:-1;chr3:180530001-180659999:0;chr3:180660000-196830000:-1;chr3:196830001-196889999:0;chr3:196890000-196950000:-1;chr3:196950001-196969999:0;chr3:196970000-199420000:-1;chr3:199420001-199501827:0;chr3:46320001-46479999:0;chr3:46480000-68000000:-1;chr3:48640000-49490000:-1;chr3:50000-17430000:1;chr3:50000-9510000:1;chr3:68000001-68159999:0;chr3:68160000-75750000:-1;chr3:75750001-75959999:0;chr3:75960000-76300000:-1;chr3:76300001-76489999:0;chr3:76490000-85260000:-1;chr3:85260001-85409999:0;chr3:85410000-90580000:-1;chr3:90580001-96099999:0;chr3:96100000-101630000:-1;chr4:0-639999:0;chr4:17180001-18929999:0;chr4:18930000-48770000:-1;chr4:190760001-191273063:0;chr4:3530001-3549999:0;chr4:3550000-3600000:-1;chr4:3600001-3619999:0;chr4:3620000-17180000:-1;chr4:48770001-52379999:0;chr4:52380000-6890000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of Breast Oncology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA	To characterize patient-derived xenografts (PDXs) for functional studies, we made whole-genome comparisons with originating breast cancers representative of the major intrinsic subtypes. Structural and copy number aberrations were found to be retained with high fidelity. However, at the single-nucleotide level, variable numbers of PDX-specific somatic events were documented, although they were only rarely functionally significant. Variant allele frequencies were often preserved in the PDXs, demonstrating that clonal representation can be transplantable. Estrogen-receptor-positive PDXs were associated with ESR1 ligand-binding-domain mutations, gene amplification, or an ESR1/YAP1 translocation. These events produced different endocrine-therapy-response phenotypes in human, cell line, and PDX endocrine-response studies. Hence, deeply sequenced PDX models are an important resource for the search for genome-forward treatment options and capture endocrine-drug-resistance etiologies that are not observed in standard cell lines. The originating tumor genome provides a benchmark for assessing genetic drift and clonal representation after transplantation. 	NCBI 36/hg18		phs000611		Yes	NA
Research	24055055	Li S, Shen D, Shao J, Crowder R, Liu W, Prat A, He X, Liu S, Hoog J, Lu C, Ding L, Griffith OL, Miller C, Larson D, Fulton RS, Harrison M, Mooney T, McMichael JF, Luo J, Tao Y, Goncalves R, Schlosberg C, Hiken JF, Saied L, Sanchez C, Giuntoli T, Bumb C, Cooper C, Kitchens RT, Lin A, Phommaly C, Davies SR, Zhang J, Kavuri MS, McEachern D, Dong YY, Ma C, Pluard T, Naughton M, Bose R, Suresh R, McDowell R, Michel L, Aft R, Gillanders W, DeSchryver K, Wilson RK, Wang S, Mills GB, Gonzalez-Angulo A, Edwards JR, Maher C, Perou CM, Mardis ER, Ellis MJ	Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts	Cell Reports	2013 Sep	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	Next Generation Sequencing	Homo 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rX:25240000-30960000:-1;chrX:270000-810000:-1;chrX:27440000-30960000:-1;chrX:30960001-31869999:0;chrX:31870000-32430000:1;chrX:32430001-32599999:0;chrX:32600000-38510000:-1;chrX:32610000-38510000:-1;chrX:3680001-3969999:0;chrX:38510001-40189999:0;chrX:3970000-6500000:-1;chrX:40190000-42790000:-1;chrX:40570000-42790000:-1;chrX:42790001-43479999:0;chrX:43480000-45230000:1;chrX:43590000-44170000:1;chrX:44640000-45230000:1;chrX:45230001-51699999:0;chrX:51700000-52110000:-1;chrX:52110001-53119999:0;chrX:53120000-54090000:1;chrX:54090001-54519999:0;chrX:54520000-57320000:-1;chrX:57320001-67859999:0;chrX:6500001-25239999:0;chrX:67860000-76140000:-1;chrX:69960000-71000000:-1;chrX:76140001-77339999:0;chrX:77340000-82140000:1;chrX:810001-829999:0;chrX:82140001-83239999:0;chrX:830000-940000:-1;chrX:83240000-85170000:1;chrX:83320000-85170000:1;chrX:85170001-86689999:0;chrX:86690000-93490000:1;chrX:93490001-93509999:0;chrX:93510000-97890000:-1;chrX:940001-1289999:0;chrX:97890001-100129999:0;chrY:0-57772954:0			Section of Breast Oncology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA	To characterize patient-derived xenografts (PDXs) for functional studies, we made whole-genome comparisons with originating breast cancers representative of the major intrinsic subtypes. Structural and copy number aberrations were found to be retained with high fidelity. However, at the single-nucleotide level, variable numbers of PDX-specific somatic events were documented, although they were only rarely functionally significant. Variant allele frequencies were often preserved in the PDXs, demonstrating that clonal representation can be transplantable. Estrogen-receptor-positive PDXs were associated with ESR1 ligand-binding-domain mutations, gene amplification, or an ESR1/YAP1 translocation. These events produced different endocrine-therapy-response phenotypes in human, cell line, and PDX endocrine-response studies. Hence, deeply sequenced PDX models are an important resource for the search for genome-forward treatment options and capture endocrine-drug-resistance etiologies that are not observed in standard cell lines. The originating tumor genome provides a benchmark for assessing genetic drift and clonal representation after transplantation. 	NCBI 36/hg18		phs000611		Yes	C1orf182,MLL3;ESR1,YAP1