Machini et al. Genetic Counseling in the era of WES/WGS Supplementary data

Supplementary Table I: Demographics I
Area of practice / WES/WGS / No WES/WGS
NSGC Region 1 / 6 / 15
NSGC Region 2 / 26 / 37
NSGC Region 3 / 14 / 14
NSGC Region 4 / 21 / 35
NSGC Region 5 / 4 / 17
NSGC Region 6 / 7 / 15
NSGC Regions 4+5 / 0 / 1
NSGC Regions 3+4 / 1 / 0
All US states / 0 / 1
International / 0 / 3
N/A / 0 / 1
Not indicated / 0 / 3
NSGC Region 1: CT, MA, ME, NH, RI, VT, Canadian Maritime Provinces
NSGC Region 2: DC, DE, MD, NJ, NY, PA, VA, WV, Quebec, Puerto Rico, Virgin Islands
NSGC Region 3: AL, FL, GA, KY, LA, MS, NC, SC, TN
NSGC Region 4: AR, IA, IL, IN, KS, MI, MN, MO, ND, NE, OH, OK, SD, WI, Ontario
NSGC Region 5: AZ, CO, MT, NM, TX, UT, WY, Alberta, Manitoba, Saskatchewan
NSGC Region 6: AK, CA, HI, ID, NV, OR, WA, British Columbia
Supplementary Table II: Demographics II
Specialty (≥50% of time) / Work Setting / WES/WGS1,2 / No WES/WGS1,2
Pediatrics / Private / 4 / 4
Public / 6 / 4
University / 31 / 5
Diagnostic / 0 / 0
Other / 1 / 1
Prenatal / Private / 1 / 14
Public / 1 / 6
University / 2 / 18
Diagnostic laboratory / 0 / 0
Other / 0 / 4
Cancer / Private / 0 / 18
Public / 2 / 21
University / 7 / 12
Diagnostic laboratory / 0 / 2
Other / 0 / 0
Laboratory / Private / 0 / 1
Public / 1 / 1
University / 1 / 1
Diagnostic laboratory / 4 / 10
Other / 1 / 0
Other / Private / 4 / 2
Public / 2 / 2
University / 16 / 10
Diagnostic laboratory / 0 / 2
Other / 1 / 7
1: 15 participants are counted twice in this table, because they divide their time between 2 specialties (50% each). This discrepancy only affects this table and does not interfere with the analysis of the data.
2: 5 individuals who do not offer WES/WGS and 1 who only offers WES do not appear in this table because they do not spend 50% of their time in any single discipline. Their responses are included in the data presented in this study.
Supplementary Table III: Demographics comparative table
Professional Status Survey 2012 / Population Sample (this study) / Not Offering WES/WGS (this study) / Offering WES/WGS (this study)
Area of practice1 / (N=1339) / (N=230) / (N=145) / (N=85)
Prenatal / 29% / 20% / 29% / 5%
Cancer / 25% / 27% / 36% / 11%
Pediatrics / 13% / 24% / 10% / 49%
Other / 33% / 29% / 25% / 35%
Primary work setting2 / (N=1339) / (N=221) / (N=141) / (N=80)
University / 36% / 48% / 31% / 65%
Private / 17% / 20% / 25% / 11%
Public / 17% / 19% / 23% / 16%
Lab / 9% / 7% / 9% / 5%
Other / 21% / 6% / 9% / 3%
1: significantly different distribution between Professional Status Survey 2012 (PSS) and Population in this study (chi square test, p=0.003) and between PSS and sample offering WES/WGS (chi square test, p=0)
2: significantly different distribution between PSS and population in this study (chi square test, p=0.005), between PSS and sample offering WES/WGS (chi square test, p=1e-8)

Supplementary Fig.1A. Recruitment notice

Subject: Student Research Project - Genetics in the era of whole exome/whole genome sequencing

I am a 2nd year graduate student in the Genetic Counseling Program at Brandeis University and I am conducting a research study to learn more about the impact of whole exome and whole genome sequencing technologies on patient care. This research study has been approved by the Brandeis University Committee for Protection of Human Subjects (IRB).

You are invited to participate in my study by taking part in an online, anonymous survey. All practicing genetic counselors (including those who work in non-traditional settings), geneticists and other healthcare professionals are eligible to participate. Your participation is valuable regardless of whether your institution currently offers whole exome and/or genome sequencing.

Your answers will enhance our knowledge of current policies regarding the integration of WES/WGS in clinic and/or research and will permit us to evaluate their impact on patient care. In addition, your answers will help us identify possible barriers to the implementation of WES/WGS.

Also, please forward this e-mail to genetic counselors (who are not members of the NSGC), geneticists and other healthcare professionals who you know are involved in WES/WGS and might be interested in participating in this study.

The survey will take approximately 20-30 minutes to complete. Upon completion of the survey, you will have the opportunity to enter a drawing to win one of two $50 Amazon.com gift cards.

Please follow the link below to access the survey:

You may contact me or my faculty advisor, Kate Kramer, at the e-mails provided below if you have any questions regarding this study.

Thank you in advance for your participation.

Kalotina Machini

Supplementary Fig.1B. Survey questions

BLOCK 1: Introduction- Consent-Demographics

Q1.1 Thank you for participating in this survey, which will take approximately 20 to 30 minutes to complete. Your participation is completely anonymous and voluntary and can be discontinued at any time. By completing the survey, you are consenting to participate in this research study.

Your answers will enhance our knowledge of the current policies in place for offering whole exome sequencing (WES) / whole genome sequencing (WGS) in clinical care and/or research and they will provide us with valuable information regarding the impact of such results on patient care. In addition, your answers will help us identify possible barriers to the implementation of WES/WGS.

Q1.2 Demographics-Background

Q1.3 What is your background? (Select all that apply)

Genetic counselor

MD (board certified in genetics)

MD (non-geneticist)

Nurse

PhD

Other (please be precise) ______

Q1.4 Which of the following best describes your work setting?

University medical center

Private hospital or medical facility

Public hospital or medical facility

Diagnostic laboratory

Other (please be precise) ______

Q1.5 In which state(s) or province(s) do you practice?

Q1.6 What is the name of your institution? Your answer will enhance the quality of our data analysis. If you prefer not answering this question, please enter "None"

Q1.7 What percentage of your time do you spend in:

______Pediatrics

______Prenatal

______Cancer

______Laboratory services

______Other (please be precise)

Q1.8 Is whole exome sequencing (WES) and/or whole genome sequencing (WGS) offered in your practice?

WES is offered

WGS is offered

both WES and WGS are offered

neither WES or WGS is offered

BLOCK 2: WES and WGS are not offered yet

Q2.1 What are the reasons you are not offering WES and/or WGS?

Q2.2 Is your practice planning on offering WES and/or WGS in the next 12 months?

YES / NO
WES /  / 
WGS /  / 

Q2.3 What role(s) would you be interested in having in the process of WES/WGS? Please select all that apply.

deciding who should be offered WES/WGS

consenting

analyzing the data

communicating the results

other, please describe ______

Q2.4 What aspect(s) of your training (e.g., Molecular Genetics, Counseling theory, Bioethics, Statistics, Clinical Genetics, Biotechnology etc.) do you expect to be most useful in the process of WES/WGS?

Q2.5 What educational resources (e.g., webinars, formal lectures or counseling aides etc.) and on what subject(s) would you like to have in order to be best prepared for your participation in WES/WGS?

BLOCK 3: WES is offered

Q3.1 How long ago did your institution begin to offer WES?

more than 12 months

less than 12 months but more than 6 months

less than 6 months

Q3.2 Who in your practice decides whether to offer the test? Please, select all that apply.

genetic counselors

MDs

NPs

other (please be precise) ______

per patient's request

I don't know

Q3.3 How manypeople are directly involved in the process of WES in your practice (consent-data analysis-result communication)?

1

2

3

4

other, please be as precise as possible ______

I don't know

Q3.4 What are you offering WES for?

Clinical purposes

Research purposes

Both clinical and research purposes

BLOCK 4: WES for research purposes

Q4.1 What are the criteria for a patient/family to be considered for WES for research purposes?

Q4.2 To date, what percentage of patients have consented to having WES when offered?

less than 10%

10-30%

30-50%

50-70%

70-100%

I don't know

Q4.3 The consent process

Q4.4 How many sessions does the consent process involve?

0

1

2

3 or more

I don't know

Q4.5 Who consents the patient/family? Please, select all that apply.

the genetic counselor

the geneticist

other, please list: ______

I don't know

Q4.6 Who provides assent/consent on behalf of intellectually disabled patients? Please, check all that apply.

the referring physician

the parent / legal guardian

other, please be precise ______

Q4.7 Is consent via telephone permitted?

Yes

No

I don't know

Q4.8 Are there provisions for patients who do not understand English?

Yes

No

I don't know

Q4.9 Are there provisions for hearing and/or vision impaired patients?

Yes

No

I don't know

Q4.10 The results

Q4.11 Which diagnostic lab runs the sequencing?

In-house laboratory

Outside laboratory. Please, list if possible all labs used: ______

I don't know

Q4.12 Who analyzes the data?

Testing laboratory

Yourself

Other personnel in your institution, please list: ______

I don't know

Q4.13 What is the approximate turn-around-time from blood-draw to results for WES at your institution?

less than 2 months

2 to 4 months

4 to 6 months

6 to 12 months

more than 12 months

Q4.14 Does the patient receive any results?

Yes

No

If No Is Selected, Then Skip To Can results be revisited and/or data ...

Answer If Does the patient receive any results? Yes Is Selected

Q4.15 How does the patient receive the results? Please, select all that apply.

In person

By written report

Over the phone

Other, please be precise ______

Q4.16 What type of results does the patient receive? Please, select all that apply.

Results considered significant for the condition he/she was tested for

Variants of unknown significance (in loci related to patient's phenotype)

Incidental findings and/or secondary diagnosis. Please, give examples: ______

Other, please be precise ______

Q4.17 Can the patient opt not to be informed about results other than those significant for the condition he /she was tested for?

Yes

No

I don't know

If Yes Is Not Selected, Then Skip To Can results be revisited and/or data ...

Answer If Can the patient opt not to be informed about results othe... Yes Is Selected

Q4.18 Can the patient change his/her mind at a later time?

Yes

No

I don't know

Q4.19 Can results be revisited and/or data reanalyzed once the original analysis and result reporting has been completed?

Yes

No

I don't know

Q4.20 How long do you plan to keep the sequencing data files?

Less than a year

1-5 years

more than 5 years

I don't know

Q4.21 Does your institution participate in data (sequence and clinical information) sharing?

Yes

No

I don't know

BLOCK 5: WES for clinical purposes

Q5.1 What are the criteria for a patient/family to be considered for WES in clinic?

Q5.2 To date, what percentage of patients have consented to having WES when offered?

less than 10%

10-30%

30-50%

50-70%

70-100%

I don't know

Q5.3 The consent process

Q5.4 How many sessions does the consent process involve?

0

1

2

3 or more

I don't know

Q5.5 Who consents the patient/family? Please, select all that apply.

the genetic counselor

the geneticist

other, please list ______

I don't know

Q5.6 Who provides assent/consent on behalf of intellectually disabled patients? Please, select all that apply.

the referring physician

the parent / legal guardian

other, please be precise ______

Q5.7 Is consent via telephone permitted?

Yes

No

I don't know

Q5.8 Are there provisions for patients who do not understand English?

Yes

No

I don't know

Q5.9 Are there provisions for hearing and/or vision impaired patients?

Yes

No

I don't know

Q5.10 The results

Q5.11 How much does your institution bill for WES in clinic?

Q5.12 What percentage of insurers covers WES in clinic?

Q5.13 Which diagnostic lab runs the sequencing?

In-house laboratory

Outside laboratory. Please list all labs used if possible: ______

I don't know

Q5.14 Who analyzes the data?

Testing laboratory

Yourself

Other personnel in your institution, please list: ______

I don't know

Q5.15 What is the approximate turn-around-time from blood-draw to results for WES at your institution?

less than 2 months

2 to 4 months

4 to 6 months

6 to 12 months

more than 12 months

Q5.16 How does the patient receive the results? Please, select all that apply.

In person

By written report

Over the phone

Other, please be precise ______

Q5.17 What type of results does the patient receive? Please, select all that apply.

Results considered significant for the condition he/she was tested for

Variants of unknown significance (in loci related to patient's phenotype)

Incidental findings and/or secondary diagnosis. Please, give examples: ______

Other, please be precise ______

Q5.18 Can the patient opt not to be informed about results other than those significant for the condition he /she was tested for?

Yes

No

I don't know

If Yes Is Not Selected, Then Skip To Can results be revisited and/or data ...

Answer If Can the patient opt not to be informed about results othe... Yes Is Selected

Q5.19 Can he change his/her mind at a later time?

Yes

No

I don't know

Q5.20 Can results be revisited and/or data reanalyzed once the original analysis and result reporting has been completed?

Yes

No

I don't know

Q5.21 Does your institution charge or plan to charge when data are reanalyzed?

Yes

No

I don't know

Q5.22 How long do you plan to keep the sequencing data files?

Less than a year

1-5 years

more than 5 years

I don't know

Q5.23 Does your institution participate in data(sequence and clinical information)sharing?

Yes

No

I don't know

BLOCK 6: WES success rate?

Q6.1 What percentage of the time did WES provide a clear-cut explanation for the patient's phenotype (i.e., mutation in a gene already implicated in the pathogenesis of the condition in question)?

Less than 10%

10-30%

30-50%

50-70%

70-100%

We haven't had enough results yet to draw a conclusion

Q6.2 What percentage of the time did WES provide a possible explanation for the patient's phenotype, but further research and investigation was required to confirm it (i.e., mutation in a gene that based on the literature could be responsible for the patient's pathology)?

Less than 10%

10-30%

30-50%

50-70%

70-100%

We haven't had enough results yet to draw a conclusion

Q6.3 What percentage of the time did WES lead to a diagnosis other than the one the patient was tested for (i.e., incidental findings and/or secondary diagnosis)?

Less than 10%

10-30%

30-50%

50-70%

70-100%

We haven't had enough results yet to draw a conclusion

BLOCK 7: General questions WES/WGS

Q7.1 Please, describe some of the challenges you had to face/ are facing with the introduction of WES and/or WGS in your practice:

Q7.2 Did you have to modify some of your strategies since you started offering WES and/or WGS? If yes, in what way?

Q7.3 What is your actual role in the process of WES/WGS? Please, select all that apply.

you decide who should be offered WES/WGS

you consent

you analyze the data

you communicate the results

other ______

Q7.4 What role would you be interested in having in the process of WES/WGS? Please, select all that apply.

deciding who should be offered WES/WGS

consenting

analyzing the data

communicating the results

other, please describe ______

Q7.5 What aspect(s) of your training (e.g., Molecular Genetics, Counseling theory, Bioethics, Statistics, Clinical Genetics, Biotechnology etc.) has (have) been most useful regarding your role in the process of WES/WGS?

Q7.6 What educational resources (e.g., webinars, formal lectures or counseling aides etc.) and on what subject(s) would you like to have in order to be best prepared for your participation in WES/WGS?

BLOCK 8: WGS is offered

Q8.1 How long ago did your institution begin to offer WGS?

more than 12 months

less than 12 months but more than 6 months

less than 6 months

Q8.2 Who in your practice decides whether to offer the test? Please, select all that apply.

genetic counselors

MDs

NPs

other, please be precise ______

per patient's request

I don't know

Q8.3 How manypeople are directly involved in the process of WGS in your practice (consent-data analysis-result communication)?

1

2

3

4

other, please be as precise as possible ______

I don't know

Q8.4 What are you offering WGS for?

Clinical purposes

Research purposes

Both clinical and research purposes

BLOCK 9: WGS for research purposes

Q9.1 What are the criteria for a patient/family to be considered for WGS for research purposes?

Q9.2 To date, what percentage of patients have consented to having WGS when offered?

less than 10%

10-30%

30-50%

50-70%

70-100%

I don't know

Q9.3 The consent process

Q9.4 How many sessions does the consent process involve?

0

1

2

3 or more

I don't know

Q9.5 Who consents the patient/family? Please, select all that apply.

the genetic counselor

the geneticist

other, please list: ______

I don't know

Q9.6 Who provides assent/consent on behalf of intellectually disabled patients? Please, select all that apply.

the referring physician

the parent / legal guardian

other, please be precise ______

Q9.7 Is consent via telephone permitted?

Yes

No

I don't know

Q9.8 Are there provisions for patients who do not understand English?

Yes

No

I don't know

Q9.9 Are there provisions for hearing and/or vision impaired patients?

Yes

No

I don't know

Q9.10 The results

Q9.11 Which diagnostic lab runs the sequencing?

In-house laboratory

Outside laboratory. Please, list if possible all labs used: ______

I don't know

Q9.12 Who analyzes the data?

Testing laboratory

Yourself

Other personnel in your institution, please list: ______

I don't know

Q9.13 What is the approximate turn-around-time from blood-draw to results for WGS at your institution?

less than 2 months

2 to 4 months

4 to 6 months

6 to 12 months

more than 12 months

Q9.14 Does the patient receive any results?

Yes

No

If No Is Selected, Then Skip To Can results be revisited and/or data ...

Answer If Does the patient receive any results? Yes Is Selected

Q9.15 How does the patient receive the results? Please, select all that apply.

In person

By written report

Over the phone

Other, please be precise ______

Q9.16 What type of results does the patient receive? Please, select all that apply.

Results considered significant for the condition he/she was tested for

Variants of unknown significance (in loci related to patient's phenotype)

Incidental findings and/or secondary diagnosis. Please, give examples: ______

Other, please be precise ______

Q9.17 Can the patient opt not to be informed about results other than those significant for the condition he /she was tested for?