INTERNATIONAL SARCOMA KINDRED STUDY:

FIRST GENE SCREENS

ISKS cohort

ISKS hereditary cancer syndromes

658 ISKS families

109Uninformative

104No cancer in

1o/2o rels

337No defined syndrome

108Recognised syndrome

69 Clinically

suspicious

268Not

suspicious

56Chomp/

LFS

21BRCA

17Lynch like

14Other

16++

42+

11+++

658 ISKS families

109Uninformative

104No cancer in

1o/2o rels

337No defined syndrome

108Recognised syndrome

69 Clinically

suspicious

268Not

suspicious

56Chomp/

LFS

21BRCA

17Lynch like

14Other

16++

42+

11+++

19% of these families were referred to a familial cancer clinic

ISKS hereditary cancer syndromes

Cancer genes: frequency and penetrance

Commonlow penetrance

Rarehigh penetrance

Commonlow penetrance

Rarehigh penetrance

Cancer genes: frequency and penetrance

QUAL>60 and total read depth ≥20 and ≥8 reads with variant allele and ≥20% reads had

variant allele17,001 variants

No dbSNP ID or allele frequency<0.05, EVS EA population

26,365 variants

Class IGenomeTrax disease

mutant ANDNOT benign by Condel

Class IISTOP, FS, essential splice, initiator codon

variant

Class IIIMissense, Condel <-

0.7, ISKS:EVS>4

ISKS Filtering pipeline

582,235 variants

non-synonymous, STOP, essential splice site, frameshifts

54,718 variants

Strand bias (FS)<100 & Positional bias (ReadPosRankSum)>-10

8,701 variants

Occurs ≤3 times in cohort1452 variants

Rest

QUAL>60 and total read depth ≥20 and ≥8 reads with variant allele and ≥20% reads had

variant allele17,001 variants

No dbSNP ID or allele frequency<0.05, EVS EA population

26,365 variants

Class IGenomeTrax disease

mutant ANDNOT benign by Condel

Class IISTOP, FS, essential splice, initiator codon

variant

Class IIIMissense, Condel <-

0.7, ISKS:EVS>4

582,235 variants

non-synonymous, STOP, essential splice site, frameshifts

54,718 variants

Strand bias (FS)<100 & Positional bias (ReadPosRankSum)>-10

8,701 variants

Occurs ≤3 times in cohort1452 variants

Rest

ISKS Filtering pipeline

CLASS I

86 variants in 85 probands

CLASS II

41 variants in 38 probands

CLASS III

299 variants in 225 probands

No pathogenic variation

379 probands

•116/681 (17%) ISKS probands carry 123 Class I or II variants

•302/681 (44%) carry 426 class I-III variants

Mutation status and age of cancer onset

HR 1.28, 95%CI 1.1-1.5, P<0.0001

HR 1.46, 95%CI 0.99-2.16, P=0.026 HR 1.2, 95%CI 0.92-1.56, P=0.008

HR 1.32, 95%CI 1.1-1.6, P<0.0001

Hazard ratios: Mantel-Haenszel; Curve comparisons: Gehan-Breslow-Wilcoxon

Median tumor latency

Nil 51y

Class I 40y

Class II 41.5y

Class III 42y

All 42y

QUAL>60 and total read depth ≥20 and ≥8 reads with variant allele and ≥20% reads had

variant allele17,001 variants

No dbSNP ID or allele frequency<0.05, EVS EA population

26,365 variants

Class IGenomeTrax disease

mutant ANDNOT benign by Condel

Class IISTOP, FS, essential splice, initiator codon

variant

Class IIIMissense, Condel <-

0.7, ISKS:EVS>4

582,235 variants

non-synonymous, STOP, essential splice site, frameshifts

54,718 variants

Strand bias (FS)<100 & Positional bias (ReadPosRankSum)>-10

8,701 variants

Occurs ≤3 times in cohort1452 variants

Rest

ISKS Filtering pipeline

•90 (13%) individuals carry 2+ (214) variants•24 (4%) individuals carry 3+ (82) variants

CLASS I

86 variants in 85 probands

CLASS II

41 variants in 38 probands

CLASS III

299 variants in 225 probands

No pathogenic variation

379 probands

Polygenic contribution to age of cancer onset

Curve comparisons: Logrank for trend; Gehan-Breslow-Wilcoxon for paired comparisons

Number Median tumor latency

Nil 347 51y

1 210 44y*

2 67 37y***

3+ 23 36y**

TP53 19 36y

* P=0.008** P=0.0001*** P<0.0001

Trend: P<0.0001

Enrichment for deleterious variants in the ISKS cohort

• 950 case Australian control cohort– 55-80 years of age, selected on high/low bone density– Free of co-morbidity, including cancer

• Whole exome panel• To correct for platform bias, compare ratios of

deleterious to synonymous variation– Deleterious = FS, stop, ESS, initiator codon variant; or

missense variant with Condel score > 0.7

Gene-specific mutation patterns in the ISKS cohort

Gene-specific mutation patterns in the ISKS cohort

*

*

**

CHEK2

TP53

CDKN2A

ATM

ATM(17)

NBN(11)

RAD50(13)

MRE11A(4)

BRCA1(2)

PALB2(6)

BRCA2(18)

BRIP1(12)

RAD51C(1)

FANCI/D2(5/2)

TP53(19)

FANCA-C/E-G/L/M

(62)

CHEK2(5)

Homologous recombination/TP53 pathwayn = 201 (Classes I-III)

DNA damage and homologous recombination pathway

ATR(14)

TP53BP1(6)

FAM175A(4)

WRAP53(4)

CDKN2A(2)

LDE225

PTCH1

ISKS therapeutic implications

ISKS AcknowledgementsISKS participating families

International Steering CommitteeIsabelle Ray-CoquardAjay Puri

Study manager – Mandy BallingerData Manager – Eveline NiedermayrResearch Assistant – Kim Riddell

Thomas labDavid GoodeTiffany PangArcadi Cipponi

PeterMac FCCGillian MitchellPaul JamesMary-Anne YoungAlex Lewis

FundingRainbows for Kate FoundationNHMRCVCA

PeterMacStephen WongAlex Dobrovic

Genomics CoreRichard TothillAga Borcz

University of QueenslandMatt BrownPaul Leo

kConFab staffHeather Thorne

ATM(5)

NBN(8)

MRE11A(1)

BRCA1(1)

PALB2(2)

BRCA2(3)

BRIP1(3)

RAD51C(1)

FANCI/D2

TP53(19)

FANCA-C/E-G/L/M

(12)

CHEK2(5)

Homologous recombination/TP53 pathwayn = 62 (Class I/II)

Genetic pathways

ATR(2)

TP53BP1(1)

WRAP53(-)

RAD50(2)

• 116/681 (17%) ISKS probands carry 123 Class I or II variants

• 302/681 (44%) carry 426 class I-III variants•90 individuals carry 2+ (214) variants•24 individuals carry 3+ (82) variants

ISKS Genotypes

ISKS Phenotypes & FCC referral

Clinically suspicious

Chomp/LFS

BRCA

Lynch-like

Other

+

++

+++

ISKS Sarcoma subtypes

ISKS gene panel

APC CDH1 EXT1 FANCM MLH3 PMS2 RET SQSTM1 WRNARID1A CDKN2A EXT2 FH MRE11A POLH RMI1 STK11 WT1ATM CHEK1 FAM175A IDH1 MSH2 PPARG RMI2 TAF15 XPAATR CHEK2 FANCA IDH2 MSH3 PRKAR1A RPA3 TGFBR2 XPCAXIN1 DDB2 FANCB KIF1B MSH6 PTCH1 RPA70 TNFRSF11AXRCC2AXIN2 DICER1 FANCC KIT MUTYH PTEN RPS19 TOP1BARD1 DKC1 FANCD2 LIG1 NBN PTPN11 SDHA TOP3ABLM DNA2 FANCE LIG4 NEIL2 RAD50 SDHB TP53BRCA1 ERCC2 FANCF MDM2 NF1 RAD51C SDHC TP53BP1BRCA2 ERCC3 FANCG MEN1 NF2 RAD51L3 SDHD TSC1BRIP1 ERCC4 FANCI MET PALB2 RB1 SMARCA4 TSC2BUB1B ERCC5 FANCL MLH1 PMS1 RECQL4 SMARCB1 VHL

Batch 1 – genes in blackBatch 2 – genes in black & red

•Agilent Haloplex custom panel of 85-101 gene CDS capture

•681 ISKS probands