Machini et al. Genetic Counseling in the era of WES/WGS Supplementary data
Supplementary Table I: Demographics IArea 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 / NOWES / /
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?