a mixed-effects model for powerful association …...the american journal of human genetics, volume...

The American Journal of Human Genetics, Volume 102

Supplemental Data

A Mixed-Effects Model for Powerful Association

Tests in Integrative Functional Genomics

Yu-Ru Su, Chongzhi Di, Stephanie Bien, Licai Huang, Xinyuan Dong, GoncaloAbecasis, Sonja Berndt, Stephane Bezieau, Hermann Brenner, Bette Caan, GrahamCasey, Jenny Chang-Claude, Stephen Chanock, Sai Chen, Charles Connolly, KeithCurtis, Jane Figueiredo, Manish Gala, Steven Gallinger, Tabitha Harrison, MichaelHoffmeister, John Hopper, Jeroen R. Huyghe, Mark Jenkins, Amit Joshi, Loic LeMarchand, Polly Newcomb, Deborah Nickerson, John Potter, Robert Schoen, MarthaSlattery, Emily White, Brent Zanke, Ulrike Peters, and Li Hsu

Supplemental Information of GECCO & CCFR: Description of

Studies

Below we provide detailed description of the 14 studies in CCFR and GECCO. In addition, detailed

numbers of cases and controls along with gender distribution in each study can be found in Table

S4.

The french Association STudy Evaluating RISK for sporadic colorectal cancer (ASTER-

ISK)9. Participants were recruited from the Pays de la Loire region in France between December

2002 and March 2006. Eligibility criteria for cases included being of Caucasian origin, being

greater than or 40 years of age at diagnosis, and having no family history of colorectal cancer or

polyps. Cases were patients with first primary colorectal cancer diagnosed in one of the six public

hospitals and five clinics located in the Pays de la Loire region which participated in the study.

Cases were confirmed based on medical and pathology reports. Controls were recruited at two

Health Examination Centers of the Pays de la Loire region, and the recruitment of controls greater

than or 70 years was completed in the departments of internal medicine and hepatogastroenterol-

ogy of the University Hospital Center of Nantes, located in the same region. Controls were eligible

to participate if they were Caucasian, aged greater than or 40 years, and had no family history of

colorectal cancer or polyps. In the presence of the physician, each participant filled out a stan-

dardized questionnaire on family information, medical history, lifestyle, and dietary intake. Cases

and controls provided a blood sample.

Colon Cancer Family Registry (CCFR). The CCFR is an NCI-supported consortium consisting

of six centers dedicated to the establishment of a comprehensive collaborative infrastructure for in-

terdisciplinary studies in the genetic epidemiology of colorectal cancer.13 The CCFR includes data

from approximately 30,500 total subjects (10,500 probands, and 20,000 unaffected and affected

relatives and unrelated controls). Cases and controls, age 20 to 74 years, were recruited at the

six participating centers beginning in 1998. CCFR implemented a standardized questionnaire that

is administered to all participants, and includes established and suspected risk factors for colorec-

tal cancer, which includes questions on medical history and medication use, reproductive history

(for female participants), family history, physical activity, demographics, alcohol and tobacco use,

and dietary factors. The Set 1 scan, which has been described previously,4 includes population-

based cases and age-matched controls from the three population-based centers: Seattle, Toronto

and Australia. Cases were genetically enriched by over-sampling those with a young age at on-

set or positive family history. Controls were matched to cases on age and sex. All cases and

controls were self-reported as White, which was confirmed with genotype data. The Set 2 scan

includes population-based cases and matched controls from all six Colon CFR centers including

Mayo Clinic, Hawaii Cancer Registry, University of Southern California, Fred Hutchinson Cancer

Research Center, Cancer Care Ontario and University of Melbourne. As with Set 1, cases were

genetically enriched by over-sampling those with a young age at onset or positive family history.

Controls were same generation family controls.

Darmkrebs: Chancen der Verhutung durch Screening (DACHS).2,12 This German study was

initiated as a large population-based case-control study in 2003 in the Rhine-Neckar-Odenwald

region (southwest region of Germany) to assess the potential of endoscopic screening for re-

duction of colorectal cancer risk and to investigate etiologic determinants of disease, particularly

lifestyle/environmental factors and genetic factors. Cases with a first diagnosis of invasive colorec-

tal cancer (International Classification of Diseases 10 codes C18-C20) who were at least 30 years

of age (no upper age limit), German speaking, a resident in the study region, and mentally and

physically able to participate in a one-hour interview, were recruited by their treating physicians

either in the hospital a few days after surgery, or by mail after discharge from the hospital. Cases

were confirmed based on histologic reports and hospital discharge letters following diagnosis of

colorectal cancer. All hospitals treating colorectal cancer patients in the study region participated.

Based on estimates from population-based cancer registries, more than 50% of all potentially eli-

gible patients with incident colorectal cancer in the study region were included. Community-based

controls were randomly selected from population registries, employing frequency matching with

respect to age (5-year groups), sex, and county of residence. Controls with a history of colorectal

cancer were excluded. Controls were contacted by mail and follow-up calls. The participation rate

was 51%. During an in-person interview, data were collected on demographics, medical history,

family history of CRC, and various life-style factors, as were blood and mouthwash samples. This

analysis includes participants recruited up to 2010 in this ongoing study.

Diet, Activity, and Lifestyle Study (DALS).17 DALS is a population-based case-control study

of colon cancer. Participants were recruited between 1991 and 1994 from three locations: the

Kaiser Permanente Medical Care Program (KPMCP) of Northern California, an eight-county area

in Utah, and the metropolitan Twin Cities area of Minnesota. Eligibility criteria for cases included

age at diagnosis between 30 and 79 years, diagnosis with first primary colon cancer (Interna-

tional Classification of Diseases for Oncology-2 codes 18.0 and 18.2-18.9) between October 1st

1991 and September 30th 1994, English speaking, and competency to complete the interview.

Individuals with cancer of the rectosigmoid junction or rectum were excluded, as were those with

a pathology report noting familial adenomatous polyposis, Crohn’s disease, or ulcerative colitis.

A rapid-reporting system was used to identify all incident cases of colon cancer resulting in the

majority of cases being interviewed within four months of diagnosis. Controls from KPMCP were

randomly selected from membership lists. In Utah, controls under 65 years of age were randomly

selected through random-digit dialing and driver license lists. Controls, 65 years of age and older,

were randomly selected from Health Care Financing Administration lists. In Minnesota, controls

were identified from Minnesota driver’s license or state ID lists. Controls were matched to cases

by 5-year age groups and sex. The Set I scan consisted of a subset of the study designed above,

from Utah, Minnesota, and KPMCP, and was restricted to subjects who self-reported as White

non-Hispanic. The Set 2 scan consisted of subjects from Utah and Minnesota that 2 were not

genotyped in Set 1. Set 2 was restricted to subjects who self-reported as White non-Hispanic and

those that had appropriate consent to post data to dbGaP.

Hawaii Colorectal Cancer Studies 2 & 3 (Colo2&3).11 Patients with colorectal cancer were

identified through the rapid reporting system of the Hawaii SEER registry and consisted of all

Japanese, Caucasian, and Native Hawaiian residents of Oahu who were newly diagnosed with an

adenocarcinoma of the colon or rectum between January 1994 and August 1998. Control subjects

were selected from participants in an on-going population-based health survey conducted by the

Hawaii State Department of Health and from Health Care Financing Administration participants.

Controls were matched to cases by sex, ethnicity, and age (within two years). Personal interviews

were obtained from 768 matched pairs, resulting in a participation rate of 58.2% for cases and

53.2% for controls. A questionnaire, administered during an in-person interview, included ques-

tions about demographics, lifetime history of tobacco, alcohol use, aspirin use, physical activity,

personal medical history, family history of colorectal cancer, height and weight, diet (Food Fre-

quency Questionnaire), and postmenopausal hormone use. A blood sample was obtained from

548 (71%) of interviewed cases and 662 (86%) of interviewed controls. SEER staging information

was extracted from the Hawaii Tumor Registry. In GECCO, self-reported Caucasian subjects with

DNA, and clinical and epidemiologic data were selected for genotyping.

Health Professionals Follow-up Study (HPFS).16 The HPFS is a parallel prospective study to

the Nurses’ Health Study (NHS). The HPFS cohort comprises 51,529 men who, in 1986, re-

sponded to a mailed questionnaire. The participants are U.S. male dentists, optometrists, os-

teopaths, podiatrists, pharmacists, and veterinarians born between 1910 and 1946. Participants

have provided information on health related exposures, including: current and past smoking his-

tory, age, weight, height, diet, physical activity, aspirin use, and family history of colorectal cancer.

Colorectal cancer and other outcomes were reported by participants or next-of-kin and followed up

through review of the medical and pathology record by physicians. Overall, more than 97% of self-

reported colorectal cancers were confirmed by medical record review. Information was abstracted

on histology and primary location. Incident cases are defined as those occurring after the subject

provided the blood sample. Prevalent cases are defined as those occurring after enrollment in

the study, but prior to the subject providing the blood sample. Follow-up has been excellent, with

94% of the men responding to date. Colorectal cancer cases were ascertained through January

1, 2008. In 1993-95, 18,825 men in HPFS mailed in blood samples by overnight courier which

were aliquoted into buffy coat and stored in liquid nitrogen. In 2001-04, 13,956 men in HPFS

who had not previously provided a blood sample mailed in a ”swish-and-spit” sample of buccal

cells. Incident cases are defined as those occurring after the subject provided a blood or buccal

sample. Prevalent cases are defined as those occurring after enrollment in the study in 1986,

but prior to the subject providing either a blood or buccal sample. After excluding participants

with histories of cancer (except non-melanoma skin), ulcerative colitis, or familial polyposis, two

case-control sets were constructed from which DNA was isolated from either buffy coat or buccal

cells for genotyping: 1) a case-control set with cases of colorectal cancer matched to randomly se-

lected controls who provided a blood sample and were free of colorectal cancer at the same time

the colorectal cancer was diagnosed in the cases; 2) a case-control set with cases of colorectal

cancer matched to randomly selected controls who provided a buccal sample and were free of

colorectal cancer at the same time the colorectal cancer was diagnosed in the case. For both

case-control sets, matching criteria included year of birth (within 1 year) and month/year of blood

or buccal cell sampling (within six months). Cases were pair matched 1:1, 1:2, or 1:3 with a control

participant(s). In addition to colorectal cancer cases and controls, a set of adenoma cases and

matched controls with available DNA from buffy coat were selected for genotyping. Over follow-up,

data were collected on endoscopic screening practices and, if individuals have been diagnosed

with polyp, the polyps were confirmed to be adenomatous by medical record review. Adenoma

cases were ascertained through January 1, 2008. A separate case-control set was constructed of

participants diagnosed with advanced adenoma matched to control participants who underwent a

lower endoscopy in the same time period and did not have an adenoma. Advanced adenoma was

defined as an adenoma ≥1 cm in diameter and / or with tubulovillous, villous, or high-grade dys-

plasia / carcinoma-in-situ histology. Matching criteria included year of birth (within one year) and

month/year of blood sampling (within six months), the reason for their lower endoscopy (screening,

family history, or symptoms) and the time period of any prior endoscopy (within two years). Con-

trols matched to cases with a distal adenoma either had a negative sigmoidoscopy or colonoscopy

exam and controls matched to cases with proximal adenoma all had a negative colonoscopy.

Multiethnic Cohort Study (MEC).8 MEC was initiated in 1993 to investigate the impact of dietary

and environmental factors on major chronic diseases, particularly cancer, in ethnically diverse

populations in Hawaii and California. The study recruited 96,810 men and 118,441 women aged

45 to 75 years between 1993 and 1996. Incident colorectal cancer cases occurring since Jan-

uary 1995, and controls were contacted for blood or saliva samples. The median interval between

diagnosis and blood draw was 14 months (interquartile range, 10-19) among cases and the par-

ticipation rate 74%. A sample of cohort participants was randomly selected to serve as controls at

the onset of the nested case-control study (participation rate 66%). The selection was stratified by

sex, age, and race/ethnicity. Colorectal cancer cases are identified through the Rapid Reporting

System of the Hawaii Tumor Registry and through quarterly linkage to the Los Angeles County

Cancer Surveillance Program. Both registries are members of SEER. In GECCO, self-reported

White subjects from the nested case-control study described above with DNA, and clinical and

epidemiologic data were selected for genotyping.

Nurses’ Health Study (NHS).1 The NHS cohort began in 1976 when 121,700 married female

registered nurses aged 30 to 55 years returned the initial questionnaire that ascertained a variety

of important health-related exposures. Since 1976, follow-up questionnaires have been mailed ev-

ery two years. Colorectal cancer and other outcomes were reported by participants or next-of-kin

and followed up through review of the medical and pathology record by physicians. Overall, more

than 97% of self-reported colorectal cancers were confirmed by medical-record review. Informa-

tion was abstracted on histology and primary location. Follow-up has been high: as a proportion

of the total possible follow-up time, follow-up has been over 92%. Colorectal cancer cases were

ascertained through June 1, 2008. In 1989-90, 32,826 women in NHS I, mailed in blood samples

by overnight courier which were aliquoted into buffy coat and stored in liquid nitrogen. In 2001-04,

29,684 women in NHS I who did not previously provide a blood sample mailed in a ”swish-and-spit”

sample of buccal cells. Incident cases are defined as those occurring after the subject provided

a blood or buccal sample. Prevalent cases are defined as those occurring after enrollment in the

study in 1976, but prior to the subject providing either a blood or buccal sample. After excluding

participants with histories of cancer (except non-melanoma skin), ulcerative colitis, or familial poly-

posis, two case-control sets were constructed from which DNA was isolated from either buffy coat

or buccal cells for genotyping: 1) a case-control set with cases of colorectal cancer matched to

randomly selected controls who provided a blood sample and were free of colorectal cancer at the

same time the colorectal cancer was diagnosed in the case; 2) a case-control set with cases of

colorectal cancer matched to randomly selected controls who provided a buccal sample and were

free of colorectal cancer at the same time the colorectal cancer was diagnosed in the cases. For

both case-control sets, matching criteria included year of birth (within one year) and month / year

of blood or buccal cell sampling (within six months). Cases were pair matched 1:1, 1:2, or 1:3

with a control participant(s). In addition to colorectal cancer cases and controls, a set of adenoma

cases and matched controls with available DNA from buffy coat were selected for genotyping. Over

follow-up, data were collected on endoscopic screening practices and, if individuals have been di-

agnosed with polyp, the polyps confirmed to be adenomatous by medical record review. Adenoma

cases were ascertained through June 1, 2008. A separate case-control set was constructed of

participants diagnosed with advanced adenoma matched to control participants who underwent a

lower endoscopy in the same time period and did not have an adenoma. Advanced adenoma was

defined as an adenoma ¿ 1 cm in diameter and / or with tubulovillous, villous, or high-grade dys-

plasia / carcinoma-in-situ histology. Matching criteria included year of birth (within one year) and

month/year of blood sampling (within six months), the reason for their lower endoscopy (screening,

family history, or symptoms) and the time period of any prior endoscopy (within two years). Con-

trols matched to cases with a distal adenoma either had a negative sigmoidoscopy or colonoscopy

exam and controls matched to cases with proximal adenoma all had a negative colonoscopy.

Physicians’ Health Study (PHS).3,7 The PHS was established as a randomized, double-blind,

placebo-controlled trial of aspirin and s-carotene among 22,071 healthy U.S. male physicians, be-

tween 40 and 84 years of age in 1982. Participants completed two mailed questionnaires before

being randomly assigned, additional questionnaires at six and 12 months, and questionnaires

annually thereafter. In addition, participants were sent postcards at six months to ascertain sta-

tus. From August 1982 to December 1984, 14,916 baseline blood samples were collected from

the physicians during the run-in phase before randomization. When participants report a diagno-

sis of cancer, medical records and pathology reports are reviewed by study physicians who are

blinded to exposure data. Among those who provided baseline blood samples, colorectal cases

were ascertained through March 31, 2008, and controls were matched on age (within one year for

younger participants, up to five years for older participants) and smoking status (never, past, cur-

rent). Cases were pair matched 1:1, 1:2 or 1:3 with a control participant(s). Due to DNA availability

samples were genotyped in two batches on the same platform at the same genotyping center at

different time points.

Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). PLCO enrolled

154,934 participants (men and women, aged between 55 and 74 years) at ten centers into a large,

randomized, two-arm trial to determine the effectiveness of screening to reduce cancer mortality.

Sequential blood samples were collected from participants assigned to the screening arm. Partic-

ipation was 93% at the baseline blood draw. In the observational (control) arm, buccal cells were

collected via mail using the “swish-and-spit” protocol and participation rate was 65%. Details of

this study have been previously described5,15 and are available online (http://dcp.cancer.gov/plco).

The Set 1 scan included a subset of 577 colon cancer cases self-reported as being non-Hispanic

White with available DNA samples, questionnaire data, and appropriate consent for ancillary epi-

demiologic studies. Cases were excluded if they had a history of inflammatory bowel disease,

polyps, polyposis syndrome or cancer (excluding basal or squamous cell skin cancer). Controls

come from the Cancer Genetic Markers of Susceptibility (CGEMS) prostate cancer scan 18,20 (all

male) and the GWAS of Lung Cancer and Smoking10 (enriched for smokers) along with an addi-

tional 92 non-Hispanic White female controls. For the Set 2 scan, cases were colorectal cancers

from both arms of the trial, which were not already included in Set 1. Samples were excluded

if participants did not sign appropriate consents, if DNA was unavailable, if baseline question-

naire data with follow-up were unavailable, if they had a history of colon cancer prior to the trial,

if they were a rare cancer, and if they were already in colon GWAS, or if they were a control in

the prostate or lung populations. Controls were frequency matched 1:1 to cases without replace-

ment, and cases were not eligible to be controls. Matching criteria were age at enrollment (two

year blocks), enrollment date (two year blocks), sex, race / ethnicity, trial arm, and study year of

diagnosis (i.e. controls must be cancer free into the case’s year of diagnosis).

Postmenopausal Hormones Supplementary Study to the Colon Cancer Family Registry

(PMH-CCFR).14 Eligible case patients included all female residents, ages 50 to 74 years, residing

in the 13 counties in Washington State reporting to the Cancer Surveillance SEER program, who

were newly diagnosed with invasive colorectal adenocarcinoma (ICD-O C18.0, C18.2-.9, C19.9,

C20.0-.9) between October 1998 and February 2002. Eligibility for all individuals was limited to

those who were English-speaking with available telephone numbers, in which they could be con-

tacted. On average, cases were identified within four months of diagnosis. The overall response

proportion of eligible cases identified was 73%. Community-based controls were randomly se-

lected according to age distribution (in 5-year age intervals) of the eligible cases by using lists of

licensed drivers from the Washington State Department of Licensing for individuals, ages 50 to

64 years, and rosters from the Health Care Financing Administration (now the Centers for Medi-

care and Medicaid) for individuals older than 64 years. The overall response proportion of eligible

controls was 66%. In GECCO, samples with sufficient DNA extracted from blood were genotyped.

Only participants that were not part of the CCFR Seattle site were included in the sample set.

VITamins And Lifestyle (VITAL). The VITamins And Lifestyle (VITAL) cohort comprises of 77,721

Washington State men and women aged 50 to 76 years, recruited from 2000 to 2002 to investigate

the association of supplement use and lifestyle factors with cancer risk. Subjects were recruited

by mail, from October 2000 to December 2002, using names purchased from a commercial mail-

ing list. All subjects completed a 24 page questionnaire and buccal-cell specimens for DNA were

self-collected by 70% of the participants. Subjects are followed for cancer by linkage to the west-

ern Washington SEER cancer registry and are censored when they move out of the area covered

by the registry or at time of death. Details of this study have been previously described.19 In

GECCO, a nested case-control set was genotyped. Samples included, colorectal cancer cases

with DNA, excluding subject with colorectal cancer before baseline, in situ cases, (large cell) neu-

roendocrine carcinoma, squamous cell carcinoma, carcinoid tumor, Goblet cell carcinoid, any type

of lymphoma, including non-Hodgkin, Mantle cell, large B-cell, or follicular lymphoma. Controls

were matched on age at enrollment (within one year), enrollment date (within one year), sex, and

race / ethnicity. One control was randomly selected per case among all controls that matched on

the four factors above and where the control follow-up time was greater than follow-up time of the

case until diagnosis.

Women’s Health Initiative (WHI). WHI is a long-term health study of 161,808 post-menopausal

women aged 50 to 79 years at 40 clinical centers throughout the U.S. WHI comprises a Clinical

Trial (CT) arm, an Observational Study (OS) arm, and several extension studies. The details of

WHI have been previously described6,18 and are available online (https://cleo.whi.org/SitePages/Home.aspx).

In GECCO, Set 1 cases were selected from the September 12, 2005 database and were com-

prised of centrally adjudicated colon cancer cases from the Observational Study (OS) who self-

reported as White. Controls were first selected among controls previously genotyped as part

of a Hip Fracture GWAS conducted within the WHI OS and matched to cases on age (within

three years) enrollment date (within 365 days), hysterectomy status, and prevalent conditions at

baseline. For 37 cases, there was not a control match in the Hip Fracture GWAS. For these par-

ticipants, we identified a matched control in the WHI OS based on same criteria. In the Set 2

scan, cases were selected from the August 2009 database and were comprised of centrally ad-

judicated colon and colorectal cancer cases from the OS and CT who were not genotyped in Set

1. In addition, case and control participants were subject to the following exclusion criteria: a prior

history of colorectal cancer at baseline, IRB approval not available for data submission into db-

GaP, and not sufficient DNA available. Matching criteria included age (within years), race/ethnicity,

WHI date (within three years), WHI Calcium and Vitamin D study date (within three years), and

randomization arms (OS flag, hormone therapy assignments, dietary modification assignments,

calcium/vitamin D assignments). In addition, they were matched on the four regions of randomiza-

tion centers. Each case was matched with one control (1:1) that exactly met the matching criteria.

Control selection was done in a time-forward manner, selecting one control for each case first

from the risk set at the time of the case’s event. The matching algorithm was allowed to select the

closest match based on a criterion to minimize an overall distance measure. Each matching factor

was given the same weight. Additional available controls that were genotyped as part of the Hip

Fracture GWAS were included to improve power.

rs28

8847

9rs

4133

195

rs10

9327

45rs

6729

308

rs13

3976

73

CAF

0.0 0.2 0.4 0.6 −0.10 0.00 0.05 0.10

Marginal Association

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●

−0.02846382−0.00927794−0.01621705

−0.05220258−0.01286155−0.03003672

−3.709907e−05−0.009414035

0.04122352−0.006633132

0.04025030.008547796−0.02141662−0.04155728−0.02272229−0.02386906

−0.0097879680.0089906690.003643506

1.17e−023.29e−033.95e−03

4.81e−043.43e−043.16e−043.84e−043.21e−04

1.14e−048.64e−05

5.38e−056.06e−055.75e−055.26e−053.62e−052.59e−05

2.73e−021.07e−021.16e−02

Gene CXCR1

−1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1

rs10193383

rs4674267

rs13397673

rs13389420

rs3762562

rs2081777

rs730947

rs6436101

rs2552517

rs2571455

rs3791957

rs6744219

rs6729308

rs6729330

rs6745037

rs890049

rs13426335

rs7573770

rs6709815

rs10932738

rs12694425

rs12694427

rs10932745

rs12694426

rs4672870

rs10804264

rs7426289

rs6723449

rs4674257

rs6436033

rs13035513

rs6726126

rs4133195

rs12471773

rs897877

rs3731860

rs4674218

rs16858298

rs4674219

rs2033306

rs10490759

rs2888479

Gene CXCR1

(a) CAF and marginal associations (b) LD structure

Figure S1: Genetic structures of CXCR1 in simulations for power comparisons The left penal shows the countallele frequencies (CAF) and the middle panel shows marginal association log-odds ratio estimates and 95% confidenceintervals for each regulatory variants. The LD structures are presented in the right penal with each ellipse in the matrix-type plot representing the Pearson correlation between a pair of variants. Marginally significant variants (at level 0.05)are marked in dark colors, and the rest of variants are marked in light colors.

rs99

5756

2rs

1108

2750

rs12

3273

41rs

6507

940

rs29

9728

CAF

0.0 0.2 0.4 0.6 0.8 −0.15 −0.05 0.05 0.15


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−0.124020359−0.002857278

0.0118254150.002688852

0.001148669

−0.00142366−0.003362775

0.072527076

3.88e−021.58e−02

1.43e−021.36e−02

1.42e−02

3.59e−094.06e−04

1.64e−02

Gene C18orf32

−1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1

rs17803280

rs894771

rs11874293

rs299728

rs2337012

rs11082678

rs7227023

rs698611

rs2337104

rs12962825

rs9960507

rs6507940

rs7233748

rs11659469

rs2000812

rs4939583

rs6507927

rs7233208

rs12954680

rs8092472

rs12327341

rs11661249

rs9954569

rs6417104

rs9807152

rs2337547

rs1628233

rs2852091

rs7242374

rs11082750

rs12458813

rs4939879

rs7237871

rs1540039

rs12454509

rs12953717

rs9946510

rs920660

rs9957562

Gene C18orf32


Figure S2: Genetic structures of C18orf32 in simulations for power comparisons The left penal shows the countallele frequencies (CAF) and the middle panel shows marginal association log-odds ratio estimates and 95% confidenceintervals for each regulatory variants. The LD structures are presented in the right penal with each ellipse in the matrix-type plot representing the Pearson correlation between a pair of variants. Marginally significant variants (at level 0.05)are marked in dark colors, and the rest of variants are marked in light colors.

rs16

9640

74rs

2141

437

rs17

8168

98rs

1107

1887

rs47

8005

2

CAF

0.0 0.2 0.4 0.6 0.8 −0.1 0.0 0.1 0.2


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0.037447786−0.000923535−0.1935873081

0.0198045104−0.0089400664

0.3577350153−0.04620651570.0146864611−0.0185126713

−0.0026562105

−0.0372174155

−0.010676953

0.0115460609−0.0326503573

0.0439357278−0.0834837359−0.0001958362

0.02161887880.0074062024

−0.0073132747

3.08e−029.16e−033.09e−03

2.55e−021.65e−03

3.58e−033.52e−023.63e−023.82e−02

4.71e−02

4.17e−02

1.58e−03

1.89e−081.77e−04

3.25e−037.72e−034.66e−02

2.15e−021.76e−03

4.78e−02

Gene ARHGAP11A

−1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1

rs28457217rs12593101

rs12438479rs1258746rs11071936

rs17228669rs10519740

rs17816285rs4780052rs10519756

rs4780042rs4343247rs11630548

rs12904522rs7178622rs11858940

rs8035668rs16966853

rs8035130rs12591992

rs12443212rs12593288

rs2291730rs3816940

rs4414465rs7177812rs17229055

rs8028021rs12914342

rs7179733rs11071887

rs11632524rs8037818rs11634439

rs11633925rs4780094rs11638698

rs1961021rs4611425

rs2339165rs12911648

rs2611603rs16959052

rs16969816rs11072570

rs12148690rs11853673

rs17817299rs597850

rs658750rs8037033rs17816892

rs17816898rs17816904

rs12915870rs2292548rs17235975

rs17236010rs8030946

rs6495180rs11632252

rs28409665rs11638089

rs12101641rs11071882

rs10318rs10519750

rs16959212rs7180085

rs3826029rs1514246

rs965435rs3108629

rs2141437rs2141438

rs2596170rs2676014

rs7175488rs2596187rs17816441

rs12594918rs10519800

rs11633650rs2670944

rs4780111rs16953863

rs7167430rs2676049

rs2596195rs17236035

rs12913333rs347932rs4780058rs11635997

rs16964074

Gene ARHGAP11A


Figure S3: Genetic structures of ARHGAP11A in simulations for power comparison The left penal shows thecount allele frequencies (CAF) and the middle panel shows marginal association log-odds ratio estimates and 95%confidence intervals for each regulatory variants. The LD structures are presented in the right penal with each ellipsein the matrix-type plot representing the Pearson correlation between a pair of variants. Marginally significant variants(at level 0.05) are marked in dark colors, and the rest of variants are marked in light colors.

2 3 4 5 6

0.0

0.2

0.4

0.6

0.8

1.0

Signal through GREx (v2=1)

−log10(sig. level)

Pow

er

2 3 4 5 6 7

0.0

0.2

0.4

0.6

0.8

1.0

Signal through both GREx and individual associations (v2=0.5)


Pow

er

2 3 4 5 6 7 8

0.0

0.2

0.4

0.6

0.8

1.0

Signal through individual associations (v2=0)


Pow

er

PrediXcan mSKAT fMiST aMiST oMiST

Binary outcomes, simulated genomewide analysis

Figure S4: Power comparison for genome-wide analysis. Power curves of PrediXcan (grey dashed curve), modifiedSKAT (yellow dashed curve), and three combination methods in MiST (red, dark blue and light blue solid curve forfMiST, aMiST and oMiST, respectively) on a simulated genome-wide analysis mimicking genetic structures available inPrediXcan whole blood database under various proportion of signal explained by gene expression (v2 = 1 for left panel,v2 = 0.5 for middle panel, and v2 = 0 for right panel).

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

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●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●

●●●●●●●●●●●●●

●●●●●●●●●

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PrediXcanmSKATfMiSTaMiSToMiST

Figure S5: Examination on hidden population substructures in GECCO & CCFR. This figure presents quantile-quantile plots of various tests after permutations on the case-control status following the method proposed in Epstein etal. (2012) to verify if the adjusted covariates in the analyses accounted for population substructure. The coloring codesare as following: Gray dots for PrediXcan, yellow dots for modified SKAT, red dots for Fisher’s combination method(fMiST ), dark and light blue dots for aMiST and oMiST respectively. The light grey line stands for the 45-degree line.

rs66

9117

0rs

6678

807

rs10

7372

35rs

4575

047

CAF

0.0 0.1 0.2 0.3 0.4 0.5 −0.10 0.00 0.05


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0.002591558

−0.029307731

−0.010100108

−0.133287683

−0.02406317

−0.023073717

−0.005801122

−0.005075676

−0.0075946

−0.158159024

−0.026091265

2.98e−03

7.01e−03

3.14e−05

1.27e−05

1.75e−05

1.40e−05

1.79e−05

1.53e−05

1.63e−05

4.90e−06

6.24e−06

2.66e−06

Gene LAMC1

−1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1

rs12025917

rs536586

rs10911269

rs8179361

rs4575047

rs4233192

rs4420053

rs10911186

rs10752881

rs10737235

rs12739316

rs6678517

rs10752878

rs12137908

rs6678807

rs3904696

rs72647484

rs10911251

rs6691170

Gene LAMC1


Figure S6: Genetic structures of regulatory variants on LAMC1. This figure presents count allele frequencies (CAF)(left), marginal association log-odds ratio estimates and 95% confidence intervals (middle), and LD structures (right) ofregulatory variants on LAMC1 along with known CRC risk SNPs on chromosome 1. Known CRC risk SNPs are markedin dark red, marginally significant variants at level 0.05 are marked in dark blue, and those marginally insignificantones are marked in light blue. The ellipses in the matrix-type correlation plot in the right penal represent the Pearsoncorrelation between a pair of variants.

rs69

8326

7rs

7014

346

rs12

5481

56rs

2385

676

rs12

6800

47

CAF

0.0 0.2 0.4 0.6 0.8 −0.1 0.0 0.1 0.2 0.3


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−0.0170221229−0.0090091535

0.0113309456

0.0132182736−0.0094114162−0.0399756007

−0.034384715

−0.1433159313−0.0219095982

6.65e−044.60e−04

6.41e−03

2.82e−022.53e−02

1.34e−03

9.07e−03

4.24e−109.69e−10

3.99e−101.10e−02

5.09e−12

Gene POU5F1B

−1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1

rs1472026rs7833011

rs901592rs785003

rs12680047rs6651166

rs13248347rs2445611

rs13275200rs1551510

rs7825118rs16902118

rs16902104rs16902103

rs6998726rs2385676

rs4871721rs16901814

rs1516952rs13259479

rs4870985rs10505508

rs4733828rs727373

rs7839958rs16901435

rs12548156rs16901453

rs12546489rs6470532

rs7388649rs10110900

rs9785095rs7819084

rs12549845rs6985419

rs7013278rs7014346

rs6996426rs976226

rs4266612rs10096900

rs16901432rs1487232

rs979201rs16892766

rs2450115rs6469656

rs6983267

Gene POU5F1B


Figure S7: Genetic structures of regulatory variants on POU5F1B. This figure presents count allele frequencies(CAF) (left), marginal association log-odds ratio estimates and 95% confidence intervals (middle), and LD structures(right) of regulatory variants on POU5F1B along with known CRC risk SNPs on chromosome 8. Known CRC riskSNPs are marked in dark red, marginally significant variants at level 0.05 are marked in dark blue, and those marginallyinsignificant ones are marked in light blue. The ellipses in the matrix-type correlation plot in the right penal representthe Pearson correlation between a pair of variants.

rs38

0284

2rs

1757

7003

rs10

5021

39rs

7122

375

rs71

1965

8

CAF

0.0 0.2 0.4 0.6 −0.15 −0.05 0.05


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−0.03952386

−0.01781985

0.02888497

0.02272773

7.08e−06

1.94e−07

2.02e−07

1.82e−07

1.41e−04

3.33e−05

1.94e−07

Gene C11orf92

−1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1

rs7119658

rs12225049

rs12575797

rs7950145

rs6589220

rs3802842

rs7122375

rs3802840

rs17471196

rs12574149

rs12785346

rs4144344

rs10502139

rs7944798

rs7104680

rs10891268

rs4938535

rs12362765

rs17577003

rs1876197

rs949279

rs174537

rs60892987

rs3824999

rs3802842.1

Gene C11orf92


Figure S8: Genetic structures of regulatory variants on C11orf92. This figure presents count allele frequencies(CAF) (left), marginal association log-odds ratio estimates and 95% confidence intervals (middle), and LD structures(right) of regulatory variants on C11orf92 along with known CRC risk SNPs on chromosome 11. Known CRC riskSNPs are marked in dark red, marginally significant variants at level 0.05 are marked in dark blue, and those marginallyinsignificant ones are marked in light blue. The ellipses in the matrix-type correlation plot in the right penal representthe Pearson correlation between a pair of variants.

rs73

2081

20rs

1077

4214

rs73

0537

5rs

7979

165

CAF

0.0 0.2 0.4 0.6 0.8 −0.8 −0.4 0.0


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−0.018868959

0.103369816

−0.020139391

−0.008802125

0.019482621

0.116767316

0.016967438

−0.044309727

−0.006507015

0.084433098

2.41e−03

4.60e−03

4.58e−03

2.02e−02

1.31e−02

1.37e−02

1.12e−02

1.08e−02

5.12e−03

5.23e−03

1.16e−02

2.33e−06

1.09e−02

1.80e−06

7.02e−05

2.54e−05

Gene ATF1

−1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1

rs4388959

rs876080

rs7316864

rs2700479

rs1613835

rs7979165

rs7978559

rs2554862

rs829112

rs2292220

rs3935138

rs7305375

rs4768933

rs4768934

rs7305655

rs10747586

rs10849432

rs10774214

rs3217810

rs11064437

rs11169552

rs3184504

rs72013726

rs73208120

Gene ATF1


Figure S9: Genetic structures of regulatory variants on ATF1. This figure presents count allele frequencies (CAF)(left), marginal association log-odds ratio estimates and 95% confidence intervals (middle), and LD structures (right) ofregulatory variants on ATF1 along with known CRC risk SNPs on chromosome 12. Known CRC risk SNPs are markedin dark red, marginally significant variants at level 0.05 are marked in dark blue, and those marginally insignificantones are marked in light blue. The ellipses in the matrix-type correlation plot in the right penal represent the Pearsoncorrelation between a pair of variants.

Table S1: Evaluation on type I error rate of oMiST with Liu’s moment matching approximation. In this table, wedemonstrate how the traditional quantile approximation via Liu’s moment matching method affects the type I error rate ofoMiST. Empirical type I error rates of oMiST are shown at significance levels from 0.05 to 10−5 with Liu’s third momentmatching method on quantile approximation under the three genetic structures mimicking genes CXCR1, C18orf32,and ARHGAP11A on continuous and binary outcomes. As observed from the table, the Liu’s moment matching methodin quantile approximation causes inflation in type I error at relaxed significance levels 0.05, but results in conservativeerror rate at more stringent levels, say < 10−4.

Significance level 5.00E-02 1.00E-02 5.00E-03 1.00E-03 5.00E-04 1.00E-04 5.00E-05 1.00E-05

Continuous outcomes

CXCR1 5.35E-02 1.05E-02 5.04E-03 9.01E-04 4.18E-04 4.70E-05 1.80E-05 0.00E+00C18orf32 5.44E-02 1.07E-02 5.22E-03 9.43E-04 4.71E-04 6.10E-05 3.00E-05 7.00E-06

ARHGAP11A 5.23E-02 1.03E-02 5.08E-03 9.01E-04 4.43E-04 6.90E-05 3.00E-05 4.00E-06

Binary outcomes

CXCR1 5.48E-02 1.09E-02 5.38E-03 9.47E-04 4.32E-04 7.00E-05 2.50E-05 0.00E+00C18orf32 5.52E-02 1.12E-02 5.54E-03 9.93E-04 4.98E-04 9.00E-05 4.00E-05 8.00E-06

ARHGAP11A 5.48E-02 1.12E-02 5.60E-03 1.04E-03 4.72E-04 7.00E-05 3.30E-05 1.00E-05

Table S2: Results from additional power simulations on continuous outcomes. This table presents additionalpower simulations on PrediXcan, modified SKAT (mSKAT), and the three combination methods in MiST (oMiST, aMiST,and fMiST ). We considered various v2 values, 0, 0.25, 0.5, 0.75, and 1, and three genetic structures based on CXCR1,C18orf32, and ARHGAP11A on continuous outcomes. v1 values is fixed as 0.25 and the significance level is set as10−6.

v2 PrediXcan mSKAT oMiST aMiST fMiST

CXCR1

0 0.000 0.884 0.856 0.858 0.7950.25 0.006 0.661 0.740 0.687 0.7650.50 0.086 0.299 0.574 0.478 0.6750.75 0.279 0.040 0.417 0.383 0.5461 0.525 0.000 0.464 0.475 0.390

C18orf32

0 0.000 0.886 0.855 0.859 0.8000.25 0.009 0.634 0.716 0.653 0.7380.5 0.086 0.266 0.589 0.467 0.6680.75 0.279 0.028 0.448 0.357 0.5371 0.542 0.000 0.463 0.484 0.396

ARHGAP11A

0 0.000 0.774 0.732 0.734 0.6510.25 0.011 0.455 0.551 0.488 0.5990.50 0.081 0.132 0.364 0.304 0.5050.75 0.268 0.006 0.297 0.309 0.4211 0.507 0.000 0.453 0.461 0.382

Table S3: Results from additional power simulations on dichotomous outcomes. This table presents additionalpower simulations on PrediXcan, modified SKAT (mSKAT), and the three combination methods in MiST (oMiST, aMiST,and fMiST ). We considered various v2 values, 0, 0.25, 0.5, 0.75, and 1, and three genetic structures based on CXCR1,C18orf32, and ARHGAP11A on binary outcomes. v1 values is fixed as 0.25 and the significance level is set as 10−6.

v2 PrediXcan mSKAT oMiST aMiST fMiST

CXCR1

0 0.000 0.881 0.842 0.851 0.7860.25 0.009 0.631 0.700 0.651 0.7310.50 0.074 0.308 0.599 0.484 0.6820.75 0.273 0.031 0.468 0.356 0.5391 0.527 0.000 0.457 0.470 0.388

C18orf32

0 0.000 0.902 0.863 0.876 0.8150.25 0.007 0.654 0.722 0.677 0.7510.50 0.084 0.272 0.580 0.458 0.6580.75 0.256 0.033 0.455 0.355 0.5131 0.512 0.000 0.452 0.462 0.386

ARHGAP11A

0 0.000 0.781 0.721 0.735 0.6460.25 0.006 0.452 0.542 0.472 0.6050.50 0.087 0.131 0.441 0.310 0.5200.75 0.260 0.010 0.385 0.291 0.4291 0.519 0.000 0.455 0.462 0.391

Table S4: Descriptive characteristics of studies in GECCO & CCFR. This table shows the numbers of cases andcontrols along with gender distribution in the 14 studies in the two consortia CCFR and GECCO used in the associationanalyses for colorectal cancer.

Study Subset Cases (Female / Male) Controls (Female / Male) Total

ARCTIC – 598 (353 / 245) 522 (227 / 295) 1120ASTERISK – 892 (340 / 552) 947 (423 / 524) 1839

CCFRCCFR1 1168 (563 / 605) 978 (509 / 469) 2146CCFR2 266 (143 / 123) 252 (134 / 118) 518

Colo2&3 – 87 (40 / 47) 124 (54 / 70) 211

DACHSDACHS 1 1707 (708 / 999) 1702 (685 / 1017) 3409DACHS 2 666 (260 / 406) 498 (175 / 323) 1164

DALSDALS 1 705 (305 / 400) 709 (309 / 400) 1414DALS 2 405 (191 / 214) 461 (220 / 241) 866

HPFSHPFS 1 173 (0 / 173) 229 (0 / 229) 402HPFS Ad 313 (0 / 313) 343 (0 / 343) 656

MEC – 326 (148 / 178) 346 (163 / 183) 672

NHSNHS 1 298 (298 / 0) 774 (774 / 0) 1072NHS Ad 513 (513 / 0) 577 (577 / 0) 1090

PHS – 375 (0 / 375) 389 (0 / 389) 764

PLCOPLCO 1 497 (213 / 284) 447 (153 / 294) 944PLCO 2 482 (206 / 276) 414 (175 / 239) 896

PMH – 276 (276 / 0) 122 (122 / 0) 398VITAL – 282 (132 / 150) 287 (138 / 149) 569

WHIWHI 1 457 (457 / 0) 521 (521 / 0) 978WHI 2 984 (984 / 0) 1007 (1007 / 0) 1991

Total 11470 (6130 / 5340) 11649 (6366 / 5283) 23119

Table S5: Top results from association analyses on GECCO & CCFR with false discovery rate less than 0.2. Thetable lists p-values of top genes in the genome-wide analysis on GECCO identified by PrediXcan, modified SKAT, andthe three combination methods in MiST, respectively, with FDR less than 0.2. Basic information, including gene names,chromosome where the genes locate, number of genetic variants in the defined set, and predictive R2 from PrediXcandatabases, is presented accordingly. For the ease of presentation, p-values which do not reach the criterion of FDR< 0.2 are not shown in the table. The total number of identified genes by each method is listed in the last row of thetable.

Chr Gene Number of snps R2 PrediXcan mSKAT oMiST aMiST fMiST

1 ARPC5 66 0.1164 – 1.69E-05 2.13E-05 2.57E-05 1.29E-051 LAMC1 13 0.2311 2.59E-06 – 6.95E-06 5.74E-06 2.81E-051 SLC44A3 26 0.1075 – 2.73E-04 7.25E-04 6.48E-04 –1 SMG7 30 0.1914 – 4.45E-04 8.14E-04 – 5.18E-042 ANKRD36 22 0.0571 – – 6.69E-04 5.79E-04 7.69E-042 ARPC2 13 0.0270 – – – – 5.90E-042 CXCR1 42 0.1692 6.22E-05 – 1.59E-04 1.44E-04 5.96E-042 CXCR2 32 0.1496 7.84E-05 – 2.01E-04 1.81E-04 6.30E-042 MERTK 63 0.3632 – – 4.08E-04 3.88E-04 –3 LRIG1 9 0.1227 – 3.83E-04 – – –3 SLC25A26 20 0.2761 – – – – 9.33E-045 C5orf34 32 0.1453 – 3.92E-04 – – –6 DCBLD1 22 0.3499 – – – – 8.84E-046 PHACTR2 22 0.0181 8.76E-05 – 2.26E-04 2.04E-04 8.13E-047 MRPL32 11 0.0512 – – 5.88E-04 – 1.86E-048 LEPROTL1 29 0.0526 – 4.44E-04 – – 9.20E-048 MBOAT4 29 0.2479 – 2.66E-04 6.75E-04 5.85E-04 9.16E-048 POU5F1B 45 0.0765 – 6.08E-12 5.00E-10 9.92E-12 5.15E-129 ANXA1 34 0.1003 – – 7.19E-04 – 2.84E-0410 C10orf88 38 0.1341 – – – – 4.83E-0411 C11orf10 19 0.0785 – – – – 8.34E-0411 C11orf84 28 0.0399 – 6.07E-04 – – –11 C11orf92 21 0.4191 – 1.71E-06 4.24E-06 3.43E-06 5.36E-0611 EIF3M 31 0.0161 – 2.09E-04 5.36E-04 4.64E-04 7.98E-0411 FADS1 13 0.2352 – – 5.91E-04 – 2.21E-0411 KCNE3 42 0.1617 – 1.44E-05 3.77E-05 3.25E-05 1.56E-0411 PRRG4 60 0.0643 – 3.85E-05 9.34E-05 8.20E-05 1.39E-0411 TCP11L1 23 0.5431 – 3.12E-04 5.79E-04 5.51E-04 3.92E-0412 ATF1 16 0.1501 – 1.33E-06 3.13E-06 2.62E-06 3.87E-0612 BCDIN3D 51 0.0643 – 1.10E-04 2.71E-04 2.55E-04 7.29E-0412 CCND2 14 0.0130 – – – – 3.71E-0412 DIP2B 7 0.5453 8.44E-05 – 1.33E-04 1.44E-04 9.64E-0512 DYRK4 27 0.0820 – 9.22E-06 2.52E-05 2.07E-05 7.95E-0512 LIMA1 31 0.1507 – – 3.91E-04 4.11E-04 1.66E-0412 PRPF40B 64 0.0244 – 1.25E-04 3.13E-04 2.92E-04 –12 SMARCD1 7 0.0126 – – 6.88E-04 – 2.39E-0412 TUBA1B 32 0.0726 – 5.39E-04 7.88E-04 – 4.12E-0415 ARHGAP11A 92 0.2589 – 9.04E-05 1.60E-04 1.53E-04 1.00E-0415 SMAD6 26 0.0385 – – 3.04E-04 4.42E-04 1.74E-0416 DPEP2 13 0.0334 – 2.35E-04 6.03E-04 5.10E-04 7.53E-0416 PAM16 33 0.0805 – – – – 4.09E-0417 ATP1B2 19 0.3167 – 5.09E-04 – – –17 CENPV 53 0.2774 – 9.44E-05 2.49E-04 2.18E-04 6.38E-0417 MYO15A 44 0.0921 – – – – 6.19E-0417 PLD6 36 0.2500 – – – – 3.52E-0417 PPP1R1B 33 0.3215 – – – – 7.45E-0417 ST6GALNAC1 84 0.4196 – 3.79E-04 6.38E-04 6.18E-04 3.67E-0418 C18orf32 38 0.0604 – 6.49E-06 1.75E-05 1.46E-05 7.11E-0520 BMP2 41 0.1327 – 3.88E-04 6.92E-04 6.67E-04 4.45E-0420 CRLS1 40 0.1311 – 2.87E-04 7.47E-04 6.78E-04 –20 PLTP 36 0.6551 – 6.00E-04 – – –22 C1QTNF6 91 0.5014 – – 2.05E-04 4.41E-04 9.69E-0522 PICK1 56 0.5084 – – 1.49E-04 3.11E-04 4.51E-05

Total number of genes 5 28 37 31 44

Table S6: Conditional association analysis of top variants in POU5F1B and ATF1 adjusting for known loci. Topvariants were selected based on a forward selection procedure. Both the marginal association (left panel) and the jointconditional association (right panel) given known loci are presented.

POU5F1B

Variant Marginal association Conditional association

Estimate Std. Error P-value Estimate Std. Error P-value8:128414892 -0.1220 0.0194 2.923E-10 -0.0374 0.0304 2.19E-018:128032251 -0.0713 0.0206 5.283E-04 -0.0886 0.0226 8.88E-058:128571059 -0.0614 0.0191 1.279E-03 -0.0635 0.0191 9.00E-048:128238105 0.0577 0.0227 1.098E-02 0.0607 0.0228 7.84E-038:128058014 0.0095 0.0200 6.350E-01 0.0431 0.0219 4.94E-028:127855936 -0.0332 0.0191 8.141E-02 -0.0380 0.0192 4.85E-02

ATF1

Variant Marginal association Conditional association

Estimate Std. Error P-value Estimate Std. Error P-value12:51128414 0.0646 0.0213 2.42E-03 0.1057 0.0370 4.25E-0312:51207704 -0.0518 0.0201 1.01E-02 -0.1048 0.0229 4.71E-06

Acknowledgement

This work was supported by grants R01 CA189532, R01 CA195789, P01 CA53996 (to L.H.). The

funding for the studies in GECCO and CCFR are listed below.

GECCO: National Cancer Institute, National Institutes of Health, U.S. Department of Health and

Human Services (U01 CA164930; U01 CA137088; R01 CA059045).

ASTERISK: a Hospital Clinical Research Program (PHRC-BRD09/C) from the University Hospital

Center of Nantes (CHU de Nantes) and supported by the Regional Council of Pays de la Loire,

the Groupement des Entreprises Francaises dans la Lutte contre le Cancer (GEFLUC), the Asso-

ciation Anne de Bretagne Genetique and the Ligue Regionale Contre le Cancer (LRCC).

COLO2& 3: National Institutes of Health (R01 CA60987).

CCFR : This work was supported by grant UM1 CA167551 from the National Cancer Institute and

through cooperative agreements with the following CCFR centers :

Australasian Colorectal Cancer Family Registry (U01 CA074778 and U01/U24 CA097735) Mayo

Clinic Cooperative Family Registry for Colon Cancer Studies (U01/U24 CA074800) Ontario Famil-

ial Colorectal Cancer Registry (U01/U24 CA074783) Seattle Colorectal Cancer Family Registry

(U01/U24 CA074794) University of Hawaii Colorectal Cancer Family Registry (U01/U24 CA074806)

USC Consortium Colorectal Cancer Family Registry U01/U24 CA074799) The Colon CFR GWAS

was supported by funding from the National Cancer Institute, National Institutes of Health (U01

CA122839 and R01 CA143237 to Graham Casey). The content of this manuscript does not nec-

essarily reflect the views or policies of the National Cancer Institute or any of the collaborating

centers in the Colon Cancer Family Registry (CCFR), nor does mention of trade names, commer-

cial products, or organizations imply endorsement by the US Government or the CCFR.

DACHS: German Research Council (Deutsche Forschungsgemeinschaft, BR 1704/6-1, BR 1704/6-

3, BR 1704/6-4 and CH 117/1-1), and the German Federal Ministry of Education and Research

(01KH0404 and 01ER0814).

DALS: National Institutes of Health (R01 CA48998 to M. L. Slattery)

HPFS is supported by the National Institutes of Health (P01 CA055075, UM1 CA167552, R01

CA137178, R01 CA151993, R35 CA197735, K07 CA190673, and P50 CA127003)

NHS by the National Institutes of Health (R01 CA137178, P01 CA087969, UM1 CA186107, R01

CA151993, R35 CA197735, K07 CA190673, and P50 CA127003,) and PHS by the National Insti-

tutes of Health (R01 CA042182).

MEC: National Institutes of Health (R37 CA54281, P01 CA033619, and R01 CA063464).

OFCCR: National Institutes of Health, through funding allocated to the Ontario Registry for Studies

of Familial Colorectal Cancer (U01 CA074783); see CCFR section above. Additional funding

toward genetic analyses of OFCCR includes the Ontario Research Fund, the Canadian Institutes

of Health Research, and the Ontario Institute for Cancer Research, through generous support

from the Ontario Ministry of Research and Innovation.

PLCO: Intramural Research Program of the Division of Cancer Epidemiology and Genetics and

supported by contracts from the Division of Cancer Prevention, National Cancer Institute, NIH,

DHHS. Additionally , a subset of control samples were genotyped as part of the Cancer Ge-

netic Markers of Susceptibility (CGEMS) Prostate Cancer GWAS (Yeager, M et al. Genome-wide

association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007

May;39(5):645-9), CGEMS pancreatic cancer scan (PanScan) (Amundadottir, L et al. Genome-

wide association study identifies variants in the ABO locus associated with susceptibility to pan-

creatic cancer. Nat Genet. 2009 Sep;41(9):986-90, and Petersen, GM et al. A genome-wide as-

sociation study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1

and 5p15.33. Nat Genet. 2010 Mar;42(3):224-8), and the Lung Cancer and Smoking study (Landi

MT, et al. A genome-wide association study of lung cancer identifies a region of chromosome

5p15 associated with risk for adenocarcinoma. Am J Hum Genet. 2009 Nov;85(5):679-91). The

prostate and PanScan study datasets were accessed with appropriate approval through the db-

GaP online resource (http://cgems.cancer.gov/data/) accession numbers phs000207.v1.p1 and

phs000206.v3.p2, respectively, and the lung datasets were accessed from the dbGaP website

(http://www.ncbi.nlm.nih.gov/gap) through accession number phs000093.v2.p2. Funding for the

Lung Cancer and Smoking study was provided by National Institutes of Health (NIH), Genes, En-

vironment and Health Initiative (GEI) Z01 CP 010200, NIH U01 HG004446, and NIH GEI U01 HG

004438. For the lung study, the GENEVA Coordinating Center provided assistance with genotype

cleaning and general study coordination, and the Johns Hopkins University Center for Inherited

Disease Research conducted genotyping.

PMH: National Institutes of Health (R01 CA076366 to P.A. Newcomb).

VITAL: National Institutes of Health (K05 CA154337).

WHI: The WHI program is funded by the National Heart, Lung, and Blood Institute, National Insti-

tutes of Health, U.S. Department of Health and Human Services through contracts HHSN268201100046C,

HHSN268201100001C, HHSN268201100002C, HHSN268201100003C, HHSN268201100004C,

and HHSN271201100004C.

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