SNP associations with risk and
outcome in Myeloma
University of Minnesota
ECOG
SWOG
Brian Van Ness
Emily Blood
Brian Durie
Christine Ramos
Philip Greipp
Bart Barlogie
Suzanne Grindle
Mike Katz
Cancer Research & Biostatistics
Royal Marsden Clinic (UK)
John Crowley
Gareth Morgan
Erik Rasmussen
David Johnson
Antje Hoering
Faith Davies
Genetic deregulation in the tumor as well as
genetic variation in the individual contribute
to differences in risk and response
DNA sequence
Biological trait
(Genotype)
(Phenotype)
Environment
ATTCGCATGGACC (3 billion)
C
A
SNPs
Single Nucleotide Polymorphisms
} Disease risk
Outcome / response
~ 1/1000 bp
Why are SNPs Important?
·
Frequency ~ .1%, but account for 90% of
human genetic variations
·
Stable: SNPs do not appear to change from
generation to generation, making them easy
to track through populations.
·
Have been shown to contribute to variability
in therapeutic responses (affecting effective
dose, toxicities)
·
May contribute to ethnic differences of risk,
response, toxicities
·
They are amenable to high throughput
analysis
Initial approach
Targeted SNP selection
· Gene is involved in myeloma growth responses,
drug metabolism or transport, or DNA repair
AND
·
The frequency of the SNP is >5% in the population
AND
·
The SNP has a functional consequence
· Candidate SNP targets
Cytokine/growth factors:
IL-6, IL-1, IL-1RA, IL-10,
TNF-, LT- , TGF
Drug metabolism or
transport: MDR1, MPO, CYP3A4,
GST(M,T,P)
DNA repair: ERCC2, XRCC1
GST-P1 genotype association
with 4 year survival
(High dose melphalan)
A/A
65%
A/G
56%
G/G
35%
p=.003
From: Dasgupta RK, et al. Polymorphic variation in GSTP1
modulates outcome following therapy for multiple myeloma. Blood
102:2345-50, 2003.
DNA repair gene SNPs in
E9486 - using DNA alkylators
Progression free survival in Arm B
ERCC312
XRCC 399
Progression-Free Survival
Arm C
1.0
1.0
Log Rank Test p=0.020
0.9
Log Rank Test p=0.027
0.9
0.8
0.8
0.7
p=.02
p=.008
0.7
0.6
0.6
Probability
0.5
Probability
0.5
0.4
0.4
0.3
AA
AG/GG
AA
AG/GG
Survival
Survival
0.3
0.2
0.2
0.1
0.1
0.0
0.0
0
1020
3040
506070
80
90
100
110
0
10203040506070
8090
100
110
120
Time in Months
Time in Months
ercc312aa
0
1.000000
LT-a genotype and therapeutic response
E9486 - Arm B
N=101
100
%
Response
50
}P=.004
A/A
A/G
G/G
and risk
Davies, F.E., et al., High-producer haplotypes of tumor necrosis factor alpha and
lymphotoxin alpha are associated with an increased risk of myeloma and have an
improved progression-free survival after treatment. J Clin Oncol, 2000. 18(15): p.
2843-51.
Myeloma and Race
Mortality Trends
Incidence Trends
(1950-1999)
(SEER, 1975-1999)
20
20
Black Male
10
Black Male
10
Black M
Blackale
Male
Black Fem
Black
ale
Female
earsy
Black Female
Black Female
White Male
White Male
White Ma
White le
person-
Male
White Fe
White male
Female
White Fe
White male
Female
100,000
pere
Rat
1
1
0.5
0.5
1950 1960 1970 1980 1990 2000
1970 1980 1990 2000
Year of death
Year of diagnosis
pgm185/plot01
Contributions to race differences in
incidence or outcomes in myeloma?
Environment
Diet
No Consensus
Socioeconomic status
No Consensus
Alcohol
No consensus
Tobacco
No consensus
Obesity
OR 2.0
African Amer 2x incidence obesity
Immune activation OR 2.0 urinary tract infection (=IgA)
Genetics
Family history of myeloma
African Amer,
OR 17.4
Caucasian
OR 1.5
* From: M Benjamin, S Reddy, O Brawley. Myeloma and Race: A review of the
literature. Cancer and Metastasis Reviews 22: 87, 2003
Racial disparity in myeloma
%
associated SNPs
100.00
AFRICAN AMERICAN
*
*
*
*
CAUCASIAN
*
80.00
*
*
*
*
*
*p < 0.001
60.00
*
40.00
*
*
*
*
20.00
0.00
00
00
00
00
00
00
9321
9487
P5
9321
9487
P5
9321
9487
P5
9321
9487
P5
9321
9487
P5
9321
9487
P5
SN
SN
SN
SN
SN
SN
GG
GG
GG
GG
CC
GG
IL6
ERCC2
XRCC1
LT
MDR1
CYP3A4
Impact Of SNPs
· Single, targeted SNPs show associations with
Complications (eg. bone disease)
Response
Toxicities
·
There are significant ethnic differences in SNP
frequencies
May impact risk and response
· BUT,
·
Single SNPs need to be replaced by global SNP
analyses
BOAC Custom global SNP Chip to target pathways,
SNP clusters
Correct SNP associations for ethnic variations
Need to examine common haplotypes
Overall Survival: >4 Years vs <1 Year in
S9321 shows cSNP clustering
>4
<1
Homozygous rare
Homozygous common
No data
Top SNPs associated with survival differences
Table 1. 10K cSNP Array - SNPs Declared Significant with a 15% False Discovery Rate
P-value
dbSNPid
Gene Symbol
Gene Name
Gene Class
(Exact Test)
rs2287622
0.000885 ABCB11
ATP-binding cassette; sub-family B
ADME/DMET
rs2228226
0.004729 GLI1
glioma-associated oncogene homolog 1
DNA Repair
rs2479383
0.006319 PSMB4
proteasome
Angiogenesis
Liver transport of
DNA Repair,
rs3730477
0.006761 POLL
polymerase
Inflammation
adriamycin
Inflammation and
rs679899
0.011796 APOB
apolipoprotein B
Immunity, Pharmacology
Inflammation and
rs2165627
0.011836 PTPRB
protein tyrosine phosphatase; receptor type; B
Immunity
Angiogenesis,
rs2305030
0.013362 LTK
leukocyte tyrosine kinase
Pharmacology
Angiogenesis
rs757081
0.014203 NUCB2
nucleobindin 2
Neuropathy
rs3177980
0.015238 SELL
selectin L
DNA Repair
rs6679793
0.017674 FCRL5
Fc receptor-like 5
Kinase
rs3088142
0.021339 DUSP13
dual specificity phosphatase 13
Kinase
Inflammation and
rs1042034
0.021519 APOB
apolipoprotein B
Immunity, Pharmacology
Inflammation and
rs676210
0.021519 APOB
apolipoprotein B
Immunity, Pharmacology
Inflammation and
rs2664538
0.021875 MMP9
matrix metalloproteinase 9
Immunity
rs2292954
0.024475 SPG7
spastic paraplegia 7; paraplegin
Environmental Response
rs12500797
0.02855 PTPN13
protein tyrosine phosphatase; non-receptor type 13
Angiogenesis
Inflammation and
rs766173
0.030429 BRCA2
breast cancer 2; early onset
Immunity, Pharmacology
Expression profile
Inflammation and
rs1801701
0.037251 APOB
apolipoprotein B
Immunity, Pharmacology
hits
Inflammation and
rs2070150
0.037251 ATF6
activating transcription factor 6
Immunity, Pharmacology
rs3808553
0.042044 FZD6
frizzled homolog 6
Kinase
rs770087
0.04658 DUSP6
dual specificity phosphatase 6
Kinase
Inflammation and
rs4459610
0.049211 ACE
angiotensin I converting enzyme
Immunity
rs7871785
0.051507 PSMB7
proteasome
Obesity/Cholesterol
rs8192284
0.052333 IL6R
interleukin 6 receptor
ADME/DMET
rs1051061
0.052547 VRK2
vaccinia related kinase 2
DNA Repair
Pathway Nodal Analysis (PNAn)
(from Ingenuity Systems)
Top ranked SNPs
associated with survival
in S9321 converge on
TNF
TNF
MYELOMA CUSTOM SNP CHIP
GENE FUNCTIONS
ADME
Cardio
Cell cycle
Death
Morphology
Cell-cell
Differentiation
Growth&proliferation
Movement
1007
801
819
1521
400
791
712
1345
395
DNA repair Gene expression Hematologic systems Signaling Metabolic
Immunity
Structures
851
819
1325
301
697
786
948
IGF-1 IL-2
IL-4 IL-6 JAK/STAT NFkB AKT
PATHWAYS
---
GENES
---
IL-6R SOS GRAB RAF RAS MAPK ERK AP-1
rs123124
rs232675 rs7456456 rs56687965
rs4560690 rs8485968
---
SNPs
OUT
IN
<2%
>2% (+5% ethnic specific)
Unvalidated
Validated
Synonymous cDNA
Non-synonymous cDNA
3,590
Non-coding
Promoter / regulatory
+ Admixture for ethnic
SNPs
correction
+ Selected Hap Tags
Custom SNP Chip Priorities:
Toxicities associated with thal, rev, mel, dex
· dvt
· neuropathy
· myelodysplasia
· hyperglycemia
Bone disease
Response - Pharmacogenetics (esp drug metabolism)
Epidemiology & ethnicity
· Risk assessments to include demographics and exposures
· Partnership with NCI - patient survey forms in development
Analysis: SNP Groupings: biologic interactions,
common pathways, common nodes