doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`
`
`1111
`
`
`
`6.46.4
`
`Physical coverage (x haploid genomes)
`
`
`6.7
`4.4
`5.9
`4.94.9
`6.96.9
`
`9.1
`
`7.6
`
`Neither end mapped
`One end mapped
`Chimaeras
`Correct
`
`125
`
`100
`
`75
`
`50
`
`02
`
`0
`
`5
`
`ns)
`
`Reads (million
`
`HCC1187 HCC1395 HCC1599 HCC1937 HCC1954 HCC2157 HCC2218 HCC38 HCC1143
`
`Physical coverage (x haploid genomes)
`
`
`6 4 5 7 4 2 5 7 6 3 3 8 5 36.4 5.7 4.2 5.7 6.3 3.8 5.3
`6 11 4 7 8 6 3 4 8 6 9 6 8 6 66 11.4 7.8 6.3 4.8 6.9 6.8 6.6
`
`Neither end mapped
`One end mapped
`Chimaeras
`Correct
`
`125
`
`
`
`100100
`
`75
`
`50
`
`25
`
`0
`
`s)
`Reads (millions
`
`PD3695a
`PD3690a
`PD3688a
`PD3672a
`PD3670a
`PD3668a
`PD3666a
`PD3664a
`PD3665a
`PD3667a
`PD3669a
`PD3671a
`PD3687a
`PD3689a
`PD3693a
`
`Supplementary Figure 1 Haploid physical coverage of breast cancer samples. Physical
`coverage indicates the number of DNA fragments of which both ends have been sequenced
`that on average overlie any position in the genome.
`
`www.nature.com/nature
`
`1
`
`Personalis EX2162
`
`
`
`SUPPLEMENTARY INFORMATION
`
`
`
`1111
`
`
`
`6.46.4
`
`Physical coverage (x haploid genomes)
`
`
`6.7
`4.4
`5.9
`4.94.9
`6.96.9
`
`9.1
`
`7.6
`
`Neither end mapped
`One end mapped
`Chimaeras
`Correct
`
`125
`
`100
`
`75
`
`50
`
`02
`
`0
`
`5
`
`ns)
`
`Reads (million
`
`HCC1187 HCC1395 HCC1599 HCC1937 HCC1954 HCC2157 HCC2218 HCC38 HCC1143
`
`Physical coverage (x haploid genomes)
`
`
`6 4 5 7 4 2 5 7 6 3 3 8 5 36.4 5.7 4.2 5.7 6.3 3.8 5.3
`6 11 4 7 8 6 3 4 8 6 9 6 8 6 66 11.4 7.8 6.3 4.8 6.9 6.8 6.6
`
`Neither end mapped
`One end mapped
`Chimaeras
`Correct
`
`125
`
`
`
`100100
`
`75
`
`50
`
`25
`
`0
`
`s)
`Reads (millions
`
`PD3695a
`PD3690a
`PD3688a
`PD3672a
`PD3670a
`PD3668a
`PD3666a
`PD3664a
`PD3665a
`PD3667a
`PD3669a
`PD3671a
`PD3687a
`PD3689a
`PD3693a
`
`Supplementary Figure 1 Haploid physical coverage of breast cancer samples. Physical
`coverage indicates the number of DNA fragments of which both ends have been sequenced
`that on average overlie any position in the genome.
`
`www.nature.com/nature
`
`1
`
`Personalis EX2162
`
`
`
`doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`HCC2157
`
`HCC1395
`
`HCC2218
`
`PD3667a
`
`PD3671a
`
`PD3689a
`
`HCC1954
`
`HCC1187
`
`PD3664a
`
`PD3668a
`
`PD3672a
`
`PD3690a
`
`HCC1937
`
`HCC1143 PD3665a
`
`PD3669a
`
`PD3687a
`
`PD3693a
`
`HCC1599
`
`HCC38 PD3666a
`
`PD3670a
`
`PD3688a
`
`PD3695a
`
`Supplementary Figure 2 Genome wide circos plots of somatic rearrangements in all 24
`breast cancers in the study.
`
`www.nature.com/nature
`
`2
`
`Personalis EX2162
`
`
`
`doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`bps
`600
`400
`
`200
`
`bps
`
`300
`
`200
`
`T
`
`N
`
`Genomic PCR
`
`T
`
`N
`
`RT-PCR
`
`a
`
`b
`
`
`
`cc
`
`NFIA
`(exons 1-2)
`
`MH(cid:3)1
`
`DNA
`Binding
`
`CTF/NF1
`Binding
`
`
`
`dd
`
`e
`
`EHF
`(exons 5-9)
`
`ETS
`
`DNA
`Binding
`
`
`
`Dual colour FISHDual colour FISH
`
`exon 2
`NFIA
`
`exon 5
`EHF
`
`Supplementary Figure 3 NFIA-EHF, an expressed, in frame fusion gene caused by an
`interchromosomal rearrangement
`in breast cancer cell
`line HCC1937. (a) Across
`rearrangement PCR to confirm the presence of the somatic rearrangement in the cancer but
`not in normal DNA; (b) RT-PCR of RNA between NFIA exon 2 and EHF exon 5 to confirm
`the presence of a chimeric expressed transcript; (c) Representative picture of dual colour
`FISH confirming a translocation in HCC1937. Red probe corresponds to BAC RP11-
`364M11, chromosome 1: 61,064,196-61,228,554. Green probe corresponds to BAC RP11-
`277N08, chromosome 11: 34,772,104-34,965,946. (d) Schematic diagram of the protein
`domains fused in the predicted NFIA/EHF fusion protein. Domains from NFIA are blue,
`domains from EHF are red (e) Sequence from RT-PCR product shown in (b) confirming
`NFIA exon 2 fused to EHF exon 5.
`
`www.nature.com/nature
`
`3
`
`Personalis EX2162
`
`
`
`doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`HCC1599
`
`HCC38
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`HCC2157
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`HCC1954
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`
`
`100100
`
`50
`
`0
`
`HCC1937
`
`HCC1395
`
`HCC1187
`
`HCC1143
`
`200
`150
`100
`50
`0
`
`
`
`HCC2218HCC2218
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`ements
`
`No(cid:3)of(cid:3)rearrang
`
`ngements
`
`No(cid:3)of(cid:3)rearran
`
`200
`
`150
`
`100
`
`50
`
`0
`
`ements
`
`No(cid:3)of(cid:3)rearrange
`
`
`
`PD3664PD3664a
`
`
`
`PD3665PD3665a
`
`
`
`PD3666PD3666a
`
`PD3670a
`
`PD3688a
`
`PD3668a
`
`PD3672a
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`150
`100
`50
`0
`
`PD3669a
`
`PD3687a
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`PD3667a
`
`PD3671a
`
`200
`150
`100
`50
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`150
`100
`50
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`200
`
`150
`
`100
`
`50
`
`0
`
`ements
`
`No(cid:3)of(cid:3)rearrang
`
`ements
`
`No(cid:3)of(cid:3)rearrange
`
`gements
`
`No(cid:3)of(cid:3)rearrang
`
`PD3689a
`PD3689
`
`PD3690a
`PD3690
`
`PD3693a
`PD3693
`
`PD3695a
`PD3695
`
`Supplementary Figure 4 SLC26A6-PRKAR2A, an expressed, in-frame fusion gene
`generated by a tandem duplication in the breast cancer cell line HCC38. (a) Across
`
`www.nature.com/nature
`
`4
`
`Personalis EX2162
`
`
`
`doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`rearrangement PCR to confirm the presence of the somatic rearrangement in the cancer but
`not in normal DNA; (b) RT-PCR of RNA between SLC26A6 exon 17 and PRKAR2A exon 4
`to confirm the presence of a chimeric expressed transcript; (c) Dual colour FISH confirming
`the 3p21.31 tandem duplication in HCC38. Green-labelled BAC RP11-148G20 is within the
`tandem duplication. Red-labelled BAC RP11-527M10 is located ~3 Mb telomeric of the
`tandem duplication. (d) Schematic diagram of the protein domains in the predicted
`SLC26A6-PRKAR2A fusion protein. Domains from SLC26A6 are blue, domains from
`PRKAR2A are red. (e) Sequence from RT-PCR product shown in (b) confirming SLC26A6
`exon 17 fused to PRKAR2A exon 4.
`
`www.nature.com/nature
`
`5
`
`Personalis EX2162
`
`
`
`doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`bps
`
`600(cid:3)
`400
`
`200
`
`bps
`
`600
`400
`200
`
`T
`
`N
`
`Genomic(cid:3)(cid:3)PCR
`
`T
`
`N
`
`RT(cid:882)PCR
`
`a
`
`b
`
`cc
`
`d
`d
`
`e
`
`SLC26A6
`(exons 1-17)
`
`PRKAR2A
`(exons 4-11)
`
`Sulphate
`Transporter
`
`cNMP
`Binding
`
`cAMP/cGMP
`Kinase
`
`cNMP
`Binding
`
`Dual colour FISH Dual colour FISH of 3p21.31of 3p21.31
`
`
`
`tandem duplicationtandem duplication
`
`exon 17
`SLC26A6
`
`exon 4
`PRKAR2A
`
`Supplementary Figure 5 Prevalence of architectures of rearrangements in all 24 breast
`cancers in the study: Deletion (dark blue), tandem duplication (red), inverted orientation
`(green), interchromosomal (light blue), breakpoint(s) within an amplicon (orange).
`
`www.nature.com/nature
`
`6
`
`Personalis EX2162
`
`
`
`doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`0
`
`1
`
`5 >5
`4
`3
`2
`HCC1599
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`1
`
`4
`3
`2
`HCC1954
`
`5 >5
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`1
`
`4
`3
`2
`HCC1937
`
`5 >5
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`40
`30
`20
`10
`0
`
`0
`
`1
`
`4
`3
`2
`HCC2157
`
`5 >5
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`No of rearrangements
`
`No of rearrangements
`
`0
`
`1
`
`5 >5
`
`4
`3
`2
`HCC1143
`
`0
`
`1
`
`5 >5
`
`2
`
`4
`3
`HCC38
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`0
`
`1
`
`5 >5
`4
`3
`2
`HCC1187
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`0
`
`1
`
`4
`3
`2
`HCC1395
`
`5 >5
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`No of rearrangements
`
`0
`
`1
`
`5 >5
`
`0
`
`1
`
`5 >5
`
`0
`
`1
`
`4
`3
`2
`PD3664a
`
`4
`3
`2
`PD3665a
`
`5 >5
`
`0
`
`1
`
`5 >5
`
`4
`3
`2
`HCC2218
`
`4
`3
`2
`PD3666a
`
`0
`
`1
`
`5 >5
`
`2
`3
`4
`PD3670a
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`0
`
`1
`
`4
`3
`2
`PD3668a
`
`5 >5
`
`0
`
`1
`
`5 >5
`
`4
`3
`2
`PD3669a
`
`50
`40
`30
`20
`10
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`0
`
`1
`
`2
`3
`4
`PD3667a
`
`5 >5
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`40
`30
`20
`10
`0
`
`No of rearrangements
`
`No of rearrangements
`
`0
`
`1
`
`2
`3
`4
`PD3671a
`
`5 >5
`
`0
`
`1
`
`4
`3
`2
`PD3672a
`
`5 >5
`
`0
`
`1
`
`4
`3
`2
`PD3687a
`
`5 >5
`
`0
`
`1
`
`4
`3
`2
`PD3688a
`
`5 >5
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`0
`
`1
`
`5 >5
`4
`3
`2
`PD3693a
`
`0
`
`4
`3
`2
`1
` PD3695a
`
`5 >5
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`50
`
`40
`
`30
`
`20
`
`10
`
`0
`
`No of rearrangements
`
`0
`
`1
`
`4
`3
`2
`PD3689a
`
`5 >5
`
`0
`
`1
`
`4
`3
`2
`PD3690a
`
`5 >5
`
`Supplementary Figure 6 Number of nucleotides of overlapping microhomology at
`rearrangement junctions in the 24 breast cancers.
`
`www.nature.com/nature
`
`7
`
`Personalis EX2162
`
`
`
`doi: 10.1038/nature08645
`
`SUPPLEMENTARY INFORMATION
`
`300
`
`250
`
`200
`
`150
`
`100
`
`50
`
`0
`
`Number of rearrangements
`
`0
`
`1
`
`2
`
`3
`
`4
`
`5
`
`6-20
`
`>20
`
`Non-templated sequence (bps)
`Supplementary Figure 7 Nucleotides of non-templated DNA sequence at rearrangement
`breakpoints in the 24 breast cancers.
`
`www.nature.com/nature
`
`8
`
`Personalis EX2162
`
`
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