Short Term Costs of Integrating Whole Genome Sequencing into Primary Care and

Cardiology Settings: A Pilot Randomized Trial

Appendices

1

Table of Contents

Additional Members of the MedSeq Project Team........................................................................4

Appendix 1. Additional methodological details..............................................................................5

Appendix 2. Cost weights for patient-reported procedures.........................................................10

Appendix 3. Hospitalizations.......................................................................................................13

Appendix 4. Sources and costing strategy for family history and whole genome sequencing

reporting...........................................................................................................................16

Appendix 5. Study flow diagram..................................................................................................17

Appendix 6. Monogenic disease risk findings among patient participants who received whole

genome sequencing........................................................................................................18

Appendix 7. Carrier status findings among patient participants who received whole genome

sequencing, reported.......................................................................................................21

Appendix 8. Summary of polygenic risk predictions and pharmacogenomic findings among

patient participants who received whole genome sequencing.........................................32

Appendix 9. The ten most frequent outpatient care procedures or tests observed within each

cohort...............................................................................................................................33

Appendix 10. Healthcare utilization in the six months preceding disclosure sessions and six

months following disclosure sessions..............................................................................34

Appendix 11. Healthcare costs in the six months preceding disclosure sessions and six months

following disclosure sessions...........................................................................................35

Appendix 12. Immediately attributable health care utilization and associated costs...................36

Appendix 13. Additional procedures that were not ordered following disclosure of WGS results,

but judged as potentially informative after review of the Genome Resource Center.......37

Appendix References..................................................................................................................40

2

Additional Members of the MedSeq Project Team

Members of the MedSeq Project are as follows: David W. Bates, MD, Allison L. Cirino, MS,

Carolyn Y. Ho, MD, Joel B. Krier, MD, William J. Lane, MD, PhD, Lisa S. Lehmann, MD, PhD,

MSc, Calum A. MacRae, MD, PhD, Cynthia C. Morton, PhD, Christine E. Seidman, MD, Shamil

R. Sunyaev, PhD, Tiffany Nguyen, Eleanor Steffens, Wendi Nicole Betting, Brigham and

Women’s Hospital and Harvard Medical School; Samuel J. Aronson, ALM, MA, Ozge Ceyhan-

Birsoy, PhD, Matthew S. Lebo, PhD, Heather M. McLaughlin, PhD, Ellen A. Tsai, PhD, Partners

Healthcare Personalized Medicine; Jennifer Blumenthal-Barby, PhD, Kai Lee, Hayley Peoples,

Baylor College of Medicine, Center for Medical Ethics and Health Policy; Pamela M. Diamond,

PhD, University of Texas Houston School of Public Health; Kelly Davis, Peter A. Ubel, MD,

Duke University; Peter Kraft, PhD, Harvard School of Public Health; J. Scott Roberts,

PhD, University of Michigan; Judy E. Garber, MD, MPH, Dana-Farber Cancer Institute; Tina

Hambuch, PhD, Illumina, Inc.; Michael F. Murray, MD, Geisinger Health System; Isaac Kohane,

MD, PhD, Sek Won Kong, MD, Boston Children’s Hospital.

3

Appendix 1. Additional methodological details.

Recruitment, Education, and Enrollment

We recruited a convenience sample of primary care physicians and cardiologists from

the Partners HealthCare system through individual invitations and presentations at practice staff

meetings. Physician participants were consented in person just prior to study initiation by

MedSeq Project personnel. They then attended a 1-hour in-person didactic genomics education

session taught by medical geneticists and genetic counselors, followed by 12 online self-guided

educational modules requiring approximately 4 hours to complete. Lastly, they attended a 1-

hour follow-up in person education session that reviewed important self-taught concepts as well

as providing important study-specific information such as criteria for variant reporting and the

format of reports. Physician participants were awarded 6 hours of continuing medical education

credits for educational curriculum completion. The educational curriculum is presented in more

detail in a separate manuscript.1 Financial incentives were also provided to physicians to

support clinical time devoted on study specific actives.

Patient participants were identified and recruited by their physicians through direct

patient contact (phone or in person) and mailings from 2012 through 2015. MedSeq Project staff

assisted physicians as needed by reviewing patient lists for eligibility, sending recruitment

letters, and calling patients to assess study interest. Eligible cardiology patients were adults of

any age with diagnoses of hypertrophic or dilated cardiomyopathy. Eligible primary care patients

were adults between 40-65 years of age at the time of recruitment, inclusive, and deemed

generally healthy by their PCPs. Patients were excluded if they had a diagnosis of

cardiovascular disease or diabetes. Participants from both cohorts were also excluded if they or

their spouses/significant others were pregnant, if they were not fluent in English, or if they

scored in ranges associated with severe anxiety or depression per the Hospital Anxiety and

Depression Scale.2 Patient participants were enrolled until study goals to disclose results to 100

4

cardiology patients and 100 primary care patients were fulfilled. Patients were followed for a

period of six months following disclosure, with final six month surveys collected in November

2016.

Physicians were provided access to a Genome Resource Center staffed by genetic

counselors and medical geneticists designed to answer questions related to family history

reports, WGS reports, or study specific procedures at no charge and without the need for formal

consultations. Physicians otherwise received no guidance about how to communicate or

respond to FH or WGS reports. Each physician participant disclosed results to between 2 and

28 patients.

Family History Review

At the initial study visit, all patients reported their family health history using a

customized version of the U.S. Surgeon General’s “My Family Health Portrait” web tool.3

MedSeq Project staff sent the resulting pedigrees and an associated FH summary chart to

physicians approximately 2 weeks before all disclosure sessions. Providers were also sent

decision support sheets about the implications of FH on screening recommendations for breast

cancer, colon cancer, coronary artery disease, glaucoma, osteoporosis, and diabetes. Family

history pedigrees and physician notes surrounding the family history collections, as well as any

rationale for further work-ups based upon any of this information, were incorporated into

patients’ medical records after disclosure sessions.

Whole Genome Sequencing

WGS, variant interpretation, and reporting within the MedSeq Project are described in

detail separately.4,5 Briefly, Illumina Clinical Services Laboratory (San Diego, CA), a CLIA-

certified, CAP-accredited facility, performed sequencing using paired-end 100 base pair reads

on the Illumina HiSeq platform.6 Genomes were sequenced to at least 30X mean coverage, and

≥ 95% of bases were sequenced to at least 8X coverage. Lossless BAM files were converted to

5

FASTQ format to obtain sequence read data and reads were realigned to the NCBI reference

sequence (GRCh37) using the Burrows-Wheeler Aligner 0.6.1-r104.7 Variant calls were made

using the Genomic Analysis Tool Kit (GATK) version 2.3-9-gdcdccbb8 for all positions with ≥8X

coverage. We derived variant annotation using ALAMUT HT version 1.1.2, Variant Effect

Predictor version 2.6 and the Laboratory for Molecular Medicine’s (LMM’s) GeneInsight

laboratory database. Annotated variants were subsequently filtered to identify: (1) variants with

minor allele frequencies less than <5% and classified as DM (disease causing) or DM?

(probable/possible pathogenic) per the Human Gene Mutation Database9 or the LMM’s clinical

testing database, (2) nonsense, frameshift, and canonical splice-site (+/−1,2) variants with a

MAF <1% in disease-associated genes, and (3) pharmacogenomic variants for metformin,

clopidogrel, warfarin, simvastatin, and digoxin metabolism. We used LMM’s variant

interpretation protocol10 to classify variants, which is consistent with current ACMG

recommendations.11 Disease-associated variants and pharmacogenomic variants were

confirmed via Sanger sequencing or the Illumina HumanOmni2.5 array (pharmacogenomic

variants only) before reporting.

WGS reports for cardiology patients included monogenic variant findings related to the

indication of HCM or DCM and classified as pathogenic, likely pathogenic, or of uncertain

significance. In addition, WGS reports for both cardiology and primary care patients disclosed

monogenic disease risks, including disease-causing variants classified as pathogenic, likely

pathogenic, and “variant of uncertain significance: favor pathogenic” (VUS:FP) in Mendelian

disease genes; carrier status, including pathogenic, likely pathogenic, and VUS:FP variants for

autosomal recessive conditions; pharmacogenomic findings, as described above; and (4) red

blood cell and platelet antigen predictions, using novel algorithms.12 Participants in both cohorts

also received a “Cardiac Risk Supplement” that predicted fasting lipid profiles and risks for eight

common complex cardiovascular phenotypes: abdominal aortic aneurysm, atrial fibrillation,

6

coronary heart disease, type 2 diabetes, hypertension, obesity, platelet aggregation, and QT

prolongation.13 The format and content of genome reports were developed with assistance from

a multi-disciplinary advisory committee and modified based on feedback from primary care

physicians.5 Physicians were oriented to the format of WGS reports during the in-person

education sessions. As with FH reports, MedSeq Project staff sent WGS reports to physicians

approximately 2 weeks before disclosure sessions, and WGS reports were incorporated into

patients’ medical records after results disclosure with facilitation by the GeneInsight Clinic

software,14 along with all physician notes describing the disclosure sessions and subsequent

work-ups.

Methods for Assigning Costs

We identified health care utilization by reviewing administrative data, medical records,

and patient surveys, and multiplying utilization by cost weights. When billing codes were

available for outpatient services, we applied 2015 reimbursement rates using CMS fee

schedules. For outpatient services in medical records that lacked billing codes (24% of total

services), we assigned billing codes based on the mode of related services in RPDR data.

Patient-reported outpatient services that were not identified in RPDR or medical records were

assigned costs based on the weighted mean of related services (see Appendix 2), with the

exception of clinical visits which we treated as level 4 evaluation and management encounters.

Costs for inpatient services were estimated by assigning a Diagnosis-Related Group based on

admitting diagnoses and then applying cost weights based on the length-of-stay per the CMS

Hospital Inpatient Prospective Payment System. We adjusted inpatient care costs by a factor of

20% to account for physician services.15 A summary of hospitalizations is presented in

Appendix 3.

7

Methods for Imputation

Missing survey data included a combination of survey non-response and item non-

response. Regarding survey non-response, patients randomized to the WGS arm were more

likely to complete the 6 week survey than patients randomized to the control arm (99% vs 89%,

respectively, p=0.005), but differences were not significant for the 6 month survey (97% vs 92%,

respectively, p=0.21).

We assumed survey data were missing at random, and imputed non-response using R

package mice 2.30.16 For continuous variables such as laboratory personnel time for variant

interpretation, medication costs, and medical equipment costs, we used fully conditional

specification procedures with predictive means matching. For dichotomous outcomes related to

cholesterol tests, blood sugar tests, heart disease screening, or cancer screening, we used fully

conditional specification procedures that implement a logistic regression model to impute

missing values.17 For imputation of missing variables, and following creation of 1,000 samples of

200 participants each created with replacement for bootstrapping, twenty imputed datasets for

each bootstrapping sample were created by running 20 iterations apiece, and the following

variables were included in the imputation process: randomization status in interaction with

cohort, gender, age, baseline health status, presence or absence of a previously-unidentified

monogenic disease risk, and number of eight cardiometabolic phenotypes for which participants

scored in the 80th and 90th percentiles.

8

Appendix 2. Cost weights for patient-reported procedures.

Patient participants reported whether or not they had received cholesterol tests, blood sugar tests, heart disease screening, or cancer screening on the post-disclosure survey (time frame: enrollment through disclosure), 6-week follow-up survey (time frame: disclosure through 6 weeks post-disclosure) and 6-month follow-up survey (time from: 6 weeks post-disclosure through 6 months post-disclosure). Survey items for cholesterol tests were adapted from the Be-havioral Risk Factor Surveillance System.18 Survey items for blood sugar tests and heart dis-ease screening were adapted from the Impact of Personal Genomics Study.19 Survey items for cancer screening were adapted from consensus measures of the Clinical Sequencing Ex-ploratory Research Consortium.20 Costs for procedures that were patient-reported and for which a corresponding procedure was not observed in the RPDR or medical records data were im-puted using the average costs for related procedures, including professional and facility fees, as detailed below, weighted for the number of times the procedures was observed from disclosure through six months post-disclosure. Costs were derived from 2015 CMS fee schedules for the metropolitan Boston area, and are adjusted for multiple procedure payment reductions, where applicable.

CPT Code Description Cost Times Ob-served

“Blood cholesterol is a fatty substance found in the blood. Blood can be taken and used to determine your cholesterol level. Since ___, have you had a blood test to check your cholesterol?”

$17.37

80061 Lipid panel $18.22 7082172 Apolipoprotein test $21.09 183690 Lipase test $9.38 883695 Lipoprotein (a) test $17.62 3

“A blood sugar test is a blood test that measures your blood glu-cose or blood sugar. Since ___, have you had a blood sugar test?”

$13.00

80053 Comprehensive metabolic panel $14.37 7683036 Hemoglobin A1C test $13.21 4480048 Glucose test $11.51 76

“Since ____, have you had any tests in which a physician or healthcare professional looked for signs of heart disease?”

$150.09

36620 Arterial catheterization or cannulation $53.44 471010 Chest X-ray, single view $69.10 8671020 Chest X-ray, two views $70.97 2971250 CT scan of thorax without contrast $174.28 674174 CT angiography abdomen and pelvis, with contrast $492.31 175561 Cardiac MRI without contrast, followed by contrast $619.65 676536 Ultrasound, soft tissues of head and neck $164.53 376604 Ultrasound, chest, B-scan $29.12 476770 Ultrasound, retroperitoneal, B-scan $173.84 378492 Myocardial imaging, PET, perfusion; multiple studies $1382.72 282172 Apolipoprotein test $21.09 182550 CK test, total $8.86 1382553 CK test, MB fraction only $10.55 683695 Lipoprotein (a) test $17.62 383880 Natriuretic peptide test $46.19 3084484 Troponin test, quantitative $13.39 1293000 ECG with interpretation and report $18.78 593005 ECG, tracing only, without interpretation and report $88.30 13793017 Cardiovascular stress test; tracing only $284.23 11

9

CPT Code Description Cost Times Ob-served

“Tests for signs of heart disease,” continued

93016 Cardiovascular stress test; physician supervision only $23.57 1293225 Electrocardiographic monitoring for 24 hours; recording $110.03 293228 External mobile cardiovascular telemetry with ECG recording;

physician review and interpretation with report$27.61 2

93289 Interrogation device evaluation with physician analysis and re-port

$83.64 4

93306 Echocardiography, transthoracic, real-time with image documen-tation (2D); M-mode recording with spectral and color flow Doppler echocardiography

$489.95 54

93307 Echocardiography, transthoracic, real-time with image documen-tation (2D); M-mode recording without spectral or color Doppler echocardiography

$365.14 1

93308 Echocardiography, transthoracic, real-time with image documen-tation (2D); follow-up or limited study

$216.95 5

93312 Echocardiography, transesophageal, real-time with image docu-mentation (2D); including probe placement, image acquisition, interpretation, and report

$722.86 3

93325 Doppler echocardiography color flow velocity mapping $3.62 493350 Echocardiography, transthoracic, real-time with image documen-

tation (2D), during rest and cardiovascular stress test, with inter-pretation and report

$498.53 2

93571 Intravascular Doppler velocity and/or pressure derived coronary flow reserve measurement during coronary angiography includ-ing pharmacologically induced stress; initial vessel

$100.78 1

93613 Intracardiac elecrophysiologic 3-D mapping $412.11 193642 Electrophysiologic evaluation of single or dual chamber pacing

cardioverter-defibrillator (includes defibrillation threshold evalua-tion, arrhythmia induction, evaluation of sensing and pacing, and programming parameters)

$1155.87 1

93654 Comprehensive electrophysiologic evaluation $0.00 193662 Intracardiac echocardiography during therapeutic/diagnostic in-

tervention, including imaging supervision and interpretation $154.60 2

93880 Duplex scan of extracranial arteries; complete bilateral study $231.25 393931 Duplex scan of upper extremity arteries or arterial bypass grafts;

unilateral or limited study$160.92 2

93978 Duplex scan of aorta, inferior vena cava, iliac vasculature, or by-pass grafts; complete study

$183.04 1

“Since ___, have you been screened for any of the following types of cancer?”

$188.82

11100 Biopsy of skin, subcutaneous tissue and/or mucous membrane, unless otherwise listed; single lesion

$198.02 3

43239 Upper gastrointestinal endoscopy including esophagus, stom-ach, and either duodenum and/or jejunum as appropriate; with biopsy, single or multiple

$904.76 2

45378 Colonoscopy, flexible, proximal to splenic flexure; diagnostic, with or without collection of specimen(s) by brushing or washing, with or without colon decompression

$1018.20 1

45380 Colonoscopy, flexible, proximal to splenic flexure; with biopsy, single or multiple

$1062.92 4

45385 Colonoscopy, flexible, proximal to splenic flexure; with removal of tumor(s), polyp(s), or other lesion(s) by snare technique

$1113.48 1

58100 Endometrial biopsy $318.46 176642 Ultrasound, breast, unilateral, real time with image documenta-

tion, including axilla when performed; limited$128.10 1

10

CPT Code Description Cost Times Ob-served

Cancer screening, continued77063 Screening digital breast tomosynthesis, bilateral $31.79 1082105 Alpha fetoprotein test $22.83 282272 Blood, occult, by peroxidase activity, qualitative, feces, single

specimen $4.43 1

84153 Prostate specific antigen (PSA) test; total $25.03 488141 Cytopathology, cervical or vaginal; requiring physician interpreta-

tion $35.43 3

88175 Cytopathology, cervical or vaginal, collected in preservative fluid, automated thin layer preparation; screening by automated sys-tem and manual rescreening

$36.05 3

88307 Level V - Surgical pathology, gross and microscopic examination $275.25 693505 Endomyocardial biopsy $908.98 3G0103 Prostate Specific Antigen Test (PSA), total $25.03 16G0105 Colonoscopy on individual at high risk $871.32 3G0121 Colonoscopy on individual not meeting criteria for high risk $871.32 1G0145 Screening vaginal/cervical smear $36.05 7G0202 Screening mammography, producing direct digital image, bilat-

eral, all views$36.92 27

G0204 Diagnostic mammography, direct digital image, bilateral, all views

$46.28 3

G0206 Diagnostic mammography, producing direct digital image, unilat-eral, all views

$36.92 1

G0279 Diagnostic digital breast tomosynthesis, unilateral or bilateral $32.01 1

11

Appendix 3. Hospitalizations.Hospitalizations were identified through review of medical records and through patient self-report on surveys completed at disclosure sessions and six weeks and six months after disclosure sessions. They did not need to be associated with family history or WGS findings disclosed as part of the MedSeq Project. Costs were assigned based on the CMS Inpatient Prospective Payment System (IPPS) for care received at Brigham and Women’s Hospital based on the Medicare Severity-Diagnosis Related Group (DRG) assigned to services and length of stay. DRGs were assigned by MedSeq Project staff based on patients’ descriptions of services received when they were not available. IPPS costs are adjusted up 20% to account for professional fees, as recommended.15

Patient # Encounter Days DRG Cost Description

Six months prior to disclosure sessions

Cardiology Cohort1 1 4 378 $3,200 Dieulafoy's lesion*

2 3 384 $2,724 Gastric ulcer*3 1 384 $2,586 Gastric ulcer*

2 1 13 315 $15,508 Pulmonary compromise2 6 292 $13,719 Heart failure

3 1 2 309 $10,360 Ventricular tachycardia2 1 309 $10,070 Ventricular tachycardia

4 1 5 164 $31467 Lung excision2 2 312 $9,816 Orthostatic hypotension

5 1 1 217 $72,344 Cardiac catheterization6 1 1 227 $62,459 Implantable defibrillator7 1 5 342 $17,123 Acute appendicitis8 1 0 315 $12,034 Syncope9 1 3 312 $10,095 Syncope10 1 1 308 $14,776 Paroxysmal atrial flutter11 1 4 392 $10,339 Abdominal pain12 1 0 556 $9,266 Subcutaneous hematoma

Primary Care Cohort

No hospitalizations

* One patient reported three hospitalizations in the six-week follow-up survey with uncertain dates of admittance. Associated costs were distributed to time periods proportional to likelihood that the hospitalizations occurred within them.

12

Patient # Encounter Days DRG Cost Description

Six months after disclosure sessions

Cardiology Cohort1 1 4 378 $1,154 Dieulafoy's lesion*

2 3 384 $983 Gastric ulcer*3 1 384 $933 Gastric ulcer*4 2 369 $13,548 Bleeding esophageal varicies

2 1 13 292 $15,596 Congestive heart failure2 18 292 $17,192 Congestive heart failure

9 1 5 251 $25,311 Ventricular tachycardia10 1 1 38 $19,064 Left carotid artery stenosis / carotid endarteretomy

2 1 253 $29,920 Repair of right femoral arteriovenous fistula12 1 2 920 $12,533 Hematoma caused by cardiac catheterization13 1 1 287 $13,919 Chest pain and heart catheterization

2 3 138 $10,675 Bradycardia3 3 234 $55,460 Circumflex stenosis and moderate mid LAD stenosis. Performed left heart catheteriza-

tion, coronary angiography, FFR of LAD, and PCI.14 1 16 291 $25,432 Chronic heart failure, prolonged by VT, septic shock, hypoxia requiring intubation.

2 95 525 $45,114 LVAD implantation15 1 2 138 $10,337 Observation after starting a new medication

2 1 251 $24,301 Cardiac ablation16 1 1 143 $1,234 Chest pain17 1 6 308 $16,284 Chest pain and atrial fibrillation18 1 5 307 $11,041 Septal myectomy, bilateral pulmonary vein isolation, resection of left atrial appendage19 1 2 179 $12,414 Asthma exacerbation and bacterial pneumonia20 1 2 138 $10,386 Atrial fibrillation, s/p direct current cardioversion21 1 1 312 $9,574 Syncope22 1 1 312 $9,535 Fainted23 1 1 143 $1,234 Palpitations, chest discomfort and lightheadednessPrimary Care Cohort1 1 5 864 $11,774 Fever2 1 2 392 $9,777 Gastroenteritis3 1 2 310 $7,656 Heart palpitations and anemia

* One patient reported three hospitalizations in the six-week follow-up survey with uncertain dates of admittance. Associated costs were distributed to time periods proportional to likelihood that the hospitalizations occurred within them.

13

Appendix 4. Sources and costing strategy for family history and whole genome sequencing reporting. Costs were assigned to sequencing and downstream services by multiplying utilization data by cost weights, as described below. All costs are presented in 2015 dollars.

Component Data Source Cost Weight Cost/UnitMicrocosting analysis of intervention costsTime for informed

consentLength of study

consent sessionsMean wage for registered

nurse21$55.41/hr

Sequencing Market rate National Human Genome Research Institute estimates22

$4,000/sample

Sanger confirmation Patient records Familial variant testing rate at the Laboratory for Molecular Medicine (LMM)

$500 for 3 variants + $50/additional variant

Variant interpretation and report drafting

LMM tracker Mean wage for medical scientist23

$57.32/hr

Laboratory report review and signout

LMM tracker Mean wage for lab director23

$73.60/hr

Data storage Market rate Partners Healthcare storage fees

$150/yr per patient

Consultation with Genome Resource Center (GRC)

GRC records Mean wage for genetic counselor21

$44.82/hr

Disclosure of results Length of disclosure sessions

CMS reimbursement for evaluation and management visit*

$106.05 to $213.26, depending on length of session

* A Current Procedural Terminology (CPT) code between 99211 and 99215 was assigned to each disclosure session based on its length.

14

Appendix 5. Study flow diagram.

15

Appendix 6. Monogenic disease risk findings among patient participants who received whole genome sequencing.Findings in primary care and cardiology (hypertrophic cardiomyopathy patients, only) were published previously.24,25 Classifications are reported as interpreted at the time of the study and as communicated to physicians and patients during disclosure sessions. Classifications may have changed since reports were issued.

Gene Disease Variant (Nucleotide) Variant (Protein) Classification* Inheritance†

Cardiology CohortResults Related to IndicationMYBPC3 Hypertrophic cardiomyopathy (X2) c.772G>A p.Glu258Lys P ADMYBPC3 Hypertrophic cardiomyopathy c.927-9G>A P ADMYBPC3 Hypertrophic cardiomyopathy c.2747G>A p.Trp916X P ADMYBPC3 Hypertrophic cardiomyopathy c.2827C>T p.Arg943X P ADMYBPC3 Hypertrophic cardiomyopathy c.2905C>T p.Gln969X P ADMYH7 Hypertrophic cardiomyopathy c.1357C>T p.Arg453Cys P ADMYH7 Dilated cardiomyopathy c.1594T>C p.Ser532Pro P ADMYH7 Hypertrophic cardiomyopathy c.1987C>T p.Arg663Cys P ADMYH7 Hypertrophic cardiomyopathy c.2609G>A p.Arg870His P ADMYH7 Hypertrophic cardiomyopathy c.2717A>G p.Asp906Gly P ADPTPN11 LEOPARD syndrome c.1403C>T p.Thr468Met P ADBAG3 Dilated cardiomyopathy c.1067delC p.Pro356HisfsX7 LP ADMYBPC3 Hypertrophic cardiomyopathy c.3742_3759dup p.Gly1238_Cys1253dup LP‡ ADTTN Dilated cardiomyopathy c.73617C>G p.Tyr24539X LP ADTTN Dilated cardiomyopathy c.91330A>T p.Lys30444X LP ADMYBPC3 Hypertrophic cardiomyopathy c.3771C>A p.Asn1257Lys VUS:FP ADMYH7 Hypertrophic cardiomyopathy c.4031G>A p.Arg1344Gln VUS:FP ADMYL2 Hypertrophic cardiomyopathy c.484G>A p.Gly162Arg VUS:FP§ ADTNNI3 Hypertrophic cardiomyopathy c.568G>T p.Asp190Tyr VUS:FP‖ ADABCC9 Dilated cardiomyopathy c.1982G>A p.Arg661His VUS ADACTN2 Dilated cardiomyopathy c.343G>A p.Val115Met VUS ADACTN2 Hypertrophic cardiomyopathy c.1839+5G>C VUS ADFLNC Adult onset myopathy c.2450T>C p.Ile817Thr VUS ADILK Dilated cardiomyopathy c.211del p.Leu71CysfsX26 VUS ADMYBPC3 Hypertrophic cardiomyopathy c.103C>T p.Arg35Trp VUS ADRBM20 Dilated cardiomyopathy c.2662G>A p.Asp888Asn VUS AD

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic; VUS: variant of uncertain significance† AD: autosomal dominant‡ Reclassified as pathogenic in June 2016.§ Reclassified as likely pathogenic in April 2016.‖ Reclassified as likely pathogenic in September 2015.

16

Reported monogenic disease risks, continued

Gene Disease Variant (Nucleotide) Variant (Protein)Classification*

Inheritance†

Cardiology Cohort (continued)Secondary Findings among Cardiology PatientsCHEK2 CHEK2-related cancer risk c.1100del p.Thr367MetfsX15 P ADELN Supravalvular aortic stenosis c.1150+1G>A p.? P ADEYA4 Deafness, postlingual c.1739-1G>A LP ADSQSTM1 Paget disease of the bone (X2) c.1175C>T p.Pro392Leu LP ADAPP Alzheimer’s disease, late onset c.2137G>A p.Ala713Thr VUS: FP ADF5 Factor V Leiden Thrombophilia (X2) c.1601G>A p.Arg534Gln Risk allele MF

Primary Care CohortLHX4 Combined pituitary hormone deficiency c.452-2A>C P ADPPOX Variegate porphyria c.199delC p.Leu67X P ADHFE Hereditary hemochromatosis (x2) c.845G>A‡ p.Cys282Tyr‡ P ARHFE Hereditary hemochromatosis c.845G>A

c.187C>Gp.Cys282Tyr p.His63Asp

P AR

RDH5 Fundus albipunctatus c.285G>A‡ p.Trp95X‡ P ARANK2 Ankyrin-B related cardiac arrhythmia c.4373A>G p.Glu1458Gly LP ADCOL2A1 Spondyloepiphyseal dysplasia

congenitalc.4316C>T p.Thr1439Met LP AD

KCNQ1 Romano-Ward syndrome c.826delT p.Ser276ProfsX13 LP ADPDE11A Primary pigmented micronodular

adrenocortical diseasec.171delT p.Thr58ProfsX41 VUS: FP§ AD

TNNT2 Hypertrophic cardiomyopathy c.832C>T p.Arg278Cys VUS: FP ADARSE Chondrodysplasia punctata c.410G>C p.Gly137Ala VUS: FP XLF5 Factor V Leiden thrombophilia c.1601G>A p.Arg534Gln Risk allele MF

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic† AD: autosomal dominant; AR: autosomal recessive; XL: X-linked; MF: multi-factorial‡ Participant was homozygous for this variant.§ Reclassified as VUS in November 2016.

17

Appendix 7. Carrier status findings reported among patient participants who received whole genome sequencing.

Findings in primary care and cardiology (hypertrophic cardiomyopathy patients, only) were published previously.24,25 Classifications are reported as interpreted at the time of the study and as communicated to physicians and patients during disclosure sessions. Classifications may have changed since reports were issued.

Cardiology Patients (n=49)Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*

1 SERPINA1 Alpha-1 Antitrypsin Deficiency Disorder c.1096G>A p.Glu366Lys P1 USH2A Usher syndrome type II c.1214delA p.Asn405fs P1 C2 C2 deficiency c.f_849+19del LP†

1 MYO7A Usher syndrome type I c.5648G>A p.Arg1883Gln LP†

2 LAMA2 Congenital muscular dystrophy type 1A c.5563-2A>G LP3 LTBP4 Cutis laxa, autosomal recessive, type IC c.254delT p.Leu85ArgfsX15 P3 RAPSN Congenital myasthenic syndrome c.264C>A p.Asn88Lys P3 TCTN2 Joubert syndrome c.1877T>A p.Leu626X P4 TCIRG1 Infantile malignant osteopetrosis c.1674-1G>A P5 HFE Hereditary hemochromatosis c.845G>A p.Cys282Tyr P5 ACOX1 Peroxisomal acyl-CoA oxidase deficiency c.1851delT p.Gly618AlafsX24 LP6 PHYH Refsum disease c.766_767delGT p.Val256PhefsX14 LP7 CFTR Cystic fibrosis c.1521_1523delCTT p.Phe508del P7 CRTAP Osteogenesis imperfecta type II c.471+2C>A P8 GPR56 Bilateral frontoparietal polymicrogyria c.10C>T p.Gln4X P8 HFE Hereditary Hemochromatosis c.187C>G p.His63Asp P8 HFE2 Hemochromatosis type 2 c.959G>T p.Gly320Val P8 TSHR Hypothyroidism c.545+2_545+3del LP9 CFTR Cystic fibrosis c.1521_1523delCTT p.Phe508del P9 VWF von Willebrand disease type 2N c.2561G>A p.Arg854Gln P

10 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P10 HEXA HEXA pseudodeficiency c.745C>T p.Arg249Trp PD11 GJB2 Hearing loss c.109G>A p.Val37Ile P12 HFE Hereditary hemochromatosis c.845G>A p.Cys282Tyr P12 PINK1 Parkinson disease c.620del p.Arg207Glnfs*14 LP13 NPHS2 Idiopathic steroid-resistant nephrotic syndrome c.868G>A p.Val290Met LP14 GJB2 Nonsyndromic hearing loss c.167del p.Leu56ArgfsX P14 TYRP1 Oculocutaneous albinism type III c.1057_1060del p.Asn353ValfsX31 P

* P: pathogenic; LP: likely pathogenic; PD: Pseudodeficiency allele† Reclassified as pathogenic in June 2015.

18

Carrier findings among cardiology patients, continued

Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*15 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P15 SGCG Limb girdle muscular dystrophy type 2C c.525delT p.Leu85ArgfsX15 P16 MUTYH MUTYH-associated polyposis c.536A>G p.Tyr179Cys P16 SLC35C1 Congenital disorder of glycosylation, type IIc c.464_466del p.Phe155del LP17 GJB2 Nonsyndromic hearing loss c.109G>A p.Val37Ile P17 LOXHD1 Nonsyndromic hearing loss c.4714C>T p.Arg1572X P17 TMCO1 Cerebrofaciothoracic dysplasia c.240_243delGGTT p.Val81ThrfsX9 P17 MUTYH MUTYH-associated polyposis c.934-2A>G LP†

17 EYS Retinitis pigmentosa c.6416G>A p.Cys2139Tyr VUS:FP18 LIFR Stuve-Wiedemann syndrome c.2074C>T p.Arg692X LP18 PAH Phenylketonuria (PKU) c.842+5G>A p.(?) LP19 AMT Glycine encephalopathy c.870G>A p.Trp290X P19 SERPINA1 Alpha-1 Antitrypsin Deficiency Disorder c.1096G>A p.Glu366Lys P19 FGF23 Hyperphosphatemic familial tumoral calcinosis c.211A>G p.Ser71Gly VUS:FP19 LIPC Hepatic lipase deficiency c.866C>T p.Ser289Phe VUS:FP19 POLG POLG-related mitochondrial disorder c.2209G>C p.Gly737Arg VUS:FP†

20 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P20 TYR Oculocutaneous albinism type 1 c.1118C>A p.Thr373Lys P20 ABCB4 Familial progressive intrahepatic cholestasis c.959C>T p.Ser320Phe VUS:FP21 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P21 PRX Charcot-Marie-Tooth disease type 4F c.2289delT p.Asp765ThrfsX10 LP22 CBS Homocystinuria c.833T>C p.Ile278Thr P22 ESCO2 Roberts syndrome c.294_297del p.Arg99SerfsX2 P23 MYH2 Myopathy with external ophthalmoplegia c.3002delA p.Glu1001GlyfsX26 LP24 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P24 POLG POLG-related mitochondrial disorder c.2209G>C p.Gly737Arg VUS:FP‡

24 TTC8 Bardet Biedl syndrome c.489G>A p.Thr163Thr VUS:FP25 RAB3GAP2 Warburg-Micro syndrome c.713-2A>G LP25 SPINK5 Netherton syndrome c.2812_2813delGT p.Val938CysfsX7 VUS:FP26 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P27 ADAMTSL4 Isolated ectopia lentis c.767_786del p.Gln256ProfsX38 P28 BBS2 Bardet-Biedl syndrome c.661delC p.Leu221PhefsX25 P28 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P28 PROM1 Retinitis pigmentosa c.1177_1178delAT p.Ile393ArgfsX21 P

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic† Reclassified as variant of uncertain significance in September 2017.‡ Reclassified as likely pathogenic in December 2016.

19

Carrier findings among cardiology patients, continued

Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*29 BTD Biotinidase deficiency c.1330G>C p.Asp444His P29 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P29 LOXHD1 Hearing loss c.4480C>T p.Arg1494X P29 MMAB Methylmalonic acidemia c.700C>T p.Gln234X LP30 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P30 SLC52A2 Brown-Vialetto-Van Laere syndrome c.916G>A p.Gly306Arg P30 TALDO1 Transaldolase deficiency c.516dupC p.Ala173ArgfsX23 P31 SERAC1 3-methylglutaconic aciduria with deafness,

encephalopathy, and Leigh-like syndromec.262_265dupCATG p.Gly89AlafsX32 LP

32 ASPA Canavan disease c.854A>C p.Glu285Ala P32 AURKC Spermatogenic failure 5 c.94_101dup p.Met35AlafsX40 P33 IFT172 Short-rib thoracic dysplasia c.112C>T p.Arg38X LP33 SLC26A4 DFNB4/Pendred syndrome c.1003T>C p.Phe335Leu LP33 SLC12A3 Gitelman syndrome c.2221G>A p.Gly741Arg VUS:FP34 BTD Biotinidase deficiency c.1330G>C p.Asp444His P34 HFE Hereditary hemochromatosis c.845G>A p.Cys282Tyr P34 SPG11 Spastic paraplegia c.1951C>T p.Arg651X P34 TMEM5 Congenital muscular dystrophy-dystrophoglycanopathy

with brain and eye anomaliesc.1018C>T p.Arg340X P

34 PARK2 Parkinson disease c.1289G>A p.Gly430Asp LP34 TRDN Catecholaminergic polymorphic ventricular tachychardia c.613C>T p.Gln205X LP35 DNAH11 Primary ciliary dyskinesia c.7508_7509insTTG p.Lys2504X P35 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P36 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P37 ATP7B Wilson disease c.383delG p.Gly128GlufsX25 P37 LIPA Lysosomal acid lipase A deficiency c.253C>T p.Gln85X P38 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P39 BTD Biotinidase deficiency c.1330G>C p.Asp444His P39 TREX1 Aicardi-Goutieres syndrome c.341G>A p.Arg114His P40 BTD Biotinidase deficiency c.1330G>C p.Asp444His P40 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P40 HPS6 Hermansky-Pudlak syndrome c.238dupG p.Asp80GlyfsX96 LP41 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic

20

Primary Care Patients (n=50)

Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*1 MMACHC Methylmalonic aciduria and homocystinuria cblC type c.271dupA p.Arg91LysfsX14 P1 SPATA7 Leber congenital amaurosis c.94+2T>C LP2 CFTR Cystic fibrosis c.3846G>A p.Trp1282X P2 PFKM Glycogen storage disease 7 c.237+1G>A P3 ERCC5 Xeroderma pigmentosum c.3238C>T p.Arg1080X LP4 CUBN Imerslund-Gräsbeck syndrome c.6928_6934delGAG

GTTAp.Glu2310CysfsX3 P

4 RAB27A Familial hemophagocytic lymphohistiocytosis c.259G>C p.Ala87Pro VUS:FP5 ABCA4 Stargardt disease c.5882G>A p.Gly1961Glu P5 MPO Myeloperoxidase deficiency c.2031-2A>C P5 CNGA3 Achromatopsia c.1669G>A p.Gly557Arg VUS:FP6 DUOX2 Hypothyroidism c.3847+2T>C P7 BTD Biotinidase deficiency c.1330G>C p.Asp444His P7 PYGL Glycogen storage disease 6 c.25_44dup p.Ser15ArgfsX21 P7 SPG7 Spastic paraplegia type 7 c.1529C>T p.Ala510Val P†

7 WFS1 Wolfram syndrome c.124C>T p.Arg42X P8 COL7A1 Epidermolysis bullosa dystrophica c.7557+1G>T LP9 CLRN1 Usher syndrome type III c.528T>G p.Tyr176X P9 CYP1B1 Primary congenital glaucoma c.171G>A p.Trp57X P9 NLRP7 Recurrent hydatidiform mole c.337_338insG p.Glu113GlyfsX7 P9 KCNQ1 Jervell and Lange-Nielsen syndrome c.826delT p.Ser276ProfsX13 LP9 NAGA Alpha-N-acetylgalactosaminidase deficiency c.479C>G p.Ser160Cys LP

10 HFE Hereditary hemochromatosis c.845G>A p.Cys282Tyr P11 ABCA4 Stargardt disease c.5882G>A p.Gly1961Glu P11 CYP1B1 Primary congenital glaucoma c.1103G>A p.Arg368His P11 SP110 Hepatic veno-occlusive disease with immunodeficiency c.877A>T p.Lys293* LP12 C2 C2 deficiency c.841_849+19del LP‡

12 KHDC3L Hydatidiform mole, recurrent c.334C>T p.Gln112X LP13 DUOX2 Congenital hypothyroidism c.2895_2898del p.Phe966Serfs*29 P13 ARSB Mucopolysaccharidosis type VI c.1450A>G p.Arg484Gly LP13 BEST1 Autosomal recessive bestrophinopathy c.602T>C p.Ile201Thr LP

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic† Reclassified as pathogenic in June 2016.‡ Reclassified as pathogenic in January 2017.

21

Carrier findings among primary care patients, continued

Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*14 ALOX12B Autosomal recessive congenital ichthyosis c.1562A>G p.Tyr521Cys P14 BTD Biotinidase deficiency c.1330G>C p.Asp444His P14 C8B C8 deficiency, type II c.1282C>T p.Arg428X P14 CYP1B1 Primary congenital glaucoma c.1103G>A p.Arg368His P14 POLG POLG-related mitochondrial disorders c.1399G>A p.Ala467Thr P14 ITGB4 Epidermolysis bullosa with pyloric atresia c.2783-2A>G LP15 SLC6A19 Hartnup disorder c.517G>A p.Asp173Asn P16 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P17 BBS10 Bardet Biedl syndrome c.1091delA p.Asn364Thrfs*5 P18 CHRNE Congenital myasthenic syndrome c.1033-2A>T P19 GJB2 Nonsyndromic hearing loss c.101T>C p.Met34Thr P19 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P19 NEK8 Renal-hepatic-pancreatic dysplasia 2 c.47+1delG VUS:FP20 CAPN3 Calpainopathy c.1468C>T p.Arg490Trp P20 SERPINA1 Alpha-1 antitrypsin deficiency disorder c.1096G>A p.Glu366Lys P20 USH2A Usher syndrome type II c.920_923dupGCCA p.His308fs P20 FOXRED1 Mitochondrial complex I deficiency c.611_614dupGAGT p.Ala206SerfsX15 LP21 DNAH11 Primary ciliary dyskinesia c.8746C>T p.Gln2916X P21 EYS Retinitis pigmentosa c.6528C>A p.Tyr2176X P21 GNRHR Isolated hypogonadotropic hypogonadism c.317A>G p.Gln106Arg P21 COG4 Congenital disorder of glycosylation c.529C>T p.Arg177X LP21 USH2A Usher syndrome c.10073G>A p.Cys3358Tyr LP†

22 BTD Biotinidase deficiency c.1330G>C p.Asp444His P22 SPG7 Spastic paraplegia type 7 c.1529C>T p.Ala510Val P‡

22 EIF2B2 Leukoencephalopathy with vanishing white matter c.599G>T p.Gly200Val LP22 MPDZ Congenital hydrocephalus c.4906C>T p.Arg1636X LP23 ANO5 ANO5-Related Muscle diseases c.2272C>T p.Arg758Cys P23 GBE1 Glycogen storage disease IV c.691+2T>C P23 HFE Hereditary hemochromatosis c.845G>A p.Cys282Tyr P23 USH2A Usher syndrome type II c.920_923dupGCCA p.His308GlnfsX16 P

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic † Reclassified as pathogenic in January 2016.‡ Reclassified as likely pathogenic in June 2016.

22

Carrier findings among primary care patients, continued

Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*24 TG Congenital hypothyroidism c.5184C>A p.Cys1728X P24 C6 Complement component 6 deficiency c.1786C>T p.Arg596X LP25 ACE Renal tubular dysgenesis c.12_31del p.Ser5AlafsX31 P25 PAH1 Phenylketonuria c.691T>C p.Ser231Pro P26 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P26 MRAP Familial glucocorticoid deficiency c.3G>A p.Met? P26 SLC4A11 Corneal endothelial dystrophy 2 c.554_562delinsC p.Arg185ProfsX4 P26 TH Segawa syndrome c.283delG p.Ala95ArgfsX6 P27 CYP21A2 Congenital adrenal hyperplasia c.844G>T p.Val282Leu P†

27 GJB2 Hearing loss c.109G>A p.Val37Ile P27 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P27 CACNA2D4 Retinal cone dystrophy c.1882C>T p.Arg628X VUS:FP28 PAH Phenylketonuria c.1208C>T p.Ala403Val P29 SERPINA1 Alpha-1 antitrypsin deficiency disorder c.1096G>A p.Glu366Lys P29 SLC6A19 Hartnup disorder c.517G>A p.Asp173Asn P29 TCTN3 Orofaciodigital syndrome 4 c.877C>T p.Gln293X P30 DBH Dopamine beta-hydroxylase deficiency c.339+2T>C P30 UBR1 Johanson-Blizzard syndrome c.4107T>A p.Cys1369X P31 SERPINA1 Alpha-1 antitrypsin deficiency disorder c.1096G>A p.Glu366Lys P31 FANCF Fanconi anemia c.690delT p.Gly231GlufsX7 LP32 PKHD1 Polycystic kidney disease c.9559delT p.Ser3187LeufsX33 P32 PLCE1 Nephrotic syndrome c.1845_1846insA p.Gly616ArgfsX52 P32 SGCG Limb girdle muscular dystrophy type 2C c.195+4_195+7del P33 MUTYH MUTYH-associated polyposis c.536A>G p.Tyr179Cys P33 COL17A1 Junctional epidermolysis bullosa c.2435-6_2440del p.? LP34 TNXB Ehlers-Danlos-like syndrome due to tenascin X deficiency c.4996C>T p.Arg1666X VUS:FP35 ABCC2 Dubin-Johnson syndrome c.3741+1G>A p. ? P35 MUT Methylmalonic acidemia c.1207C>T p.Arg403X P36 USH2A Usher syndrome type II c.2276G>T p.Cys759Phe P36 CYP24A1 Infantile hypercalcemia c.1039C>T p.Gln347X LP

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic† Removed from the genome report after reanalysis, when it was determined that the Sanger validation of the variant was unable to distinguish between the functional gene and multiple pseudogenes.

23

Carrier findings among primary care patients, continued

Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*37 ABCC6 Pseudoxanthoma elasticum c.3306+1del p.? P37 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P38 ABCA4 Stargardt disease c.5882G>A p.Gly1961Glu P38 HSD17B3 17 beta-hydroxysteroid dehydrogenase 3 deficiency c.277+4A>T p.? P38 IDUA Mucopolysaccharidosis type I c.208C>T p.Gln70X P38 MRAP Familial glucocorticoid deficiency c.3G>A p.Met1? P38 NEK1 Short rib-polydactyly syndrome type II c.3107C>G p.Ser1036X LP38 GFPT1 Limb-girdle myasthenia syndrome c.*22C>A p.? VUS:FP38 SLC7A9 Cystinuria c.1399+4_1399+7del p.? VUS:FP39 GJB2 Hearing loss c.109G>A p.Val37Ile P39 CFTR Cystic fibrosis c.2909G>A p.Gly970Asp LP39 PAPSS2 Brachyolmia c.1662_1666del p.Phe555SerfsX15 LP39 RPGRIP1L Joubert syndrome c.3299_3300dup p.Ala1101SerfsX34 LP40 ASPA Canavan disease c.854A>C p.Glu285Ala P40 CPT2 Carnitine palmitoyltransferase II deficiency c.338C>T p.Ser113Leu P40 GJB2 Non-syndromic hearing loss c.167del p.Leu56ArgfsX P40 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P40 GYS1 Muscle glycogen storage disease type 0 c.989_992del p.Gly330AlafsX25 LP41 ASPA Canavan disease c.693C>A p.Tyr231X P41 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P41 CNGA3 Achromatopsia c.101+1G>A LP41 NDUFAF3 Mitochondrial complex I deficiency c.180_181insT p.Asp61X VUS:FP42 HFE Hereditary hemochromatosis c.845G>A p.Cys282Tyr P42 TTPA Ataxia with isolated vitamin E deficiency c.19delC p.Gln7SerfsX64 P43 FANCA Fanconi anemia c.987_990delTCAC p.His330AlafsX4 P43 IFNGR1 IFNGR1 deficiency c.523del p.Tyr175MetfsX2 P43 NEB Nemaline myopathy c.23848-1G>C LP44 IL36RN Generalized pustular psoriasis c.338C>T p.Ser113Leu P44 MOCS2 Molybdenum cofactor deficiency c.539_540delAA p.Lys180ArgfsX31 LP44 C2 C2 deficiency c.1063C>T p.Arg355X VUS:FP

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic

24

Carrier findings among primary care patients, continued

Patient Gene Associated Disease Variant (Nucleotide) Variant (Protein) Classification*45 ABCA4 Stargardt disease c.5882G>A p.Gly1961Glu P45 BLM Bloom syndrome c.2207_2212delinsTA

GATTCp.Tyr736LeufsX5 P

45 DHDDS Retinitis pigmentosa c.124A>G p.Lys42Glu P45 HOGA1 Primary hyperoxaluria, type III c.944_946del p.Glu315del P45 EDARADD Hypohidrotic ectodermal dysplasia c.299_300insAAC p.Cys100X VUS:FP46 DHCR7 Smith-Lemli-Opitz syndrome c.452G>A p.Trp151X P46 GNPTAB Mucolipidosis II c.3503_3504del p.Leu1168GlnfsX5 P46 HFE Hereditary hemochromatosis c.845G>A p.Cys282Tyr P46 KIF7 Acrocallosal syndrome c.2944G>T p.Glu982X P47 GRM6 Congenital stationary night blindness c.2213_2219delCCA

GAGGp. Ala738GlyfsX81 VUS:FP

48 USH2A Usher syndrome type II c.4405C>T p.Gln1469X P48 VWF von Willebrand disease type 2 N c.2561G>A p.Arg854Gln P49 FLG Ichthyosis vulgaris c.2143C>T p.Gln715X P49 SYNE1 Spinocerebellar ataxia c.3930_3931dup p.His1311ProfsX30 P50 HFE Hereditary hemochromatosis c.187C>G p.His63Asp P50 MUTYH MUTYH-related attenuated familial adenomatous

polyposisc.1187G>A p.Gly396Asp P

* P: pathogenic; LP: likely pathogenic; VUS:FP: variant of uncertain significance - favor pathogenic

25

Appendix 8. Summary of polygenic risk predictions and pharmacogenomic findings among patient participants who received whole genome sequencing.

Findings in primary care settings were published previously.24

Cardiology Cohort (n=49)

Average number (sd) of conditions where polygenic risk predictions indicated… 80th percentile of genetic risk 1.4 (1.0) 90th percentile of genetic risk 0.9 (1.0)

Pharmacogenomic results indicated…Drug Interpretation n (%)Clopidogrel Significantly decreased response 0 (0%)

Decreased response 12 (24%)Typical response 17 (35%)Increased response 20 (41%)

Digoxin Decreased metabolism and increased serum concentration 12 (24%)Typical metabolism and serum concentration 22 (45%)Increased metabolism and decreased serum concentration 15 (31%)

Metformin Decreased glycemic response 16 (33%)Typical glycemic response 24 (49%)Increased glycemic response 9 (18%)

Simvastatin Typical risk of myopathy 39 (80%)Increased risk of myopathy 10 (20%)

Warfarin Decreased dose requirement 1 (2%)Standard dose requirement 18 (37%)Increased dose requirement 30 (61%)

Primary Care Cohort (n=50)

Average number (sd) of conditions where polygenic risk predictions indicated… 80th percentile of genetic risk 1.7 (1.1) 90th percentile of genetic risk 1.0 (0.9)

Pharmacogenomic results indicated…Drug Interpretation n (%)Clopidogrel Significantly decreased response 2 (4%)

Decreased response 11 (22%)Typical response 23 (46%)Increased response 14 (28%)

Digoxin Decreased metabolism and increased serum concentration 7 (14%)Typical metabolism and serum concentration 27 (54%)Increased metabolism and decreased serum concentration 16 (32%)

Metformin Decreased glycemic response 16 (32%)Typical glycemic response 22 (44%)Increased glycemic response 12 (24%)

Simvastatin Typical risk of myopathy 41 (82%)Increased risk of myopathy 9 (18%)

Warfarin Decreased dose requirement 4 (8%)Standard dose requirement 19 (38%)Increased dose requirement 27 (54%)

26

Appendix 9. The ten most frequent outpatient care procedures or tests observed within each cohort.

Times observed Patients ReceivingCardiology patients WGS

(n=49)Control (n=51)

WGS (n=49)

Control (n=51)

p

Electrocardiogram 49 61 36 (73.5%) 40 (78.4%) 0.561Prothrombin time 37 44 10 (20.4%) 13 (25.5%) 0.546Complete blood count 30 24 13 (26.5%) 18 (35.3%) 0.344Basic metabolic panel 28 19 13 (26.5%) 14 (27.5%) 0.918Echocardiogram 18 23 18 (36.7%) 20 (39.2%) 0.798Comprehensive metabolic panel 16 21 13 (26.5%) 15 (29.4%) 0.748Lipid panel 15 13 14 (28.6%) 13 (25.5%) 0.729TSH test 14 12 11 (22.4%) 9 (17.6%) 0.548Natriuretic peptide test 13 10 8 (16.3%) 10 (19.6%) 0.669Magnesium test 19 4 6 (12.2%) 4 (7.8%) 0.463

Primary care patients WGS (n=50)

Control (n=50)

WGS (n=50)

Control (n=50)

Blood count 17 14 11 (22%) 11 (22%) >0.99Physical therapy – therapeutic exercises 15 14 2 (4%) 4 (8%) 0.400Lipid panel 18 9 16 (32%) 9 (18%) 0.106Comprehensive metabolic panel 16 6 11 (22%) 6 (12%) 0.183Physical therapy - manual therapy 10 12 3 (6%) 2 (4%) 0.646Screening mammogram 8 13 8 (16%) 13 (26%) 0.220TSH test 9 7 8 (16%) 7 (14%) 0.779Electrocardiogram 10 6 9 (18%) 5 (10%) 0.249Basic metabolic panel 6 8 5 (10%) 7 (14%) 0.538Hemoglobin A1C test 8 3 8 (16%) 3 (6%) 0.110

27

Appendix 10. Healthcare utilization in the six months preceding disclosure sessions and six months following disclosure

sessions.

Counts, 6 Months

Pre-Disclosure, Mean (SD)

Counts, 6 Months

Post-Disclosure, Mean (SD)

Mean Change (SD)

pvalue

Counts, 6 Months

Pre-Disclosure, Mean (SD)

Counts, 6 Months

Post-Disclosure, Mean (SD)

Mean Change

(SD)p

value

P Value, Comparison in

Changes by Randomization Arm

Cardiology CohortControl Arm (n=51) WGS Arm (n=49)

Visits 5.4 (4.3) 7.2 (6.5) 1.7 (7.1) 0.312 6.1 (6.1) 7.8 (6.5) 1.7 (7.8) 0.125 0.401

Labs 5.4 (7.6) 6.9 (6.8) 1.5 (7.4) 0.256 8.0 (12.9) 9.5 (15.3) 1.5 (10.6) 0.472 0.372

Imaging tests 1.1 (1.7) 2.1 (1.9) 1.0 (1.7) 0.006 1.2 (1.7) 2.1 (2.2) 0.9 (2.1) 0.047 0.473

Cardiology tests 2.2 (2.6) 3.1 (1.7) 0.9 (3.0) 0.096 2.3 (2.4) 3.1 (1.9) 0.8 (2.7) 0.066 0.446

Hospitalizations 0.2 (0.6) 0.3 (0.8) 0.1 (0.7) 0.278 0.1 (0.4) 0.2 (0.4) 0.1 (0.6) 0.426 0.454

Primary Care CohortControl Arm (n=50) WGS Arm (n=50)

Visits 4.6 (4.8) 6.9 (7.4) 2.3 (6.8) 0.091 4.5 (3.9) 8.4 (8.7) 3.9 (7.9) 0.020 0.421

Labs 4.7 (6.8) 4.4 (4.8) -0.3 (7.8) 0.434 4.1 (6.9) 5.5 (5.9) 1.4 (8.9) 0.384 0.309

Imaging tests 1.0 (2.2) 0.9 (1.5) -0.1 (2.6) 0.295 1.0 (1.6) 1.0 (1.4) 0.0 (2.1) 0.419 0.476

Cardiology tests 0.4 (1.1) 0.5 (0.6) 0.2 (0.8) 0.424 0.3 (1.0) 0.5 (0.9) 0.2 (1.0) 0.305 0.420

Hospitalizations 0.0 (0.0) 0.0 (0.2) 0.0 (0.2) 0.175 0.0 (0.0) 0.0 (0.1) 0.0 (0.1) 0.232 0.322

28

Appendix 11. Healthcare costs in the six months preceding disclosure sessions and six months following disclosure

sessions.

Control Arm (n=51) WGS Arm (n=49) WGS Arm - Control Arm

Mean Costs, 6 Months

Pre-Disclosure, USD (SD)

Mean Costs, 6 Months

Post-Disclosure, USD (SD)

Change in Mean Costs, USD (95% CI) p

Mean Costs, 6 Months

Pre-Disclosure, USD (SD)

Mean Costs, 6 Months

Post-Disclosure, USD (D)

Change in Mean Costs, USD (95% CI) p

Mean Difference in Change between

Randomization Arms, USD (95% CI) p

Cardiology Cohort

Control Arm (n=51) WGS Arm (n=49)

Visits 686 (548) 1344 (1415) 656 (341 to 1021) 0.004 790 (773) 1344 (1165) 554 (252 to 876) 0.017 -102 (-540 to 1329) 0.487

Labs 70 (95) 109 (108) 38 (-5 to 70) 0.170 104 (151) 137 (269) 32 (-19 to 103) 0.298 -6 (-73 to 304) 0.459

Imaging tests 359 (666) 638 (865) 280 (-10 to 573) 0.092 364 (743) 696 (1047) 332 (66 to 622) 0.048 52 (-357 to 736) 0.395

Cardiology tests 165 (157) 188 (102) 23 (-28 to 70) 0.320 156 (159) 192 (143) 36 (-21 to 82) 0.214 13 (-57 to 127) 0.409

Other outpatient 1470 (4645) 1489 (3958) 19 (-1866 to 1778) 0.451 1480 (4174) 2265 (6821) 853 (-1664 to 3331) 0.291 834 (-2214 to 9636) 0.358

Hospitalizations 3055 (10356) 5131 (13891) 1923 (-2930 to 6893) 0 .272 2796 (9922) 2717 (9907) -79 (-4390 to 3869) 0 .412 -2002 (-8508 to 11411) 0.334

Total, Cardiology 5805 (2911) 8898 (3188) 2939 (-2857 to 8772) 0.237 5690 (815) 7351 (2799) 1728 (-3067 to 6387) 0.352 -1211 (-8969 to 2891) 0.376

Primary Care Cohort

Control Arm (n=50) WGS Arm (n=50)

Visits 524 (638) 1347 (1366) 824 (482 to 1162) <0.001 556 (408) 1581 (1455) 1025 (699 to 1395) <0.001 202 (-294 to 1512) 0.400

Labs 74 (110) 66 (81) -8 (-48 to 28) 0.530 63 (72) 96 (113) 33 (-10 to 74) 0.254 41 (-16 to 146) 0.297

Imaging tests 113 (278) 149 (270) 35 (-46 to 127) 0.692 170 (264) 227 (330) 57 (-63 to 175) 0.560 23 (-129 to 398) 0.693

Cardiology tests 25 (56) 49 (79) 24 (3 to 45) 0.313 25 (51) 52 (94) 26 (2 to 57) 0.290 2 (-35 to 120) 0.643

Other outpatient 875 (2419) 540 (1166) -335 (-1198 to 313) 0.648 297 (356) 625 (1288) 345 (-18 to 798) 0.668 680 (-143 to 1875) 0.566

Hospitalizations 0 (0) 142 (1504) 127 (-433 to 705) 0 .836 0 (0) 449 (1306) 449 (0 to 1092) 0 .710 322 (-565 to 0) 0.799

Total 1611 (2911) 2293 (3188) 682 (-472 to 1680) 0.648 1111 (815) 3030 (2799) 1919 (1151 to 2828) 0.232 1237 (-120 to 3365) 0.572

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Appendix 12. Immediately attributable health care utilization and associated costs. Services were recommended by physicians in response to study results, through checklists they completed at the end of each results disclosure session, and identified as completed after review of medical records or patient self-report. Services among primary care patient participants received within the Partners HealthCare System were reported previously,24 and in this tally additional services have been identified through patient self-report.

Services Rationale* CostPrimary Care Cohort, Control Arm (n=50)

Colonoscopy FH of adenomas $1,159Referral to neurology and neurobehavioral exam FH of Lewy body dementia $777Referral for genetic counseling FH of breast cancer $290Referral to dermatology FH of melanoma $177C-reactive protein, homocysteine, lipoprotein(a) tests FH of heart disease $58

$2,461Primary Care Cohort, WGS Arm (n=50)

Referral to cardiovascular genetics; aldolase, creatine kinase, natriuretic peptide, troponin, and TSH tests; complete blood count; comprehensive metabolic panel; ECG; echocardiogram

MDR: Likely pathogenic KCNQ1 variant $984

Referral to cardiovascular genetics, ECG, echocardiogram MDR: Likely pathogenic ANK2 variant $800Echocardiogram Polygenic risk for AF $490Referral to medical genetics and genetic testing MDR: Pathogenic PPOX variant $462Ultrasound FH of AAA $178ECG Polygenic risk for CAD and long QT syndrome $97ECG Polygenic risk for long QT syndrome $97Hemoglobin A1c, blood glucose, and lipid panel† FH + polygenic risk for T2D, CAD $46Hemoglobin A1c and blood glucose Polygenic risk for T2D $31Ferritin test† Carrier of pathogenic HFE variant $30Ferritin test MDR: Pathogenic HFE variants $19Hemoglobin A1c Polygenic risk for T2D $13

$3,247Cardiology Cohort, Control Arm (n=51)

Referral to gastroenterology FH of pancreatic cancer $179

Cardiology Cohort, WGS Arm (n=49)Ultrasound Polygenic risk for AAA $206

* FH: family history; MDR: monogenic disease risk; AAA: abdominal aortic aneurism; T2: type 2 diabetes; CAD: coronary artery disease.† Data from the same participant.

30

Appendix 13. Additional procedures that were not ordered following disclosure of WGS results, but judged as potentially informative after review of the Genome Resource Center.Gene Disease Classification Inheri-

tanceCohort Additional Tests Considered Costs

LHX4 Combined pituitary hormone deficiency

Pathogenic AD Primary Care 1) Referral to endocrinology +a) Growth hormone testb) Total T4 c) TSH d) LH e) FSHf) Prolacting) ACTH

2) DEXA3) Testosterone4) Cortisol

$178.78 $22.70

$9.35 $22.87 $25.20 $25.29 $26.37 $52.56

$105.89 $35.13 $44 .93

$549.07RDH5 Fundus albipuncta-

tus Pathogenic AR Primary Care 1) Fundoscopy

2) Optical coherence tomography3) Electroretinogram

$126.76 $83.09$372 .02

$581.87HFE Hereditary

hemochromatosisPathogenic AR Primary Care 1) LFT

2) Transferrin saturation $11.11

$11 .90 $23.01

CHEK2 CHEK2-related can-cer risk

Pathogenic AD Cardiology 1) Referral to cancer genetics $178.78

ANK2 Ankyrin-B related cardiac arrhythmia

Likely patho-genic

AD Primary Care 1) Cardiology referral 2) ECG 3) Holter monitor 4) Exercise test

$178.78 $97.24

$104.72 $38 .93

$419.67COL2A1 Spondyloepiphyseal

dysplasia congenitaLikely Patho-genic

AD Primary Care 1) Physical exam 2) Skeletal survey 3) Vision evaluation4) Hearing evaluation

$178.78 $105.89 $191.87 $152 .44 $628.98

31

Additional potential procedures, continued

Gene Disease Classification Inheri-tance

Cohort Additional Tests Considered Costs

KCNQ1 Romano-Ward syn-drome

Likely Patho-genic

AD Primary Care 1) Referral to cardiogenetics2) CK3) Troponin 4) Exercise test5) Cardiac MRI with contrast

$178.78 $8.86

$13.39 $38.93

$619 .65 $859.61

SQSTM1 x 2 Paget disease of the bone

Likely Patho-genic

AD Cardiology 1) Referral to endocrinology2) Skeletal survey3) Alkaline phosphatase

$178.78 $105.89

$7 .04 $291.71

APP Alzheimer’s dis-ease, late onset

VUS - Favor Pathogenic

AD Cardiology 1) DNA extraction and single site mutation testing of relative

$500.00

ARSE Chondrodysplasia punctata

VUS – Favor Pathogenic

XL Primary Care 1) Skeletal survey w flex/ext2) Hearing evaluation3) Echocardiogram 4) Ophthalmology5) Clotting work up

a) PT/PTTb) Factor IIc) Factor VIId) Factor IX

6) Genetics Exam

$114.69 $152.44 $489.95 $191.87

$13.52 $17.67 $24.37 $25.91 $178 .78

$1,209.20TNNT2 Hypertrophic car-

diomyopathyVUS – Favor Pathogenic

AD Cardiology 1) Referral to cardiology2) Echocardiogram

$178.78 $489 .95 $668.73

32

Additional potential procedures, continued

Gene Disease Classification Inheri-tance

Cohort Additional Tests Considered Costs

PDE11A Primary pigmented micronodular adrenocortical dis-ease

VUS – Favor Pathogenic

AD Primary Care 1) Endocrinology referral2) Blood pressure 3) DEXA4) Spine X-ray5) Blood-cortisol6) Blood glucose7) ACTH stimulation testing 8) Dexamethasone suppression 9) MRI of adrenal glands

$178.78 $0.00

$105.89 $114.69

$44.93 $5.34

$44.39 $22.19

$603 .88 $1,120.09

33

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