Supplementary Figure 1 Expression profiles of cell-specific surface markers and T-helper cell cytokines. Numbers on Y axis are the normalized gene expression levels calculated by the Cufflinks algorithm using RNA-seq data. Controls, CD4+ T-cells from five healthy donors. Th, T-helper cells; T-reg, regulatory T cells.

0

100

200

300

400

500

600

CD

4 C

D26

C

D7

IFN

G

IL2

IL12

A IL

12B

IL18

IL

18R1

ST

AT1

STAT

4 TB

X21

IL4

IL5

IL13

IL

7R

STAT

6 G

ATA3

IL

1A

IL17

A IL

6 ST

AT3

RORC

IL

10

TGFB

1 IR

F4

FOXP

3 ST

AT5A

ST

AT5B

Th1 Th2 Th17 T-reg

Gen

e Ex

pres

sion

(FPK

M)

CD

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 2 a b Mutation validated by transcriptional expression in RNA-seq. a) Summary of the validation status for all somatic mutations identified from 32 patients who had RNA-seq data available. b) A breakdown of the validation status by mutation types. The percent of total values were labeled for all pie charts. No information, no RNA-seq reads were mapped to the particular mutation site; Mutant allele not expressed, mutation site were covered but no variant alleles were detected; Mutant allele expressed, at least one variant supporting reads were detected; VAF, variant allele fraction.

55.2%27.8%

1.7%

15.3%

Frame-shift indels

21.1%

21.1%

9.9%

47.9%

In-frame indels

30.4%

8.7%8.7%

52.2%

Missense mutations

57.0%27.2%

1.3%14.5%

Nonsense mutations

50.7%

24.7%

2.7%

22.0%

Silent mutations

54.4%30.9%

1.7%13.0%

Splice site mutations

62.7%

25.5%

11.8%

RNA-seq Validation

Mutant allele is expressed and > 5%Mutant allele is expressed but < 5%

Mutant allele is not expressedNo information

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 3 The mutation rate of Sézary syndrome estimated by whole-exome sequencing. Only non-silent somatic mutations were counted.

Mut

atio

n Co

unt (

Non-

sile

nt)

0

50

100

150

200

250

01

2

3

4

5

6

78

Nonsilent m

utation rate (per Mb)

SPZ-028

SPZ-037

SPZ-038

SPZ-022

SPZ-034

SPZ-021

SPZ-004

SPZ-010

SPZ-007

SPZ-018

SPZ-009

SPZ-001

SPZ-016

SPZ-012

SPZ-026

SPZ-002

SPZ-019

SPZ-008

SPZ-015

SPZ-031

SPZ-032

SPZ-017

SPZ-003

SPZ-005

SPZ-029

SPZ-013

SPZ-033

SPZ-036

SPZ-025

SPZ-024

SPZ-030

SPZ-027

SPZ-006

SPZ-011

SPZ-020

SPZ-023

SPZ-014

Mutation CountMutation Rate (per Mb)

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 4 a c b The UVB mutation signature in Sézary syndrome. a) The heatmap on the left shows the mutation signatures across 37 Sézary syndrome patients in the discovery cohort. Samples are ordered by the fraction of UVB signatures. Three prominent signatures, out of 21 cancer mutation signatures (Covington and Wheeler, in preparation) were observed. The top two tracks indicate total mutation frequency (0–10.5, from black to white) and the race: Orange: Caucasian; Brown: African American. The figure on the right shows the relative proportions of each base change that characterizes each of the signatures shown in the heatmap. Each signature is displayed according to the 32 sequence contexts immediately 3’ and 5’ to the mutated base. The numbers on the y-axis indicate the fraction of mutations attributed to a specific mutation type. b) The number of mutations in each patient’s tumor that are attributable to CpG and UVB signatures. Blue: UVB, Red: CpG. See Online Methods (Mutation Signatures) for computation of mutation signature count. Virtually all Sézary syndrome samples exhibited some level of CpG (NCG > NTG) mutation at a nearly constant rate with respect to overall mutation rate. Many Sézary syndrome samples had mutations corresponding to UVB exposure, which was the principal factor driving increasing mutation rate. Anova analysis indicated that 85% of the variability in mutation counts is explained by the UVB signature component. c) Correlation analysis of UVB signatures in patients with prior radiation therapies. DNM, di-nucleotide mutations.

Not UVA UVB Treated

0 0.1 0.3 0.5Value

04

812

Color Keyand Histogram

Coun

t

UVB

CpG

TCR

M.RateRace

Variant

6

14

1

0.0

0.2

0.4

0.0

0.2

0.4

0.0

0.2

0.4

CpG

UVB

TCR

ACA

ACC

ACG

ACT

ATA

ATC

ATG

ATT

CCA

CCC

CCG

CCT

CTA

CTC

CTG

CTT

GCA

GCC

GCG

GCT

GTA

GTC

GTG

GTT

TCA

TCC

TCG

TCT

TTA

TTC

TTG

TTT

C>A

C>G

C>T

T>A

T>C

T>G

CaucasianAfrican American

0.00

0.25

0.50

0.75

1.00

ALL AML CSCC Melanoma SS0.0

0.1

0.2

0.3

0.4

0.5

African American Caucasian

% U

VB S

igna

ture

Ex

posu

reA

B

Figure 5: A) Signature heatmap of the three most penetrant signatures in SS. Tracks indicate mutation count and race. Values are ordered by UVB signatureexposure. Signatures are shown to the right with numbers indicating the signature designation in the 21 signature nsNMF solution from HGSC. B) UVB signatureexposure was independent of race and consistent with skin cancers. African American (and hispanic and indian [not shown]) races had significantly less overallUVB signature exposure compared with Caucasians. This is likely because of the protective effect of malanin in absorbing UVB radiaton (left). In comparisonto other cancers, SS had a UVB signature exposure similar to that of CSCC, much higher than other liquid cancers (AML and ALL), though not as high asMelanoma.

9

Mutation rate Race

UVB

CpG

TCR

0 0.1 0.3 0.5Value

04

812

Color Keyand Histogram

Cou

nt

UVB

CpG

TCR

M.RateRace

Variant

6

14

1

0.0

0.2

0.4

0.0

0.2

0.4

0.0

0.2

0.4

CpG

UVB

TCR

ACA

ACC

ACG

ACT

ATA

ATC

ATG

ATT

CCA

CCC

CCG

CCT

CTA

CTC

CTG

CTT

GCA

GCC

GCG

GCT

GTA

GTC

GTG

GTT

TCA

TCC

TCG

TCT

TTA

TTC

TTG

TTT

C>A

C>G

C>T

T>A

T>C

T>G

CaucasianAfrican American

0.00

0.25

0.50

0.75

1.00

ALL AML CSCC Melanoma SS0.0

0.1

0.2

0.3

0.4

0.5

African American Caucasian

% U

VB

Sig

natu

re

Exp

osur

e

A

B

Figure 5: A) Signature heatmap of the three most penetrant signatures in SS. Tracks indicate mutation count and race. Values are ordered by UVB signatureexposure. Signatures are shown to the right with numbers indicating the signature designation in the 21 signature nsNMF solution from HGSC. B) UVB signatureexposure was independent of race and consistent with skin cancers. African American (and hispanic and indian [not shown]) races had significantly less overallUVB signature exposure compared with Caucasians. This is likely because of the protective effect of malanin in absorbing UVB radiaton (left). In comparisonto other cancers, SS had a UVB signature exposure similar to that of CSCC, much higher than other liquid cancers (AML and ALL), though not as high asMelanoma.

9

0 0.1 0.3 0.5Value

04

812

Color Keyand Histogram

Cou

nt

UVB

CpG

TCR

M.RateRace

Variant

6

14

1

0.0

0.2

0.4

0.0

0.2

0.4

0.0

0.2

0.4

CpG

UVB

TCR

ACA

ACC

ACG

ACT

ATA

ATC

ATG

ATT

CCA

CCC

CCG

CCT

CTA

CTC

CTG

CTT

GCA

GCC

GCG

GCT

GTA

GTC

GTG

GTT

TCA

TCC

TCG

TCT

TTA

TTC

TTG

TTT

C>A

C>G

C>T

T>A

T>C

T>G

CaucasianAfrican American

0.00

0.25

0.50

0.75

1.00

ALL AML CSCC Melanoma SS0.0

0.1

0.2

0.3

0.4

0.5

African American Caucasian

% U

VB

Sig

natu

re

Exp

osur

e

A

B

Figure 5: A) Signature heatmap of the three most penetrant signatures in SS. Tracks indicate mutation count and race. Values are ordered by UVB signatureexposure. Signatures are shown to the right with numbers indicating the signature designation in the 21 signature nsNMF solution from HGSC. B) UVB signatureexposure was independent of race and consistent with skin cancers. African American (and hispanic and indian [not shown]) races had significantly less overallUVB signature exposure compared with Caucasians. This is likely because of the protective effect of malanin in absorbing UVB radiaton (left). In comparisonto other cancers, SS had a UVB signature exposure similar to that of CSCC, much higher than other liquid cancers (AML and ALL), though not as high asMelanoma.

9

Mutation rate (Per Mb)

Caucasian

African American

0 0.1 0.3 0.5Value

04

812

Color Keyand Histogram

Cou

nt

UVB

CpG

TCR

M.RateRace

Variant

6

14

1

0.0

0.2

0.4

0.0

0.2

0.4

0.0

0.2

0.4

CpG

UVB

TCR

ACA

ACC

ACG

ACT

ATA

ATC

ATG

ATT

CCA

CCC

CCG

CCT

CTA

CTC

CTG

CTT

GCA

GCC

GCG

GCT

GTA

GTC

GTG

GTT

TCA

TCC

TCG

TCT

TTA

TTC

TTG

TTT

C>A

C>G

C>T

T>A

T>C

T>G

CaucasianAfrican American

0.00

0.25

0.50

0.75

1.00

ALL AML CSCC Melanoma SS0.0

0.1

0.2

0.3

0.4

0.5

African American Caucasian

% U

VB

Sig

natu

re

Exp

osur

e

A

B

Figure 5: A) Signature heatmap of the three most penetrant signatures in SS. Tracks indicate mutation count and race. Values are ordered by UVB signatureexposure. Signatures are shown to the right with numbers indicating the signature designation in the 21 signature nsNMF solution from HGSC. B) UVB signatureexposure was independent of race and consistent with skin cancers. African American (and hispanic and indian [not shown]) races had significantly less overallUVB signature exposure compared with Caucasians. This is likely because of the protective effect of malanin in absorbing UVB radiaton (left). In comparisonto other cancers, SS had a UVB signature exposure similar to that of CSCC, much higher than other liquid cancers (AML and ALL), though not as high asMelanoma.

9

0

50

100

150

2.5 5.0 7.5 10.0Mutations

Mut

atio

n ra

te

Figure 4: Correlation of CpG and UVB signature exposures with mutation rate. Though both are correlated with overall mutation rate, UVB is much more so.Blue: UVB, Red: CpG.

7

Mutation Rate (per Mb)

Mut

atio

ns p

er S

igna

ture

UVB CpG

C>T

at N

pCpC

%

05101520253035

DNM%

0123456

Not Trea

ted UVAUVB

Not UVA UVB Treated

P=N.S.

P=N.S.

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 5

Schematic representation of somatic mutations identified in other potential drivers in the combined cohorts (n = 105).

ARID1A

FAS

TNFRSF1B

RHOA

Extension (Deep-seq)

Colors Shapes

Discovery (WES) Missense Nonsense Splice_site Frame-shift

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 6

Conservation analysis of the CARD11 mutation hotspots. The protein sequences of all species were downloaded and aligned using Uniprot (see URLs). Two sequence segments (a, b) were selected to show the mutation hotspots. The mutations sites were marked and the amino acid changes were indicated. The two numbers in the parentheses indicate the number of mutations identified in the discovery cohort and extension cohort, respectively.

a

b

MEEECKLERNQSLKLKNDIENRPKKEQVLELERENEMLKTKNQELQSIIQAGKRSLPDSD 298

MEEECKLERNQSLKLKNDIENRPKKEQVLELERENEMLKTKNQELQSIIQAGKRSLPDSD 298

MEEECKLERNQSLKLKNDIENRPKKEQVLELERENEMLKTKNQELQSIIQAGKRSLPDSD 298

MEEECKLERNQSLKLKNDIENRPRKEQVLELERENEMLKTKIQELQSIIQAGKRSLPDSD 298

MEEECKLERNQSLKLKNDIENRPKKEQVLELERENEMLKTKIQELQSIIQAGKRSLPDSD 298

MEEECKLERNQSLKLKNDIENRPKREQVLELERENEMLKTKIQELQSIIQAGKRSLPDSD 298

MEEECKLERNQSLKLKNDIENRPKREQVLELERENEMLKTKIQELQSVIQAGKRSLPDSD 298

VEEECKLERNQSLKLKNDIENRPKKEQMLELERENEMMKTKIQELQSIIQADKRSLPDSD 300

VEEECKMERRQSLKLRNDIENRPRKEQVFELERENEVLKIKVQELQSIIQPG--PLPDSD 290

:*****:**.*****:*******::**::*******::* * *****:** *****

KAILDILEHDRKEALEDRQELVNRIYNLQEEARQAEELRDKYLEEKEDLELKCSTLGKDC 358

KAILDILEHDRKEALEDRQELVNRIYNLQEEARQAEELRDKYLEEKEDLELKCSTLGKDC 358

KAILDILEHDRKEALEDRQELVNRIYNLQEEARQAEELRDKYLEEKEDLELKCSTLGKDC 358

KAILDILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYLEEKEDLELKCSTLGKDC 358

KAILDILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYLEEKEDLELKCSTLGKDC 358

KAILDILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYLEEKEDLELKCSTLGKDC 358

KAILDILEHDRKEALEDRQELVNRIYNLQEEARQAEELRDKYLEEKEDLELKCSTLGKDC 358

KAILDILEHDRKEALEDRHELVNKIFNLQEEIRHVEDLRDKYLEEKEDLELKCSTLGKDC 360

KAILDILEHDRQEALEDRQELVDRLCNLHEEVRQAEELRDKYLEEKEDLELKCSTLVKDC 350

***********:******:***::: **:** *:.*:******************* ***

EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

Alignment [completed]

E7FB52|CARD11_Z.. 291 KAILDILEHDRQEALEDRQELVDRLCNLHEEVRQAEELRDKYLEEKEDLELKCSTLVKDC***********:******:***::: **:** *:.*:******************* ***

Q9BXL7|CARD11_H.. 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

H2QU43|CARD11_C.. 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

H9YY19|CARD11_R.. 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

Q8CIS0|CARD11_M.. 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

F1M1I1|CARD11_Rat 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

F1PZC8|CARD11_Dog 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

G3UL74|CARD11_E.. 359 EMYRHRMNTVMLQLDEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

Q5F3W0|CARD11_C.. 361 EMYKHRMNTVMIQLEEVEKERDQAFRSRDEAQTQYSHCLIEKDKYRKQIRELEERNDELR

E7FB52|CARD11_Z.. 351 EMYKNRMNTIMVQLEEVERERDQAFKSRDDSQHLVSQCLIDKDKYRKQIRELEEKSDELQ

***:.****:*:**:***:******:***::* *:***:*************:.**::

Q9BXL7|CARD11_H.. 419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS

H2QU43|CARD11_C.. 419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS

H9YY19|CARD11_R.. 419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRTLPVTIISQDFGDASPRTNGQEADDSS

Q8CIS0|CARD11_M.. 419 IEMVRREACIVNLESKLRRLSKDNGSLDQSLPRHLPATIISQNLGDTSPRTNGQEADDSS

F1M1I1|CARD11_Rat 419 IEMVRREACIVNLESKLRRLSKDSGSLDQSLPRHLPATIISQSLGDTSPRTNGQEADDSS

F1PZC8|CARD11_Dog 419 IEMVRREACIVNLESKLRRLSKDSSGLDQSLPRNLPVAIISQNFGDASPRTNGQEADDSS

G3UL74|CARD11_E.. 419 IEMVRREACIVNLESKLRRLSKDSGTLDQSLPRNLPVTIISQSFGDASPRTNGQEADDSS

Q5F3W0|CARD11_C.. 421 IEMVRKEACIVNLECKLRRLSKDNNCHDQSLPRNLPITIISQTFGNSSPKANGQEADDSS

E7FB52|CARD11_Z.. 411 IEIVRKEAKIVNLECKLRRMAKENG-LDQSLPRGITPLIIAQNFGQHDEDSGEDTV----

**:**:** *****.****::*:. ****** : **:* :*: . : : .

Q9BXL7|CARD11_H.. 479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG

H2QU43|CARD11_C.. 479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG

H9YY19|CARD11_R.. 479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG

Q8CIS0|CARD11_M.. 479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF

F1M1I1|CARD11_Rat 479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF

F1PZC8|CARD11_Dog 479 TSEESPEDSRYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----GRGHEEEG

G3UL74|CARD11_E.. 479 TSEESPEDNKYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRASDLQVLPGPGRGHEEDD

Q5F3W0|CARD11_C.. 481 TSEDSPEDNKFFLPDQARLKRRVNLKGIQINPRAKSPVSMNRTSEFQAVRAQDEDGANAS

E7FB52|CARD11_Z.. 466 ------DDVEF------RLQRRSNLKGRINRP--KSPAAGPKSPLFPAQPFTNGDLSEHA

:* .: :** **** . *** : :: : :

Q9BXL7|CARD11_H.. 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

H2QU43|CARD11_C.. 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

H9YY19|CARD11_R.. 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

Q8CIS0|CARD11_M.. 537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH-

F1M1I1|CARD11_Rat 537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH-

F1PZC8|CARD11_Dog 532 -IDASPSSSRSLPIT-----NSFSKMQPHR-SRSSIMSITAEPPGNDSILRRYKEDAPH-

G3UL74|CARD11_E.. 537 -LDASPSSSSSLPSN-----SAFAKMPPHR-NRNSIMSITAEPPGNDSIVRRYKEDAPH-

Q5F3W0|CARD11_C.. 541 NGRTDTSSSNSVSISNSISSCEVSKIQTLRNRNDSIMSTTPEPPGNDSIVRRCKEDAPP-

E7FB52|CARD11_Z.. 512 AGD-STGFSNASPMNT--PAELF--SKNIRSRNHSILSTAPEPPDNHSIVRRIKENSDAL

. . . : . . * . **:* : *** *.**:** **::

Q8CIS0|Mouse 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMRF1M1I1|Rat 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

F1PZC8|Dog 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

G3UL74|Elephant 359 EMYRHRMNTVMLQLDEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR

Q5F3W0|Chicken 361 EMYKHRMNTVMIQLEEVEKERDQAFRSRDEAQTQYSHCLIEKDKYRKQIRELEERNDELR

E7FB52|Zebrafish 351 EMYKNRMNTIMVQLEEVERERDQAFKSRDDSQHLVSQCLIDKDKYRKQIRELEEKSDELQ

***:.****:*:**:***:******:***::* *:***:*************:.**::

Q9BXL7|HUMAN 419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS

H2QU43|Chimpanzee 419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS

H9YY19|Rhesus 419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRTLPVTIISQDFGDASPRTNGQEADDSS

Q8CIS0|Mouse 419 IEMVRREACIVNLESKLRRLSKDNGSLDQSLPRHLPATIISQNLGDTSPRTNGQEADDSS

F1M1I1|Rat 419 IEMVRREACIVNLESKLRRLSKDSGSLDQSLPRHLPATIISQSLGDTSPRTNGQEADDSS

F1PZC8|Dog 419 IEMVRREACIVNLESKLRRLSKDSSGLDQSLPRNLPVAIISQNFGDASPRTNGQEADDSS

G3UL74|Elephant 419 IEMVRREACIVNLESKLRRLSKDSGTLDQSLPRNLPVTIISQSFGDASPRTNGQEADDSS

Q5F3W0|Chicken 421 IEMVRKEACIVNLECKLRRLSKDNNCHDQSLPRNLPITIISQTFGNSSPKANGQEADDSS

E7FB52|Zebrafish 411 IEIVRKEAKIVNLECKLRRMAKENG-LDQSLPRGITPLIIAQNFGQHDEDSGEDTV----

**:**:** *****.****::*:. ****** : **:* :*: . : : .

Q9BXL7|HUMAN 479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG

H2QU43|Chimpanzee 479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG

H9YY19|Rhesus 479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG

Q8CIS0|Mouse 479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF

F1M1I1|Rat 479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF

F1PZC8|Dog 479 TSEESPEDSRYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----GRGHEEEG

G3UL74|Elephant 479 TSEESPEDNKYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRASDLQVLPGPGRGHEEDD

Q5F3W0|Chicken 481 TSEDSPEDNKFFLPDQARLKRRVNLKGIQINPRAKSPVSMNRTSEFQAVRAQDEDGANAS

E7FB52|Zebrafish 466 ------DDVEF------RLQRRSNLKGRINRP--KSPAAGPKSPLFPAQPFTNGDLSEHA

:* .: :** **** . *** : :: : :

Q9BXL7|HUMAN 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

H2QU43|Chimpanzee 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

H9YY19|Rhesus 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

Q8CIS0|Mouse 537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH-

F1M1I1|Rat 537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH-

F1PZC8|Dog 532 -IDASPSSSRSLPIT-----NSFSKMQPHR-SRSSIMSITAEPPGNDSILRRYKEDAPH-

G3UL74|Elephant 537 -LDASPSSSSSLPSN-----SAFAKMPPHR-NRNSIMSITAEPPGNDSIVRRYKEDAPH-

Q5F3W0|Chicken 541 NGRTDTSSSNSVSISNSISSCEVSKIQTLRNRNDSIMSTTPEPPGNDSIVRRCKEDAPP-

E7FB52|Zebrafish 512 AGD-STGFSNASPMNT--PAELF--SKNIRSRNHSILSTAPEPPDNHSIVRRIKENSDAL

. . . : . . * . **:* : *** *.**:** **::

Q9BXL7|HUMAN 584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSIHSSSSSHQSEGLDAYDLEQVNLMFRK

H2QU43|Chimpanzee 584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK

H9YY19|Rhesus 584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK

Q8CIS0|Mouse 589 -RSTVEEDNDSCGFDALDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMLRK

F1M1I1|Rat 589 -RSTVEEDNDSCGFDVLDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK

F1PZC8|Dog 584 -RSTVEEDNDSGGFDVLDFDDDSHERSSFGPPSVHSSSSSHQSEGLDAYDLEQVNLMFRK

G3UL74|Elephant 589 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK

Q5F3W0|Chicken 600 -CSMVEEDNDSFGFDALELDDDSHDRHSHGAPSVHSSSSSHQSEGLDAYDLEHVNSIFRK

E7FB52|Zebrafish 567 HKSFLPSDT--ADTD----SGDNADMDDHEPSSINSSSSSHQSEIMDSYDLEQVNNIFRK

* : .*. * . :. : .. *:.********* :*:****:** ::**

Q9BXL7|HUMAN 643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE

H2QU43|Chimpanzee 643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE

359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418 359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

G3UL74|Elephant 359 EMYRHRMNTVMLQLDEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

Q5F3W0|Chicken 361 EMYKHRMNTVMIQLEEVEKERDQAFRSRDEAQTQYSHCLIEKDKYRKQIRELEERNDELR 420

E7FB52|Zebrafish 351 EMYKNRMNTIMVQLEEVERERDQAFKSRDDSQHLVSQCLIDKDKYRKQIRELEEKSDELQ 410

***:.****:*:**:***:******:***::* *:***:*************:.**::

419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS 478

H2QU43|Chimpanzee 419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRTLPVTIISQDFGDASPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDNGSLDQSLPRHLPATIISQNLGDTSPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSGSLDQSLPRHLPATIISQSLGDTSPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSSGLDQSLPRNLPVAIISQNFGDASPRTNGQEADDSS 478

G3UL74|Elephant 419 IEMVRREACIVNLESKLRRLSKDSGTLDQSLPRNLPVTIISQSFGDASPRTNGQEADDSS 478

Q5F3W0|Chicken 421 IEMVRKEACIVNLECKLRRLSKDNNCHDQSLPRNLPITIISQTFGNSSPKANGQEADDSS 480

E7FB52|Zebrafish 411 IEIVRKEAKIVNLECKLRRMAKENG-LDQSLPRGITPLIIAQNFGQHDEDSGEDTV---- 465

**:**:** *****.****::*:. ****** : **:* :*: . : : .

479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG 531

H2QU43|Chimpanzee 479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG 531

479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG 531

479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF 536

479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF 536

479 TSEESPEDSRYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----GRGHEEEG 531

G3UL74|Elephant 479 TSEESPEDNKYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRASDLQVLPGPGRGHEEDD 536

Q5F3W0|Chicken 481 TSEDSPEDNKFFLPDQARLKRRVNLKGIQINPRAKSPVSMNRTSEFQAVRAQDEDGANAS 540

E7FB52|Zebrafish 466 ------DDVEF------RLQRRSNLKGRINRP--KSPAAGPKSPLFPAQPFTNGDLSEHA 511

:* .: :** **** . *** : :: : :

532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH- 583

H2QU43|Chimpanzee 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH- 583

532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH- 583

537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH- 588

537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH- 588

532 -IDASPSSSRSLPIT-----NSFSKMQPHR-SRSSIMSITAEPPGNDSILRRYKEDAPH- 583

G3UL74|Elephant 537 -LDASPSSSSSLPSN-----SAFAKMPPHR-NRNSIMSITAEPPGNDSIVRRYKEDAPH- 588

Q5F3W0|Chicken 541 NGRTDTSSSNSVSISNSISSCEVSKIQTLRNRNDSIMSTTPEPPGNDSIVRRCKEDAPP- 599

E7FB52|Zebrafish 512 AGD-STGFSNASPMNT--PAELF--SKNIRSRNHSILSTAPEPPDNHSIVRRIKENSDAL 566

. . . : . . * . **:* : *** *.**:** **::

584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSIHSSSSSHQSEGLDAYDLEQVNLMFRK 642

H2QU43|Chimpanzee 584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK 642

584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK 642

589 -RSTVEEDNDSCGFDALDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMLRK 647

589 -RSTVEEDNDSCGFDVLDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK 647

584 -RSTVEEDNDSGGFDVLDFDDDSHERSSFGPPSVHSSSSSHQSEGLDAYDLEQVNLMFRK 642

G3UL74|Elephant 589 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK 647

Q5F3W0|Chicken 600 -CSMVEEDNDSFGFDALELDDDSHDRHSHGAPSVHSSSSSHQSEGLDAYDLEHVNSIFRK 658

E7FB52|Zebrafish 567 HKSFLPSDT--ADTD----SGDNADMDDHEPSSINSSSSSHQSEIMDSYDLEQVNNIFRK 620

* : .*. * . :. : .. *:.********* :*:****:** ::**

643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE 702

H2QU43|Chimpanzee 643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE 702

359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

359 EMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

359 EMYRHRMNTVMLQLDEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMR 418

361 EMYKHRMNTVMIQLEEVEKERDQAFRSRDEAQTQYSHCLIEKDKYRKQIRELEERNDELR 420

351 EMYKNRMNTIMVQLEEVERERDQAFKSRDDSQHLVSQCLIDKDKYRKQIRELEEKSDELQ 410

***:.****:*:**:***:******:***::* *:***:*************:.**::

419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRNLPVTIISQDFGDASPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSNNLDQSLPRTLPVTIISQDFGDASPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDNGSLDQSLPRHLPATIISQNLGDTSPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSGSLDQSLPRHLPATIISQSLGDTSPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSSGLDQSLPRNLPVAIISQNFGDASPRTNGQEADDSS 478

419 IEMVRREACIVNLESKLRRLSKDSGTLDQSLPRNLPVTIISQSFGDASPRTNGQEADDSS 478

421 IEMVRKEACIVNLECKLRRLSKDNNCHDQSLPRNLPITIISQTFGNSSPKANGQEADDSS 480

411 IEIVRKEAKIVNLECKLRRMAKENG-LDQSLPRGITPLIIAQNFGQHDEDSGEDTV---- 465

**:**:** *****.****::*:. ****** : **:* :*: . : : .

479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG 531

479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG 531

479 TSEESPEDSKYFLPYHP-PQRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----AKGHEEEG 531

479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF 536

479 TSEESPEDSKYFLPYHP-PRRRMNLKGIQLQ-RAKSPISMKQASEFQALMRTVKGHEEDF 536

479 TSEESPEDSRYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRTSDFQ-----GRGHEEEG 531

479 TSEESPEDNKYFLPYHP-PKRRMNLKGIQLQ-RAKSPISLKRASDLQVLPGPGRGHEEDD 536

481 TSEDSPEDNKFFLPDQARLKRRVNLKGIQINPRAKSPVSMNRTSEFQAVRAQDEDGANAS 540

466 ------DDVEF------RLQRRSNLKGRINRP--KSPAAGPKSPLFPAQPFTNGDLSEHA 511

:* .: :** **** . *** : :: : :

532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH- 583

532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH- 583

532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH- 583

537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH- 588

537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH- 588

532 -IDASPSSSRSLPIT-----NSFSKMQPHR-SRSSIMSITAEPPGNDSILRRYKEDAPH- 583

537 -LDASPSSSSSLPSN-----SAFAKMPPHR-NRNSIMSITAEPPGNDSIVRRYKEDAPH- 588

541 NGRTDTSSSNSVSISNSISSCEVSKIQTLRNRNDSIMSTTPEPPGNDSIVRRCKEDAPP- 599

512 AGD-STGFSNASPMNT--PAELF--SKNIRSRNHSILSTAPEPPDNHSIVRRIKENSDAL 566

. . . : . . * . **:* : *** *.**:** **::

584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSIHSSSSSHQSEGLDAYDLEQVNLMFRK 642

584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK 642

584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK 642

589 -RSTVEEDNDSCGFDALDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMLRK 647

589 -RSTVEEDNDSCGFDVLDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK 647

584 -RSTVEEDNDSGGFDVLDFDDDSHERSSFGPPSVHSSSSSHQSEGLDAYDLEQVNLMFRK 642

589 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK 647

600 -CSMVEEDNDSFGFDALELDDDSHDRHSHGAPSVHSSSSSHQSEGLDAYDLEHVNSIFRK 658

567 HKSFLPSDT--ADTD----SGDNADMDDHEPSSINSSSSSHQSEIMDSYDLEQVNNIFRK 620

* : .*. * . :. : .. *:.********* :*:****:** ::**

643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE 702

643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE 702

S615F (2,2)

S615C (0,1)

S618F (0,2)

S619F (1,0)

S625F (1,0)

E626K (0,1)

Q9BXL7|HUMAN 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

H2QU43|Chimpanzee 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

H9YY19|Rhesus 532 -TDASPSSCGSLPIT-----NSFTKMQPPR-SRSSIMSITAEPPGNDSIVRRYKEDAPH-

Q8CIS0|Mouse 537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH-

F1M1I1|Rat 537 -TDGSPSSSRSLPVT-----SSFSKMQPHR-SRSSIMSITAEPPGNDSIVRRCKEDAPH-

F1PZC8|Dog 532 -IDASPSSSRSLPIT-----NSFSKMQPHR-SRSSIMSITAEPPGNDSILRRYKEDAPH-

G3UL74|Elephant 537 -LDASPSSSSSLPSN-----SAFAKMPPHR-NRNSIMSITAEPPGNDSIVRRYKEDAPH-

Q5F3W0|Chicken 541 NGRTDTSSSNSVSISNSISSCEVSKIQTLRNRNDSIMSTTPEPPGNDSIVRRCKEDAPP-

E7FB52|Zebrafish 512 AGD-STGFSNASPMNT--PAELF--SKNIRSRNHSILSTAPEPPDNHSIVRRIKENSDAL

. . . : . . * . **:* : *** *.**:** **::

Q9BXL7|HUMAN 584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSIHSSSSSHQSEGLDAYDLEQVNLMFRK

H2QU43|Chimpanzee 584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK

H9YY19|Rhesus 584 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPSSVHSSSSSHQSEGLDAYDLEQVNLMFRK

Q8CIS0|Mouse 589 -RSTVEEDNDSCGFDALDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMLRK

F1M1I1|Rat 589 -RSTVEEDNDSCGFDVLDLDDENHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK

F1PZC8|Dog 584 -RSTVEEDNDSGGFDVLDFDDDSHERSSFGPPSVHSSSSSHQSEGLDAYDLEQVNLMFRK

G3UL74|Elephant 589 -RSTVEEDNDSGGFDALDLDDDSHERYSFGPPSIHSSSSSHQSEGLDAYDLEQVNLMFRK

Q5F3W0|Chicken 600 -CSMVEEDNDSFGFDALELDDDSHDRHSHGAPSVHSSSSSHQSEGLDAYDLEHVNSIFRK

E7FB52|Zebrafish 567 HKSFLPSDT--ADTD----SGDNADMDDHEPSSINSSSSSHQSEIMDSYDLEQVNNIFRK

* : .*. * . :. : .. *:.********* :*:****:** ::**

Q9BXL7|HUMAN 643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE

H2QU43|Chimpanzee 643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE

H9YY19|Rhesus 643 FSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFVHSVKPGSLAE

Q8CIS0|Mouse 648 FSLERPFRPSVTSGGHVRGTGPLVQHTTLNGDGLITQLTLLGGNARGSFIHSVKPGSLAE

F1M1I1|Rat 648 FSLERPFRPSVTSGGHVRGTSPLVQHTTLNGDGLITQLTLLGGNAHGSFIHSVKPGSLAE

F1PZC8|Dog 643 FSLERPFRPSVTSVGHVRGPGPSMQYTTLNGDSLISQLTLLGGNARGSFVHSVKPGSLAE

G3UL74|Elephant 648 FSLERPFRPSVTSGGHLRGPGSTVQHATLSGDGLITQLTVLGGNASGSFIHSVKPGSLAE

Q5F3W0|Chicken 659 FSLERPFRPSVTSVGRIRSSCHTIQRITLNGDTLNSEITLIGGNDKGSFVSSVVSGSLAE

E7FB52|Zebrafish 621 FSLERPFRPSLTSGP-PRNSLRTVQSLSLSGENLLSEITLIGGNDSGIFVNSVQSGSDAD

**********:** * :* :*.*: * :::*::*** * *: ** ** *:

Q9BXL7|HUMAN 703 KAGLREGHQLLLLEGCIRGERQSVPLDTCTKEEAHWTIQRCSGPVTLHYKVNHEGYRKLV

H2QU43|Chimpanzee 703 KAGLREGHQLLLLEGCIRGERQSVPLDTCTKEEAHWTIQRCSGPVTLHYKVNHEGYRKLV

H9YY19|Rhesus 703 KAGLREGHQLLLLEGCIRGERQSVPLDTCTKEEAHWTIQRCSGPVTLHYKVNHEGYRKLV

Q8CIS0|Mouse 708 RAGLREGHQLLLLEGCIRGERQSVPLDACTKEEARWTIQRCSGLITLHYKVNHEGYRKLL

F1M1I1|Rat 708 KAGLREGHQLLLLEGCIRGERQSVPLDACTKEEARWTIQRCSGPVTLHYKVNHEGYRRLL

F1PZC8|Dog 703 KAGLHEGHQLLLLEGCIKGERQKVPLDTCTKEEVHWTIQRCSGSVTLYYKVNQEGYRKLL

G3UL74|Elephant 708 KAGLREGHQLLLLEGCIRGERQNVPLDTCTKEEARWTIQRCSGPVTLHYKVNHEGYRKLL

Q5F3W0|Chicken 719 KAGLREGHQLLLLEGCIKGENQSVPLDTCTKEEVHWTIQRCHGPVTLQYKSNHEGYRKLL

E7FB52|Zebrafish 680 LAGVKVGFHLLMLEGNVHGKAESVSLDTSTKEEAHWTLQRCSGQVHLHYKSSYDSYRRLV

**:: *.:**:*** ::*: :.* **:.****.:**:*** * : * ** . :.**:*:

Q9BXL7|HUMAN 763 KDMEDGLITSGDSFYIRLNLNISS-QLDACTMSLKCDDVVHVRDTMYQDR---HEWLCAR

H2QU43|Chimpanzee 763 KDMEDGLITSGDSFYIRLNLNISS-QLDACTMSLKCDDVVHVRDTMYQDR---HEWLCAR

H9YY19|Rhesus 763 KDMEDGLITSGDSFYIRLNLNISS-QLDACTMSLKCDDVVHVRDTMYQDR---HEWLCAR

Q8CIS0|Mouse 768 KEMEDGLITSGDSFYIRLNLNISS-QLDACSMSLKCDDVVHVLDTMYQDR---HEWLCAR

F1M1I1|Rat 768 KEMEDGLITSGDSFYIRLNLNISSEGLDACSMPMKMNVVEGGVLDTYQDR---HEWLVCR

F1PZC8|Dog 763 KDMEEGLITSGDSFYIRLNLNISS-QLDACSLSLKCDDIVHVRDTMYQDR---HEWLCAR

G3UL74|Elephant 768 KDMEEGLITSGDSFYIRLNLNISS-QLDACSMSLKCDDVVHVRDTMYQDR---YEWLCAR

Q5F3W0|Chicken 779 SELEDGLIASGDSFHIRLNLNISS-QLDCCSLSVKCDEIVHILDTMYQGTCGGCDWLCAR

E7FB52|Zebrafish 740 KDIEDGTVVSGDSFYIRLNLNISS-QSDNCSLNVRCDEVLHVLDTMHQDK---CEWLCAR

.::*:* :.*****:********* * *:: :: : : :* :** .*

Y361C (1,0) D401N (3,0)

405405405405405405405407397

346346346346346346346348338

D357N (1,1)

D357E (1,0)

CARD11

Segment a Segment b

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 7 The PLCG1 mutations in the combined cohorts. Numbers are the PLCG1 mutant allele fractions.

SP

Z-02

2

SP

Z-02

4

2007

-046

2015

-044

2006

-049

2006

-018

2004

-127

2006

-166

2009

-136

2009

-068

2006

-063

2006

-187

2006

-193

2006

-150

2005

-158

SP

Z-00

9

SP

Z-01

8

SP

Z-02

9

2006

-054

SS origin SS origin

R48W 0.33 0.16 0.15 0.14 0.11 0.10 0.02 0.03 Evolved/from/MFS345F 0.01 0.15 0.10 0.12 0.04 De/novoS520F 0.18

P319L 0.47

472-483del 0.12

G869R 0.03

R873W 0.05

E989K 0.45

Q1016L 0.02

L1035V 0.47

E1163K 0.04

D1165H 0.02

SS origin

Evolved'from'MF

De'novo

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 8 Survival analysis for recurrent somatic alterations that have potential pathogenic significance. The Kaplan-Meier survival plots were shown and the P values were calculated by Log-Rank test.

0.0

0.2

0.4

0.6

0.8

1.0Su

rviv

ing

0 10 20 30 40 50 60 70 80 90Months after diagnosis

2q37.3 deletionDiploid

Log-Rank P=0.05

0.0

0.2

0.4

0.6

0.8

1.0

Surv

ivin

g

0 10 20 30 40 50 60 70 80 90Months after diagnosis

Log-Rank P>0.05

CCR4 Mutation or overexpressionCCR4 Wildtype

0.0

0.2

0.4

0.6

0.8

1.0

Surv

ivin

g

0 10 20 30 40 50 60 70 80 90Months after diagnosis

Log-Rank P>0.05

CDKN2A deletionCDKN2A Diploid

0.0

0.2

0.4

0.6

0.8

1.0

Surv

ivin

g

0 10 20 30 40 50 60 70 80 90Months after diagnosis

ARID1A deletion and/or mutationARID1A Diploid/Wildtype

Log-Rank P>0.05

0.0

0.2

0.4

0.6

0.8

1.0

Surv

ivin

g0 10 20 30 40 50 60 70 80 90

Months after diagnosis

Log-Rank P>0.05

ZEB1 deletionZEB1 Diploid

0.0

0.2

0.4

0.6

0.8

1.0

Surv

ivin

g

0 10 20 30 40 50 60 70 80 90Months after diagnosis

Log-Rank P>0.05

TNFAIP3 Diploid & wildtypeTNFAIP3 mutation or deletion

0.0

0.2

0.4

0.6

0.8

1.0

Surv

ivin

g

0 10 20 30 40 50 60 70 80 90Months after diagnosis

Log-Rank P>0.05

TCR Vb dominantTCR Vb Polyclonal

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 9 Correlation analysis between DNA copy number alterations and gene expression levels for 3 representative genes in the region of 2q37.3 deletion. One-way ANOVA was used to compare the means of groups and calculate the P values. The DNA copy number status was inferred by Nexus analysis of the SNP array data. The expression levels were normalized FPKM values calculated by Cufflinks using RNA-seq data. N.S., not statistically significant; LOH, loss of heterozygosity; HD, homozygous deletion.

ING

5 Ex

pres

sion

0

5

10

15

Diploid LOH Control

D2HG

DH E

xpre

ssio

n

0

5

10

15

Diploid LOH HD Control

PDCD

1 Ex

pres

sion

0

10

20

30

40

50

60

Diploid LOH HD Control

P=N.S. P=N.S.

P = N.S.

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 10 a b Correlation analysis between expression of IL32 and IL2RG, CARD11. RNA expression data was used for analysis. Numbers on Y axis are the normalized gene expression levels calculated by the Cufflinks algorithm using RNA-seq data. Bivariate fit was made by JMP algorithm.

0

100

200

300

400

500IL2RG

0 500 1000 1500 2000IL32

0

10

20

30

40

50

60

70

CARD11

0 500 1000 1500 2000IL32

RSquare=0.4 P=4.25E-4

RSquare=0.6 P=1.89E-7

Black dots: SS samples Green dots: Control samples

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 11

The landscape of TCR repertoire. RNA-seq coverage tracks were shown for the TCR-Vβ (a) and Vα (b) loci. The T-cell samples from five healthy donors were also included for comparison purpose. The recurrently rearranged TCR-Vβ and Vα genes were indicated by arrows and their names were displayed underneath. The scale was adjusted for a better visualization. The data range for all control samples was set to 0–100; the data range for samples with polyclonal TCR-Vβ or Vα expression was set to 0–500; the data range for samples with dominant TCR-Vβ or Vα expression was set to 0–5,000.

Supplementary Figure 11 TCR-Vβ TCR-Vα

a

b

!

!

Controls

Tumors

TRBV29-1

TRBV20-1

TRBV28

Unr

elat

ed

gene

s

TRBV19

TRBV7-3

TRBV2

TRBV3-1

TRBV5-1

TRBV7-1

!

!

Control

sTumors

TRAV27

Unr

elat

ed

gene

s

TRAV8-3

TRAV13-1

TRAV9-2

TRAV12-2

TRAV21

TRAV24

Nature Genetics: doi:10.1038/ng.3444

Supplementary Figure 12

Survival analysis for the combined cohorts. The Kaplan-Meier survival plots were shown and the P values were calculated by Log-Rank test.

0.0

0.2

0.4

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0.8

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Surv

ivin

g

0 20 40 60 80 100 140 180Months from diagnosis

0.0

0.2

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Surv

ivin

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0 20 40 60 80 100 140 180Months from diagnosis

0.0

0.2

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ivin

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0 20 40 60 80 100 120 160Months from diagnosis

With LCTWithout LCT

Log-Rank P=0.042 Log-Rank P=0.005

African American Caucasian

0.0

0.2

0.4

0.6

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Surv

ivin

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0 20 40 60 80 100 140 180Months from diagnosis

Log-Rank P=0.131

0.0

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1.0Su

rviv

ing

0 20 40 60 80 100 140 180Months from diagnosis

PLCG1 mutant PLCG1 Wildtype

TP53 mutant TP53 Wildtype

Log-Rank P=0.346

Log-Rank P=0.631

CARD11 mutant CARD11 Wildtype

Blue filled circles: Discovery cohort Orange filled circles: Extension cohort

Nature Genetics: doi:10.1038/ng.3444