Table 1. Genotype differences observed in 12 paired samples: Clinical samples analyzed by SureSelect and derived isolates sequenced classically.

Sample code	Clinical sample ISC genotype	Derived isolate ISC genotype	Total base difference*	Homozygous difference	Heterozygous difference	Indel difference	Karyotype (bone marrow)	Karyotype (derived isolate)
BPK77	ISC4	ISC6	47	20	7	4	almost diploid**	trisomy on ch5 and 11
BPK80	UG	ISC4	42	17	8	3	almost diploid	trisomic on ch2, 4, 7, 8, 9, 11, 12, 20, 26, 33 and 35. tetrasomic on ch23
BPK87	ISC6	ISC4	55	21	13	4	almost diploid	regular
BPK91	ISC3	ISC4	36	14	8	8	almost diploid	trisomic on ch20, 26 and 33
BPK156	ISC3	ISC1	68459	34146	167	6275	almost diploid	monosomic on ch17
BPK157	ISC4	ISC1	64254	29942	4370	8281	almost diploid	trisomic on ch23, 33 and 35
BPK177	ISC9	ISC5	55	26	3	3	almost diploid	trisomic on ch2, 5, 8, 9, 11, 12, 13, 14, 20, 23, 27 and 32. tetrasomic on ch33
BPK276	ISC5	ISC4	40	18	4	1	monosomic on ch17	trisomic on ch4, 11, 20, 23. tetrasomic on ch5
BPK280	ISC4	UG	21	9	3	4	almost diploid	trisomic on ch1, 7, 8, 10, 13. 15, 20, 22, 23. tetrasomic on ch9
BPK81	ISC4	ISC4	13	3	7	LdAQP1: frameshift G/GA insertion	almost diploid	regular
BPK181	ISC6	ISC6	5	0	5	0	almost diploid	trisomic on ch8, 9, 13 and 23
BPK208	ISC4	ISC4	11	1	9	0	almost diploid	trisomic on ch1, 7, 8, 10, 13, 15, 20, 22 and 23. tetrasomic on ch9

Total base difference* = Homozygous difference x 2 + Heterozygous difference. Almost diploid**: S-value was 2 in all chromosomes except the tetrasomic chromosome 31. Notes: (1) the S-values of chromosome 11 in all bone marrow samples were slightly higher due to amplification artefact and therefore, their values were assumed to be disomic. (2) The S-values of chromosome 31 of BPK87BM and BPK80BM were lower than the expected tetrasomic values due to lower genome coverage.