Table 2. LAM-PCR analysis of provirus... | American Society of Hematology

Table 2.

LAM-PCR analysis of provirus integrants in identified sites

Patient no. and Seq no.	Time after transplantation, d	Genomic length	LAM amplicon length, bp	Integrant-host-junction sequence	Identity, %	Chromosome	Sequence orientation	Integration locus	Genomic locus/RefSeq gene
1
80852 H02	12	54	147	TCCATTTAATACAGTtgaaagaccc	100.0	4	Plus	48114519	1777 bp upstream of TEC
78933 B06	12	177	270	GACCAGATGTGGGAAtgaaagaccc	98.4	5	Plus	94448967	6025 bp upstream of MCTP1
78933 C06	12	139	232	TGCTATAGTTACCGCtgaaagaccc	100.0	10	Minus	121145584	187767 bp in intron 3 of GRK5
80852 F01	12	26	119	ATAAAAGGGAAGCCTtgaaagaccc	100.0	11	Plus	128037827	31372 bp upstream of FLI1
78933 B07	13	38	131	CACACACACTCATAAtgaaagaccc	100.0	1	Minus	155874598	14878 bp upstream of AIM2
78933 F07	13	77	170	GACCTCAGGTGATCCtgaaagaccc	100.0	1	Plus	164251126	3588 bp in intron 1 of CREG1
78933 D07	13	52	145	TTGCTTACCCCACTGtgaaagaccc	100.0	2	Minus	136728494	19044 bp upstream of CXCR4
79697 C08	13	130	223	ATGTCACAGACAAAGtgaaagaccc	100.0	2	Plus	17225602	41799 bp upstream of VSNL1
78933 H06	13	28	121	AACAAATGAGGTTAGtgaaagaccc	100.0	6	Plus	2935514	1582 bp in exon 1 of DKFZp6861 15217
78933 E07	13	125	218	CTTGAAGGGTGGGTGtgaaagaccc	100.0	7	Minus	94707759	1187 bp in intron 1 of PON2
80852 G03	13	289	382	CTCCCTATATGATTGtgaaagaccc	100.0	7	Plus	43647712	27533 bp downstream of BLVRA
80852 C04	13	79	172	CCAATAGCCTACCTTtgaaagaccc	100.0	8	Plus	62757554	32002 bp in intron 2 of ASPH
80852 G04	13	80	173	ATCGCTTGAACCCGGtgaaagaccc	98.8	9	Minus	129009529	8983 bp downstream of IER5L
78933 F06	13	27	120	TCTGTCTTCAAGTTCtgaaagaccc	100.0	12	Minus	107639068	11307 bp upstream of CORO1C
80852 E03	13	278	371	TCCAGTAAGAGCTATtgaaagaccc	99.7	12	Minus	92744212	170593 bp in intron 2 of CRADD
80852 A04	13	26	119	GCCGTGCAATACCTTtgaaagaccc	100.0	12	Plus	15927381	768 bp in intron 1 of STRAP
79697 C09	14	26	119	GGAACTACTTTTTCCtgaaagaccc	100.0	4	Plus	185981905	35854 bp in exon 9 of FLJ33167
80852 A06	14	60	153	CATAGTTTCAAATAAtgaaaggccc	100.0	5	Minus	59965457	66256 bp in intron 7 of DEPDC1B
79697 E09	14	93	186	GTGGGAGGATCGCTTtgaaagaccc	100.0	6	Minus	109393783	117465 bp in intron 17 of ARMC2
78933 A09	14	49	142	GAAAGTTATTTAGTTtgaaagaccc	100.0	8	Plus	124166005	11904 bp in intron 4 of MGC21654
80852 G07	14	24	117	GAACGGTCCTCTGACtgaaagaccc	100.0	15	Plus	48215414	16703 bp upstream of ATP8B4
79697 F09	14	23	116	CAGGATAGGATGCAGtgaaagaccc	100.0	18	Minus	40593847	58380 bp in intron 1 of SETBP1
78933 H07	14	119	212	TTAAGAGCTTGAGGCtgaaagaccc	99.2	20	Minus	30763159	31877 bp in intron 3 of COMMD7
78933 A08	14	207	300	ATACAGGTTCCAGGGtgaaagaccc	99.1	20	Plus	237848	8887 bp downstream of ZCCHC3
80852 A08	15	76	169	GTGTGGCCTAATAAtgaaagaccc	98.7	2	Plus	36543852	48804 bp in intron 2 of CRIM1
80852 H08	15	159	252	ATCTTAACAAACAGGtgaaagaccc	100.0	3	Plus	15815709	2372 bp upstream of ANKRD28
80852 A09	15	89	182	GTTAAGATATTTCATtgaaagaccc	100.0	3	Minus	159553012	242418 bp in intron 5 of MGC12197
80852 G08	15	21	114	TTTCATTCAAGAATCtgaaagaccc	100.0	13	Plus	77171831	41659 bp upstream of FLJ30046
79697 H10	21	137	230	AATATGACTGACATCtgaaagaccc	100.0	5	Minus	10558333	40196 bp downstream of ROPN1L
78933 E11	21	167	260	TGCTTTGTGTCGCAGtgaaagaccc	98.3	7	Minus	23111987	193 bp upstream of C7orf30
78933 E02	21	22	115	AGGTGCCATTCCTTTtgaaagaccc	100.0	12	Minus	121193424	16278 bp in Intron 1 of MGC35140
78933 H10	21	176	269	CCCCCACCCACCTACtgaaagaccc	99.5	17	Minus	7181218	612 bp in intron 1/exon 1 of CENTB1
78933 A11	21	86	179	TGCAAAGATTGTTTCtgaaagaccc	100.0	18	Plus	27468862	49764 bp in intron 5 of B4GALT6
78933 D10	21	115	208	GTCTGGGGTTCAAACtgaaagaccc	97.4	19	Plus	44428610	1159 bp upstream of IL28B
80852 F12	21	101	194	TCCCCTCAGTCCTCAtgaaagaccc	100.0	20	Plus	5573746	34074 bp upstream of KIAA1434
2
78933 A02	21	54	147	CTGAATACTTACTATtgaaagaccc	100.0	16	Minus	28531941	3791 bp upstream of SULT1A1
3
9084	13	79	172	GTCTTTGTTTCATAGtgaaagaccc	100.0	2	Minus	136732882	23434 bp upstream of CXCR4
9086	14	110	203	GAGCTGAGATCGCGCtgaaagaccc	99.1	12	Minus	120560220	10060 bp in intron 1 of LOC283385
9088	15	89	182	ACATTGGCACATCGCtgaaagaccc	100.0	12	Plus	18867724	84336 bp upstream of CAPZA3
4065	152	212	305	GGGGAAGGAAAAAACtgaaagaccc	99.6	1	Plus	181568775	106526 bp in intron 5 of C1orf24
9706*	335	93	186	CAAGGAGAGTTTGATtgaaagaccc	94.6	2	Plus	128781865	10617 bp in intron 1 of HS6ST1

Patient no. and Seq no.	Time after transplantation, d	Genomic length	LAM amplicon length, bp	Integrant-host-junction sequence	Identity, %	Chromosome	Sequence orientation	Integration locus	Genomic locus/RefSeq gene
1
80852 H02	12	54	147	TCCATTTAATACAGTtgaaagaccc	100.0	4	Plus	48114519	1777 bp upstream of TEC
78933 B06	12	177	270	GACCAGATGTGGGAAtgaaagaccc	98.4	5	Plus	94448967	6025 bp upstream of MCTP1
78933 C06	12	139	232	TGCTATAGTTACCGCtgaaagaccc	100.0	10	Minus	121145584	187767 bp in intron 3 of GRK5
80852 F01	12	26	119	ATAAAAGGGAAGCCTtgaaagaccc	100.0	11	Plus	128037827	31372 bp upstream of FLI1
78933 B07	13	38	131	CACACACACTCATAAtgaaagaccc	100.0	1	Minus	155874598	14878 bp upstream of AIM2
78933 F07	13	77	170	GACCTCAGGTGATCCtgaaagaccc	100.0	1	Plus	164251126	3588 bp in intron 1 of CREG1
78933 D07	13	52	145	TTGCTTACCCCACTGtgaaagaccc	100.0	2	Minus	136728494	19044 bp upstream of CXCR4
79697 C08	13	130	223	ATGTCACAGACAAAGtgaaagaccc	100.0	2	Plus	17225602	41799 bp upstream of VSNL1
78933 H06	13	28	121	AACAAATGAGGTTAGtgaaagaccc	100.0	6	Plus	2935514	1582 bp in exon 1 of DKFZp6861 15217
78933 E07	13	125	218	CTTGAAGGGTGGGTGtgaaagaccc	100.0	7	Minus	94707759	1187 bp in intron 1 of PON2
80852 G03	13	289	382	CTCCCTATATGATTGtgaaagaccc	100.0	7	Plus	43647712	27533 bp downstream of BLVRA
80852 C04	13	79	172	CCAATAGCCTACCTTtgaaagaccc	100.0	8	Plus	62757554	32002 bp in intron 2 of ASPH
80852 G04	13	80	173	ATCGCTTGAACCCGGtgaaagaccc	98.8	9	Minus	129009529	8983 bp downstream of IER5L
78933 F06	13	27	120	TCTGTCTTCAAGTTCtgaaagaccc	100.0	12	Minus	107639068	11307 bp upstream of CORO1C
80852 E03	13	278	371	TCCAGTAAGAGCTATtgaaagaccc	99.7	12	Minus	92744212	170593 bp in intron 2 of CRADD
80852 A04	13	26	119	GCCGTGCAATACCTTtgaaagaccc	100.0	12	Plus	15927381	768 bp in intron 1 of STRAP
79697 C09	14	26	119	GGAACTACTTTTTCCtgaaagaccc	100.0	4	Plus	185981905	35854 bp in exon 9 of FLJ33167
80852 A06	14	60	153	CATAGTTTCAAATAAtgaaaggccc	100.0	5	Minus	59965457	66256 bp in intron 7 of DEPDC1B
79697 E09	14	93	186	GTGGGAGGATCGCTTtgaaagaccc	100.0	6	Minus	109393783	117465 bp in intron 17 of ARMC2
78933 A09	14	49	142	GAAAGTTATTTAGTTtgaaagaccc	100.0	8	Plus	124166005	11904 bp in intron 4 of MGC21654
80852 G07	14	24	117	GAACGGTCCTCTGACtgaaagaccc	100.0	15	Plus	48215414	16703 bp upstream of ATP8B4
79697 F09	14	23	116	CAGGATAGGATGCAGtgaaagaccc	100.0	18	Minus	40593847	58380 bp in intron 1 of SETBP1
78933 H07	14	119	212	TTAAGAGCTTGAGGCtgaaagaccc	99.2	20	Minus	30763159	31877 bp in intron 3 of COMMD7
78933 A08	14	207	300	ATACAGGTTCCAGGGtgaaagaccc	99.1	20	Plus	237848	8887 bp downstream of ZCCHC3
80852 A08	15	76	169	GTGTGGCCTAATAAtgaaagaccc	98.7	2	Plus	36543852	48804 bp in intron 2 of CRIM1
80852 H08	15	159	252	ATCTTAACAAACAGGtgaaagaccc	100.0	3	Plus	15815709	2372 bp upstream of ANKRD28
80852 A09	15	89	182	GTTAAGATATTTCATtgaaagaccc	100.0	3	Minus	159553012	242418 bp in intron 5 of MGC12197
80852 G08	15	21	114	TTTCATTCAAGAATCtgaaagaccc	100.0	13	Plus	77171831	41659 bp upstream of FLJ30046
79697 H10	21	137	230	AATATGACTGACATCtgaaagaccc	100.0	5	Minus	10558333	40196 bp downstream of ROPN1L
78933 E11	21	167	260	TGCTTTGTGTCGCAGtgaaagaccc	98.3	7	Minus	23111987	193 bp upstream of C7orf30
78933 E02	21	22	115	AGGTGCCATTCCTTTtgaaagaccc	100.0	12	Minus	121193424	16278 bp in Intron 1 of MGC35140
78933 H10	21	176	269	CCCCCACCCACCTACtgaaagaccc	99.5	17	Minus	7181218	612 bp in intron 1/exon 1 of CENTB1
78933 A11	21	86	179	TGCAAAGATTGTTTCtgaaagaccc	100.0	18	Plus	27468862	49764 bp in intron 5 of B4GALT6
78933 D10	21	115	208	GTCTGGGGTTCAAACtgaaagaccc	97.4	19	Plus	44428610	1159 bp upstream of IL28B
80852 F12	21	101	194	TCCCCTCAGTCCTCAtgaaagaccc	100.0	20	Plus	5573746	34074 bp upstream of KIAA1434
2
78933 A02	21	54	147	CTGAATACTTACTATtgaaagaccc	100.0	16	Minus	28531941	3791 bp upstream of SULT1A1
3
9084	13	79	172	GTCTTTGTTTCATAGtgaaagaccc	100.0	2	Minus	136732882	23434 bp upstream of CXCR4
9086	14	110	203	GAGCTGAGATCGCGCtgaaagaccc	99.1	12	Minus	120560220	10060 bp in intron 1 of LOC283385
9088	15	89	182	ACATTGGCACATCGCtgaaagaccc	100.0	12	Plus	18867724	84336 bp upstream of CAPZA3
4065	152	212	305	GGGGAAGGAAAAAACtgaaagaccc	99.6	1	Plus	181568775	106526 bp in intron 5 of C1orf24
9706*	335	93	186	CAAGGAGAGTTTGATtgaaagaccc	94.6	2	Plus	128781865	10617 bp in intron 1 of HS6ST1

All patient samples analyzed were derived from cloned and sequenced PB LAM products as shown in Figure 1. Each sequenced LAM-PCR amplicon was aligned to the human genome database, and the insertion site was identified using University of California, Santa Cruz BLAT search tools (http://genome.ucsc.edu/). Integrant-host-junction sequence present in the first 15 nucleotides of the genomic DNA flanking the 5′-LTR (10 nucleotides). Genomic length denotes the size of the LAM-PCR amplicon without linker and LTR sequences. A complete list of all integrants analyzed is provided in Table S1. All cells analyzed were WBCs, except as shown by the asterisk (*), where purified granulocytes were analyzed.

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