StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	2	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG014	Illumina HiSeq 2000	chr11:5741151-5765859:-1;chr12:65705844-65860964:1;chr12:81020356-81057622:1;chr2:170199813-170326345:-1;chr2:57315075-77261648:-1;chr2:58945897-64101169:1;chr2:59398168-62198357:1;chr2:61030770-64950932:1;chr2:61603741-64186434:1;chr2:61959737-65021132:-1;chr2:64107369-83051955:1;chr2:64110075-65196092:1;chr2:64113324-65011399:-1;chr2:65060073-83052605:1;chr2:79181777-83926268:-1;chr6:76460862-77861329:-1;chr6:76957466-76993247:1;chr8:129070957-129271216:1	hs17:25765380-25765380,hs2:176675354-176675354;hs17:48938937-48938937,hs2:119668564-119668564;hs17:48922187-48922187,hs2:119665556-119665556;hs2:35595408-35595408,hs2:117065447-117065447;hs2:82171889-82171889,hs2:83807361-83807361;hs2:79094169-79094169,hs2:83058298-83058298;hs2:60090711-60090711,hs2:62199561-62199561;hs2:65279526-65279526,hs2:65287675-65287675;hs2:64079006-64079006,hs2:64192609-64192609;hs2:77936878-77936878,hs2:84222375-84222375;hs2:83398215-83398215,hs6:136004781-136004781;hs2:60450993-60450993,hs2:60495932-60495932;hs2:83700519-83700519,hs2:84985328-84985328;hs2:61026746-61026746,hs2:65237642-65237642;hs2:64077491-64077491,hs2:65019980-65019980;hs2:60485726-60485726,hs2:61960697-61960697;hs4:43228837-43228837,hs17:49888087-49888087;hs6:75376489-75376489,hs6:76456545-76456545;hs6:75942261-75942261,hs6:76460877-76460877;hs6:41494848-41494848,hs6:69619654-69619654;hs6:75965673-75965673,hs6:118982169-118982169		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	1,2,9,17	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG028	Illumina HiSeq 2000	chr10:119070367-121619306:-1;chr11:35141779-35165434:-1;chr14:36701359-36840978:-1;chr14:72625917-72666602:-1;chr17:21644130-22782616:1;chr17:40668478-40735550:-1;chr18:51225332-51298777:-1;chr19:7005812-14457285:1;chr1:1297525-1346091:-1;chr1:152467650-152471574:-1;chr2:146440464-148588487:-1;chr3:189003121-189799358:-1;chr6:30004458-30022379:-1;chr6:31200494-32919822:-1;chr9:21854346-21958850:-1	hs1:56808946-56808946,hs6:106644529-106644529;hs1:56808986-56808986,hs6:106644512-106644512;hs1:204432648-204432648,hs1:210243172-210243172;hs17:24009064-24009064,hs17:36056640-36056640;hs19:54622010-54622010,hs19:63789465-63789465;hs19:62436306-62436306,hs2:146408009-146408009;hs2:113889788-113889788,hs4:191114592-191114592;hs4:49021102-49021102,hs1:141547959-141547959;hsX:136261018-136261018,hsX:153961240-153961240		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	6,9,13,15,18	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG034	Illumina HiSeq 2000	chr11:89591175-89603940:-1;chr19:10201579-10243189:-1;chr3:116907103-117124779:1;chr3:30882610-32919140:1;chr4:27509942-27522063:1;chr6:32556135-32787998:1;chr9:73648796-135984683:-1;chr9:74010545-122137819:1;chr9:74012466-135928486:-1	hs1:7917554-7917554,hs2:212411334-212411334;hs1:211480185-211480185,hs1:233469225-233469225;hs1:211480438-211480438,hs1:233470458-233470458;hs12:59079221-59079221,hs3:104717848-104717848;hs13:19333012-19333012,hs6:58448015-58448015;hs13:74231050-74231050,hs6:148187364-148187364;hs15:43161536-43161536,hs15:44265431-44265431;hs18:99044-99044,hsX:29179265-29179265;hs18:3223258-3223258,hs7:31794203-31794203;hs18:35202776-35202776,hs18:35963496-35963496;hs18:38646689-38646689,hs9:72929765-72929765;hs18:55281977-55281977,hs9:100213501-100213501;hs18:58944466-58944466,hs14:105453750-105453750;hs18:60448528-60448528,hs9:80921411-80921411;hs18:60448860-60448860,hs9:80920106-80920106;hs4:19855480-19855480,hs5:160965636-160965636;hs4:114010531-114010531,hs8:135704572-135704572;hs9:29523040-29523040,hs13:64616941-64616941;hs9:68504374-68504374,hs9:135678585-135678585;hs9:87562349-87562349,hs9:135983249-135983249;hsX:27045422-27045422,hs2:64728521-64728521		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	1	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG043	Illumina HiSeq 2000	chr11:48324097-48330277:-1;chr11:5741151-5765859:-1;chr11:5741151-5765859:-1;chr1:12250777-193382205:-1;chr1:213285864-213354216:-1;chr1:228454814-228632682:-1	hs1:6929266-6929266,hs1:223002855-223002855;hs1:9608555-9608555,hs1:17082878-17082878;hs1:16411862-16411862,hs1:204052851-204052851;hs1:41088909-41088909,hs1:211452286-211452286;hs1:193508150-193508150,hs1:197311616-197311616;hs1:209387883-209387883,hs1:215984986-215984986;hs18:58938257-58938257,hs14:105425455-105425455;hs20:28212606-28212606,hs3:84522975-84522975;hs3:80977085-80977085,hs1:158052243-158052243		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	6,8,12,15	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG065	Illumina HiSeq 2000	chr11:71343029-73802765:-1;chr12:68010736-68052393:1;chr13:49224823-50468703:-1;chr5:72192415-72193673:-1;chr6:105567621-132861645:-1;chr6:139952895-147336937:1;chr6:3009669-139952687:1	hs1:98275905-98275905,hs1:113273697-113273697;hs12:14506772-14506772,hs7:149989270-149989270;hs12:14514646-14514646,hs15:53207573-53207573;hs12:16829260-16829260,hs15:54045543-54045543;hs12:29522767-29522767,hs12:32709099-32709099;hs12:47646759-47646759,hs6:149700841-149700841;hs12:79781431-79781431,hs15:82417226-82417226;hs12:119440408-119440408,hs6:142993440-142993440;hs15:40231347-40231347,hs12:80162742-80162742;hs15:100006694-100006694,hs7:121288645-121288645;hs19:11504357-11504357,hs22:16500825-16500825;hs3:31670104-31670104,hs5:78448167-78448167;hs4:49021102-49021102,hs1:141547959-141547959;hs6:110462792-110462792,hs6:149748688-149748688;hs6:132761733-132761733,hs6:139232864-139232864;hs8:11037250-11037250,hs7:16958961-16958961;hs8:11613426-11613426,hs8:15450879-15450879;hs8:11631937-11631937,hs12:80817101-80817101;hs8:12284062-12284062,hs15:53985158-53985158;hs8:15450613-15450613,hs12:80256871-80256871;hs8:15554496-15554496,hs12:68010980-68010980;hs8:27950108-27950108,hs1:204062668-204062668		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	1,7	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG074	Illumina HiSeq 2000	chr1:161136806-164717238:-1;chr1:165516699-166573985:-1;chr1:165525571-166580798:1;chr1:169353666-169846970:1;chr1:169966121-171343966:-1;chr2:85107885-85109419:-1;chr7:105070585-106658688:-1;chr7:110440087-110968574:-1;chr7:85466212-104951519:1;chr7:87605427-106955682:-1;chr9:13774490-125208378:-1;chr9:22774444-125209873:1;chrX:151065582-151261917:-1	hs7:112055184-112055184,hs7:112094401-112094401;hs1:165837846-165837846,hs1:169870169-169870169;hs7:105066896-105066896,hs7:106645924-106645924;hs7:111796478-111796478,hs7:111806087-111806087;hs7:111916426-111916426,hs7:112093752-112093752;hs1:168679194-168679194,hs1:168895539-168895539;hs1:13101833-13101833,hs7:109944707-109944707;hsY:11929072-11929072,hs10:41706096-41706096;hs7:82539845-82539845,hs13:99069416-99069416;hs7:109852760-109852760,hs7:109873275-109873275;hs7:89334567-89334567,hs7:106168598-106168598;hs7:97968349-97968349,hs7:110474110-110474110;hs2:88942551-88942551,hs2:88978418-88978418;hs20:28252248-28252248,hs7:105752285-105752285;hs1:159430181-159430181,hs1:172193289-172193289;hs9:44010661-44010661,hs2:94838950-94838950;hs1:163359478-163359478,hs1:163382721-163382721;hs17:827988-827988,hs3:80842380-80842380;hs3:57430662-57430662,hs3:60881705-60881705		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	1,4,11,12	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG081	Illumina HiSeq 2000	chr10:135210223-135221652:-1;chr11:48324097-48330277:-1;chr11:77458412-77470894:-1;chr12:62518696-62526039:-1;chr15:42783127-42792027:-1;chr19:1839676-56743095:-1;chr19:57953041-61224839:-1;chr2:15290346-15403819:-1;chr2:228700177-228775363:-1;chr2:60515103-60536057:1;chr3:103031169-103221628:1;chr3:120755640-120766403:-1;chr5:77661760-77791264:-1;chr6:78415700-159397414:-1;chr7:31109735-31122428:1;chr8:59981864-60072798:-1;chr9:104534247-104552540:1	hs1:169413686-169413686,hs1:169451283-169451283;hs11:58248849-58248849,hs11:58291772-58291772;hs12:14067180-14067180,hs12:14086713-14086713;hs12:14076874-14076874,hs2:222123802-222123802;hs12:93617229-93617229,hs12:93641630-93641630;hs12:93624809-93624809,hs12:93640657-93640657;hs4:38520630-38520630,hs4:38536299-38536299;hs4:65363665-65363665,hs4:65373125-65373125;hs4:65364279-65364279,hs4:65411541-65411541		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	2,8	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG116	Illumina HiSeq 2000	chr10:37310572-59129250:-1;chr11:48324097-48330277:-1;chr12:126618424-126647066:1;chr13:18813546-53873925:-1;chr18:20509151-46914186:-1;chr1:237482552-237691235:1;chr1:3327087-8593408:-1;chr2:40798455-50552509:1;chr2:51424401-51528988:1;chr2:51425299-53158169:-1;chr3:1807114-3815014:1;chr6:109617475-110600692:1;chr6:109684178-109707834:1;chr6:109749781-109925749:1;chr6:136951284-139215017:-1;chr9:104573081-129090329:1;chrX:7327904-37082985:-1	hs10:109651099-109651099,hs10:109682554-109682554;hs10:127180408-127180408,hs10:127191092-127191092;hs14:86394108-86394108,hs14:99079370-99079370;hs14:105397889-105397889,hs3:189143698-189143698;hs14:105397897-105397897,hs3:189143731-189143731;hs2:53751682-53751682,hs7:158463320-158463320;hs22:15293067-15293067,hs6:165001564-165001564;hs3:2928142-2928142,hs3:5234158-5234158;hs3:3820714-3820714,hs3:5631812-5631812;hs3:5653917-5653917,hs3:5741494-5741494;hs3:23819256-23819256,hs3:23831402-23831402;hs3:26226052-26226052,hs3:28419205-28419205;hs3:27553307-27553307,hs2:34024816-34024816;hs3:156749177-156749177,hs3:192809310-192809310;hs3:178046832-178046832,hs3:192809461-192809461;hs5:2255807-2255807,hs20:51824061-51824061;hs6:108388775-108388775,hs6:110631606-110631606;hs6:109707669-109707669,hs6:109714992-109714992;hs6:109740948-109740948,hs6:109764520-109764520;hs6:109908135-109908135,hs4:150073818-150073818;hs6:109912609-109912609,hs6:109928181-109928181;hs6:112095624-112095624,hs6:114557104-114557104;hs8:4485226-4485226,hsX:57953555-57953555;hs8:19772839-19772839,hs8:137370851-137370851;hs9:5725249-5725249,hs8:121983547-121983547;		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	16,17,2,6,8,X	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG132	Illumina HiSeq 2000	chr16:28538120-29886949:-1;chr2:53036933-79163725:-1;chr2:59927998-114919109:1;chr2:66623177-84383564:-1;chr2:67023548-106133091:1;chr2:78392100-103293338:1;chr8:36998729-80575343:-1;chrX:33795147-34222789:1	hs17:21056252-21056252,hs17:21069872-21069872;hs17:21134312-21134312,hs10:41936522-41936522;hs2:50528422-50528422,hs2:103156366-103156366;hs2:67565481-67565481,hs2:94743186-94743186;hs2:99497033-99497033,hs2:106139452-106139452;hs6:58886185-58886185,hs13:106609271-106609271;hs8:2792863-2792863,hs8:43026187-43026187;hs8:29602247-29602247,hs8:30277494-30277494;hs8:36974639-36974639,hs8:36999408-36999408;hs8:40756189-40756189,hs8:56172812-56172812		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA
Research	23699601	Ryan D. Morin, Karen Mungall, Erin Pleasance, Andrew J. Mungall, Rodrigo Goya, Ryan D. Huff, David W. Scott, Jiarui Ding, Andrew Roth, Readman Chiu, Richard D. Corbett, Fong Chun Chan, Maria Mendez-Lago, Diane L. Trinh, Madison Bolger-Munro, Greg Taylor, Alireza Hadj Khodabakhshi, Susana Ben-Neriah, Julia Pon, Barbara Meissner, Bruce Woolcock, Noushin Farnoud, Sanja Rogic, Emilia L. Lim, Nathalie A. Johnson, Sohrab Shah, Steven Jones, Christian Steidl, Robert Holt, Inanc Birol, Richard Moore, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra	Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing	Blood	2013 Aug	8,11,18	Diffuse large B-cell lymphoma	Next Generation Sequencing	Homo sapiens	RG138	Illumina HiSeq 2000	chr11:18716208-45329936:1;chr1:115502658-121186800:-1;chr1:6182243-95195626:-1;chr8:128525264-129544861:1;chr8:129282247-131956016:-1;chr8:50109248-70530204:1;chrX:152759760-153024102:1	hs8:50172131-50172131,hs8:70391059-70391059;hs2:4183144-4183144,hs2:4201354-4201354;hs6:58886798-58886798,hs6:75169496-75169496;hs11:45359344-45359344,hs11:46160005-46160005;hs17:21134312-21134312,hs10:41936522-41936522;hs3:183427260-183427260,hs3:183529139-183529139;hs4:105162145-105162145,hs4:106553660-106553660;hs4:105162153-105162153,hs4:105226236-105226236;hs19:1871143-1871143,hs19:2463361-2463361;hs6:58887071-58887071,hs6:76237245-76237245;hs18:35880144-35880144,hs18:55105867-55105867;hs22:15399058-15399058,hs12:120804324-120804324;hs8:37903757-37903757,hs4:190921474-190921474;hs8:50080227-50080227,hs8:70531495-70531495;hs18:35881611-35881611,hs18:52677321-52677321;hs18:36402620-36402620,hs18:54945798-54945798;hs18:36678172-36678172,hs18:52829615-52829615		Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada	Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.	NCBI 36/hg18		phs000532		Yes	NA