Nature - USA (2019-07-18)

LETTER RESEARCH

p = 0.051

0

100

200

300

400

12345+

FOXA1 copy−number

FOXA1 expression (FPKM)

MIPOL1 RP11-356O9.1O9.^1 FOXA1 TTC6

Tandem-Duplication

ETV1 Translocation

HAPLOTYPE

MDA-PCa-2b

PCa cells

d

e

0%

25%

50%

75%

100%

Allelic read support

SNP #1 SNP #2 SNP #1

MDA-PCa-2b samples LNCaP samples

Allele type: translocated duplicated

Independent RNASeq libraries Independent RNASeq libraries

sgCTRL

sgMIPOL1-UTR

sgFOXMIND_1

sgFOXMIND_2 sgFOXMIND_3

0%

25%

50%

75%

100%

Read support

Genotype

G

A

Chr14: 37566636

0%

25%

50%

75%

100%

Read support

Genotype

C

T

Chr14: 37566514

0%

25%

50%

75%

100%

Read support

Genotype

G

A

RP11-356O9.1 SNP:Chr14: 37565229

(hg38)

Independent MDA-PCa-2b

RNASeq libraries

f

−2.0

0.0

2.0

4.0

Pearson

residuals:

p−value =1.1333e−06

Tloc/inv/del

Duplication

WT

Mut

Mut WT







p = 0.0055

0

50

100

150

Rearranged WT

Duplication (RNA)

FOXA1 / TTC6 expression ratio







p = 0.015

0

50

100

150

Rearranged WT

Duplication (WXS)









p = 0.012

0

50

100

150

Rearranged WT

Translocations (RNA)

FOXA1 / TTC6 expression ratio

ab c

g

BActin HP

RT1

Tubulin E

TV

1

TTC6

Housekeeping control genes

p<0.0001 p<0.0001

LNCaP Cells

0.0

0.2

0.4

0.6

0.8

1.0

1.2

Relative expression

FOXA1:

Extended Data Fig. 10 | See next page for caption.