SFARI Base / SSC Researcher Welcome Packet

Transcription

1 SFARI Base / SSC Researcher Welcome Packet Last Updated: Monday, April 19, 2010 Simons Foundation 160 Fifth Avenue 7th Floor New York, NY 10010

2 Welcome The mission of the Simons Foundation Autism Research Initiative (SFARI) is to improve the diagnosis, treatment, and prevention of autism and related developmental disorders. SFARI explores neuroscience from multiple directions, supporting genetic, molecular, cellular, systems, cognitive, behavioral, theoretical, and computational approaches. The SFARI Simplex Collection (SSC) is a new resource for autism research that will provide the scientific community with an increasing variety of information on a highly characterized set of simplex families. Successful analyses depend on careful and detailed characterization of the clinical picture presented by probands and their relatives, which is why the Simons Foundation has undertaken the unprecedented work to standardize and coordinate patient evaluation at over one dozen medical centers across North America. The immediate goal of the SSC is to collect high quality phenotype data and biospecimens from approximately 2,000 simplex families (8,000 individuals) by early Rigor and uniformity in data collection, as well as attaining and maintaining diagnostic reliability, characterize the SSC. All collection sites use the same inclusion and exclusion criteria, administer the same instruments, and follow the same protocols in collecting biospecimens. Descriptions of the inclusion and exclusion criteria, and of the relevant protocols, are available in this packet. Recent data indicate that many cases of autism are due to new, highly penetrant, mutations that very likely arise in germ line cells. The SSC is optimally designed to facilitate the discovery of these de novo mutations by focusing on collecting phenotypic information and biospecimens from simplex families, in which only one child (the proband) is on the autism spectrum, while both biological parents and all other siblings are not. Collections are already publicly available for studying multiplex families, in which two or more siblings are on the autism spectrum. The SFARI initiative s research repository, SFARI Base, currently provides access to the Simplex Collection s curated, de-identified phenotype data, as well as to biospecimens obtained from each SSC participant, including: DNA samples derived from whole blood and/or lymphoblastoid cell lines (LCLs), viable source LCLs, and plasma. The Simons Foundation has selected the Rutgers Cell and DNA Repository (RUCDR) to receive, process, store, and distribute SFARI biospecimens to research laboratories; phenotype data and biospecimens have already begun being distributed to multiple outside investigators. Parallel genome-wide scans of the collection are being carried out by Mike Wigler at Cold Spring Harbor Laboratory (using a Nimblegen platform) and Matthew State at Yale University (using an Illumina platform). Perhaps the most exciting aspect of SFARI is its novel approach to collaboration. Researchers using the resource are required to contribute the results of their experiments back to SFARI Base (after a sufficient grace period for publication). In this way, the entire research community benefits from a collection that is continually enriched with new -- and new types of -- searchable, leading edge scientific data. (Please see Appendix A for more information.) SFARI Researcher Welcome Packet Page 2

3 Table of Contents SSC Inclusion / Exclusion Criteria 4 Participant Classes 4 Specific Inclusion Criteria 4 Specific Exclusion Criteria 6 Other Considerations 7 Available Instruments by Family Role Table 8 SSC Instrument Details 9 Mandatory Instruments 9 Optional Instruments 16 Available Biospecimens 17 DNA 17 Cells 17 Plasma 17 Prerequisites for Access to SFARI Base 18 Required Institutional Documents 18 Online SFARI Application Instructions 19 Appendix A : Researcher Distribution Agreement Appendix B : Simons Simplex Collection IRB Appendix C : Sample SSC Consent Form SFARI Researcher Welcome Packet Page 3

4 SSC Inclusion / Exclusion Criteria Subjects are admitted into the SSC in biological family groups. Each family collected must include one (and only one) child with ASD. All siblings must be unaffected. Participant Classes Proband: the affected child in a family. Parent: biological mother and father of the proband, living at the time of submission, both unaffected with ASD. The parents may not be related to one another by blood. Unaffected Designated Sibling: the unaffected full sibling closest in age to the proband. The sibling should be at least 4 years of age. Other Sibling: any other sibling of the proband, including half-siblings. If additional siblings are available to provide a blood sample, then efforts are made to collect blood and measures from as many siblings as possible. This sibling should be at least 4 years of age. Sibling Exception: At any given site, the full sibling requirement may be waived for a maximum of 25% of families collected. These families will fall into one of the following categories: No sibling available Only half-siblings Full or half siblings < 4 years old Blood Samples will be collected for the proband, mother, father and designated (full) sibling and sent to a central biological repository to support genetic studies. Specific Inclusion Criteria Age The proband must be between 4 and 17 years, 11 months of age when the phenotype measures are administered and the data is collected. SFARI Researcher Welcome Packet Page 4

5 Note: The ADI-R, ADOS, and cognitive measures must be collected within the same 6 month period. ADI-R Scores On the ADI-R, the proband must meet one of the following four (4) criteria: Standard cutoffs on the Social and Communication domains Standard cutoff on the Social domain and within two (2) points of Communication cutoff Standard cutoff on the Communication domain and within two (2) points of Social cutoff Is within one (1) point of the standard cutoffs on both Social and Communication domains. All ADI-R data must be collected by a reliable examiner. ADOS Scores On the ADOS, the proband must have received a valid and reliable administration, and must meet cutoffs for autism spectrum or autism: The newest ADOS algorithms must be used for Modules 1 3 Original cutoff algorithms may be used for Module 4. Nonverbal Cognitive Ability Using the Mullen, DAS-II, WISC-IV, or WASI: Probands who are four (4) years of age must have a nonverbal deviation or ratio IQ score greater than or equal to 60. Participants between five (5) and eight (8) years of age (< 96 months) must have a nonverbal deviation IQ score or nonverbal ratio IQ score greater than or equal to 40. Whichever is the higher of the two scores (i.e., deviation or ratio IQ) is used. Participants eight (8) years of age or older ( 96 months) must have a nonverbal mental age of 36 months or older. Diagnosis Following the SSC Evaluation, the proband must have a clinical Best Estimate Diagnosis, of Autistic Disorder, Asperger s Disorder, or PDD-NOS, according to the DSM-IV-TR. The Best Estimate Diagnosis must be based on information from the current evaluation, including observation, chart review, and ADI-R and ADOS findings. The Best Estimate Diagnosis must be made by a psychologist or physician with appropriate credentials and experience requisite for making clinical psychiatric / psychological diagnoses. The diagnostician must have had direct observation of the proband in making the Best Estimate Diagnosis. SFARI Researcher Welcome Packet Page 5

6 Specific Exclusion Criteria Families meeting one or more of the following are excluded: For Probands: Pregnancy and Birth Fewer than 36 weeks gestation AND less than 2000 grams at birth (~4 lbs 6.5 oz) A history of extensive pregnancy or birth complications o A history of significant prenatal / birth injury or brain damage should be explored if the proband was in the NICU, or in the hospital for greater than three days. Other Disorders or Limitations Positive for Fragile Syndrome or Down Syndrome (Trisomy 21) o o Note 1: If probands meet criteria for inclusion based on clinical phenotype measures, no other genetic diagnosis (whether based on macroscopic, microscopic or sub-microscopic criteria) is excluded. The interest in these situations is to identify additional risk factors or modifier genes that may correlate with the autism phenotype. Note 2: Clinical arrays may be administered for purposes of genetic counseling, but results from clinical arrays will not be considered in the research project. Sensory or motor difficulties that would preclude valid use of the diagnostic instruments History of severe nutritional or psychological deprivation For Any Full and/or Half Siblings: Diagnosed with or referred for ASD Identified as having mental retardation (Exception: cases documented as Trisomy 21 Down Syndrome) Diagnosed with schizophrenia Diagnosed with psychiatric disorder(s) requiring treatment with more than one psychotropic medication An Adaptive Behavior Standard Score on the Vineland-II that is 70 or below An Individualized Education Plan (IEP) for extensive special education services o Note 1: For full siblings under 4 years old, stringent screening is done to eliminate any concerns of potential ASD. For this reason, if the sibling is receiving any services (even services not considered extensive ), the family is put on a wait list until the sibling reaches the age of 4. They can then be reassessed for the SSC. For Either Biological Parent: Diagnosed with ASD Identified as having mental retardation Diagnosed with schizophrenia SFARI Researcher Welcome Packet Page 6

7 For Any Second-degree Relative: Diagnosed with ASD o Second-degree relatives include aunts, uncles, nephews, nieces, grandparents, and grandchildren For Any Third-degree Relative: Diagnosed with ASD o Third-degree relatives include cousins, great-aunts, great-uncles, great-grandmothers, great-grandfathers and any first cousin s children (first cousin once-removed) Participation in Other Biomaterial Repositories A family is excluded from the SSC if they have participated or are participating in other autism repositories or repositories of disorders related to autism (e.g., Obsessive Compulsive Disorder). Other Considerations Multiplex Families Simplex families initially enrolled in the study may be discovered to be multiplex after the start of data collection. If a site identifies a sibling or parent that is on the autism spectrum (based on the SSC assessments or clinical impression) before blood is collected, these cases should be excluded. When blood has already been collected, the family must be clearly flagged as ineligible for the simplex sample using the last page of the SSC Diagnosis Summary Form. A non-designated sibling or parent later may be diagnosed with ASD through processes unrelated to and occurring after the SSC study. There is a procedure for noting late exclusion findings in the database. Monozygotic Twins with ASD If a family has monozygotic (identical) twins with ASD and one unaffected sibling, the family should be included in the SSC (the sibling exception rule can be applied for these families as well). The full protocol for the proband should be completed on both twins. Use the last page of the SSC Diagnosis Summary Form to indicate that the proband is the identical twin of another proband who has been included in the SSC. SFARI Researcher Welcome Packet Page 7

8 Available Instruments by Family Role Table Note: Protocol modifications are sometimes made to accommodate new and/or changed instruments; not all instruments are available for all participants. Aberrant Behavior Checklist (ABC) Autism Diagnostic Interview (ADI-R) Instrument/Activity Parents Probands Unaffected Siblings Autism Diagnostic Observation Schedule (ADOS) Brief family physical and dysmorphology examination Broad Autism Phenotype Questionnaire (BAPQ) Child Behavior Checklist (CBCL) OR Adult Behavior Checklist (ABCL) Cognitive Testing Developmental Coordination Disorder Questionnaire (DCDQ) Diagnosis Summary Form Interviewer s Clinical Impressions (completed by clinician) Non-Word Repetition Task (CTOPP) Parent Substance Use History Form Peabody Picture Vocabulary Test 4 th Edition (PPVT-4) Purdue Peg Board Raven s Standard Progressive Matrices Repetitive Behavior Scale - Revised (RBS-R) Social Communication Questionnaire (SCQ) - Parent report Social Communication Questionnaire (SCQ) - Teacher report Social Responsiveness Scale Adult Research Version Social Responsiveness Scale (SRS) Parent report Social Responsiveness Scale (SRS) Teacher report SSC Background History Form SSC Family Pedigree Form SSC Medical History Interview SSC Treatment History Form Teacher Report Form (TRF), OR Caregiver-Teacher Report Form (C-TRF) Vineland Adaptive Behavior Scale-II (VABS-II) SFARI Researcher Welcome Packet Page 8

9 SSC Instrument Details The following list provides detailed information on all mandatory and optional instruments used in the SSC. Mandatory Instruments ABC (Aberrant Behavior Checklist, Community Edition) Measure of: Aberrant Behaviors Format: Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: Parent Regarding Whom: Proband Publisher: Slosson ABCL (Adult Behavior Checklist for Ages 19 to 59) Measure of: Problem Behavior Format: Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: Parent Regarding Whom: Siblings 19 years and older Publisher: ASEBA ADI-R (Autism Diagnostic Interview Revised) Measure of: Parent Report of Behaviors Related to Autism Phenotype Format: Direct Interview Administered When: Stage 5.2 SSC Research Evaluation Administered by: Examiner who has achieved research levels of ADI-R reliability according to SSC standards Administered to: Parent Regarding Whom: Proband Publisher: WPS ADOS (Autism Diagnostic Observational Schedule) Measure of: Observational Measure of Autism Phenotype Format: Direct Examiner Observation Administered When: Stage 5.3 SSC Research Evaluation SFARI Researcher Welcome Packet Page 9

10 Administered by: Examiner who has achieved research levels of ADOS reliability according to SSC standards Administered to: Proband Publisher: WPS BAPQ (Broad Autism Phenotype Questionnaire) Measure of: Broader Autism Phenotype Format: Self-Report Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: Mother and Father Regarding: Self Publisher: Piven CBCL (Child Behavior Checklist for ages 1 1/2 to 5) Measure of: Problem Behavior Format: Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: Parent Regarding: Probands (age 4-5); and Siblings (ages 1 year 6 months to 5 years, 11 months and under). Publisher: ASEBA CBCL (Child Behavior Checklist for ages 6 to 18) Measure of: Problem Behavior Format: Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: Parent Regarding: Proband and Siblings who are between 6 and 18 years old Publisher: ASEBA CTOPP-NR (Comprehensive Test of Phonological Processing: Non-word Repetition Subtest) Measure of: Speech and Memory of Sounds and Non-words Format: Direct Assessment Administered When: Stage 5.3 SSC Research Evaluation Administered by: Clinical / Research Staff Administered to: Probands with a Verbal Mental Age of 60 months. Publisher: PRO-ED SFARI Researcher Welcome Packet Page 10

11 C-TRF (Caregiver-Teacher Report Form for ages 1 1/2 to 5 years) Measure of: Problem Behavior Format: Questionnaire Administered When: Stage 3.2 Included in Teacher Questionnaire Packet Completed by: Teacher/Daycare provider Most Knowledgeable Regarding: Siblings Between 1 year 6 months and 5 years, 11 Months of Age and Probands between 4 years and 5 years, 11 Months Publisher: ASEBA DAS-II (Differential Ability Scales, 2nd Edition) Measure of: Cognitive Ability Format: Direct Assessment Administered When: Stage 5.3 SSC Research Evaluation Administered by: Clinical / Research Staff Administered to: Proband ages 4 to 17yrs 11mos Publisher: Harcourt Assessments Developmental Coordination Disorder Questionnaire Measure of: motor delays Format: Questionnaire Administered When: Stage 3.1 Parent Questionnaire Packet Completed by: Parents Regarding: Proband Author: Wilson FHI-I (IMGSAC Interviewer s Impressions) Measure of: Broader Phenotype Format: Rating Administered When: Stage 5.2 Following ADI-R Interview at the SSC Research Evaluation Completed by: ADI-R Examiner Regarding Whom: Mother and Father, if both were present for interview Publisher: IMGSAC Mullen (Mullen Scales of Early Learning, AGS Edition) Measure of: Cognitive Ability Format: Direct Assessment Administered When: Stage 5.3 SSC Research Evaluation Administered by: Clinical / Research Staff SFARI Researcher Welcome Packet Page 11

12 Administered to: Proband Publisher: Pearson Assessments Parent Substance Use Form Format: Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: both Parents Regarding: Self Publisher: SSC PPVT-4 (Peabody Picture Vocabulary Test 4th Edition) Measure of: Receptive Single Word Vocabulary Format: Direct Assessment Administered When: Stage 5.3 SSC Research Evaluation Administered by: Clinical / Research Staff Administered to: Proband Publisher: NCS Pearson, INC. Purdue Pegboard Measure of: Fine Motor Dexterity Format: Direct Assessment Administered When: Stage 5.3 SSC Research Evaluation Administered by: Clinical / Research Staff Administered to: Proband Publisher: Lafayette Instrument Co. RBS-R (Repetitive Behavior Scale Revised) Measure of: Repetitive Behaviors Format: Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: Parents Regarding Whom: Proband Publisher: Bodfish SSC-Background History Form Index of: Contact Information, Family Demographic Information; Parent Report of Proband s Developmental Milestones Format: Phone Interview Administered When: Stage 3.1 Included in Parent Questionnaire Packet SFARI Researcher Welcome Packet Page 12

13 Completed by: Parent Regarding: Family and Proband Publisher: SSC SSC-Diagnosis (SSC Diagnosis Summary Form) Index of: DSM-IV-TR Diagnoses; Diagnostic Certainty; Clinicians Involved in Making Diagnosis; Deviation IQ, Ratio IQ, and Mental Age scores; Information potentially critical to the evaluation (e.g., undiagnosed problems in parents and siblings). Format: Form Administered When: Stage 5.4 Following SSC Research Evaluation Completed by: Observing senior Psychologist/Psychiatrist with Clinical / Research Staff Regarding Whom: Proband Publisher: SSC SSC-HWHC (Height, Weight, Head Circumference Form) Measure of: Physical Characteristics Format: Direct Assessment Administered When: Stage 5.1 SSC Research Evaluation Administered by: Physician or Clinical / Research Staff Administered to: Mother, Father, Proband, & Siblings SSC-MHI (SSC Medical History Interview) Measure of: Family Medical History Format: Telephone Interview Administered When: Stage 4 Parent Phone Interview following return of Parent Questionnaire Packet Administered by: Clinical / Research Staff Administered to: Parent Regarding Whom: Proband s Immediate and Extended Family Publisher: SSC SSC-Pedigree (SSC Pedigree Form) Publisher: SSC Measure of: Phenotype of Ancestry Format: Phone Interview Administered When: Stage 4 Parent Phone Interview following return of Parent Questionnaire Packet Administered by: Clinical / Research Staff Subject: Immediate and Extended Family of Proband SFARI Researcher Welcome Packet Page 13

14 Informant: Parent SSC-THF (SSC Treatment History Form) Measure: Past participation in therapeutic treatments Format: Phone Interview Administered When: Stage 4 Parent Phone Interview prior to Research Evaluation. Subject: Proband Informant: Parent Format: Interview Publisher: SSC SCQ (Social Communication Questionnaire Lifetime, and Social Communication Questionnaire-Current) Measure of: Screen of ASD markers Format: Questionnaire Administered When: Stages 3.1 and 3.2 Included in Parent Questionnaire Packet (SCQ-L) and Teacher Questionnaire Packet (SCQ-C) Completed by: Parents and Teachers Regarding Whom: Parents report on probands (age 4 years to 17 years, 11 months) and siblings (age 4 and up) using Lifetime form. Teachers report on probands age 4 years to 17 years, 11 months and siblings age 4 and up using Current form. Publisher: WPS SRS (Social Responsiveness Scale) Measure of: Autistic traits on a continuous scale Format: Questionnaire Administered When: Stages 3.1 and 3.2 Included in both Parent and Teacher Questionnaire Packets Completed by: Parents and Teachers Regarding Whom: Parents report on probands (age 4 years to 17 years, 11 months) and siblings (age 4 to 18 years). Teachers report on siblings (age 4 to 18 years) and probands (age 4 years to 17 years, 11 months). Publisher: WPS SRS-ARV (Social Responsiveness Scale Adult Research Version) Measure of: Autistic traits on a continuous scale Format: Questionnaire Administered When: Stage 3.1 Included in Parent Questionnaire Packet Completed by: Parents SFARI Researcher Welcome Packet Page 14

15 Regarding Whom: Mother reports on father; Father reports on Mother; Parent reports on adult sibling ages 19 and up Publisher: WPS TRF (Teacher Report Form for ages 6 to 18 years) Measure of: Problem Behavior and School Functioning Format: Questionnaire Administered When: Stage 3.2 Included in Teacher Questionnaire Packet Completed by: Teacher Most Knowledgeable about sibling Regarding Whom: Siblings age 6 to 18 and Probands age 6 years to 17 years 11 months Vineland-II (Vineland Adaptive Behavior Scales, Second Edition Survey Interview Form) Measure of: Adaptive Behavior Format: Interview Administered When: Stage 4 Parent Phone Interview regarding siblings and Stage 5.2 Parent Interview about proband following ADI-R at SSC Research Evaluation. Administered by: Clinical / Research Staff Administered to: Parents Regarding Whom: Probands (age 4 years to 17 years, 11 months) and Siblings. Publisher: Pearson Assessments WASI (Wechsler Abbreviated Scale of Intelligence) Measure of: Cognitive Ability Format: Direct Assessment Administered When: Stage 5.3 SSC Research Evaluation Administered by: Clinical / Research Staff Administered to: Proband ages 9 to Publisher: Harcourt Assessments WISC-IV (Wechsler Intelligence Scale for Children, Fourth Edition) Measure of: Cognitive Ability Format: Direct Assessment Administered When: Stage 5.3 SSC Research Evaluation Administered by: Clinical / Research Staff Administered to: Proband ages 9 to Publisher: Harcourt Assessments SFARI Researcher Welcome Packet Page 15

16 Optional Instruments Autism Dysmorphology Measure (Miles) Measure of: physical anomalies Format: Direct Physical Exam Administered When: Stage 5.1 Physical Exam Administered by: Medical/Clinical staff Administered to: Proband Author: Judith Miles FHI Subject (IMGSAC Family History Interview Subject) Measure of: Broader Phenotype Format: Interview Administered to: Parent Regarding Whom: Self Publisher: IMGSAC FHI Informant (IMGSAC Family History Interview Informant) Measure of: Broader Phenotype Format: Interview Administered to: Parent Regarding Whom: Spouse Publisher: IMGSAC Raven s (Raven s Coloured or Standard Progressive Matrices) Measure of: Non-verbal problem solving Format: Direct Assessment Administered by: Clinical / Research Staff Administered to: Proband Publisher: Harcourt Assessments SFARI Researcher Welcome Packet Page 16

17 Available Biospecimens DNA WB DNA Derived from whole blood. This is the preferred DNA source for epigenomics studies (for example, methylation), as well as some genome-wide scans. It is, however, a limited resource (yields are typically in the range of μg per 10 ml blood, depending on white cell count), and requests will be carefully evaluated for their scientific merit and the imperative of using WB DNA. LCL (CP) DNA Derived from a cell pellet of a Lymphocyte Cell Line (LCL). A renewable resource, LCLs can be regrown upon depletion of DNA stocks, and typically yield between μg DNA in a single extraction. This is an excellent source of DNA for most PCR-based analyses. SPIT DNA Derived from Saliva. The lowest quality genomic DNA is extracted from saliva. It is available in cases where normal means of collection (whole blood) are not feasible. Yields are generally poor (1-100 μg), and availability for distribution is subject to the same criteria as whole blood DNA samples. Potentially useful in PCR assays, it is generally not advisable to use saliva DNA in sequencing or epigenomics studies. Cells Lymphocyte Cell Lines (LCL) Can be requested as fresh (actively growing cultures shipped in growth medium) or frozen (glass ampoules of frozen cells are shipped on dry ice). Plasma Aliquots (200 μl) of plasma isolated from whole blood are shipped frozen (in 2D barcoded tubes) on dry ice. SFARI Researcher Welcome Packet Page 17

18 Prerequisites for Access to SFARI Base Answers to Frequently Asked Questions are available ion n the Researcher Welcome Packet. Please direct specific inquiries about obtaining access to the Research Liaison. Required Institutional Documents Please note that each principal investigator (PI) who wishes to conduct one or more research projects using SFARI data and/or materials must obtain the following from their institution before applying: 1. A signed Researcher Distribution Agreement (RDA) for the PI and any collaborators (see Appendix A). The RDA specifies the legal issues pertaining to research data and specimens, and requires approval from the PI's institution. A separate RDA is required for each collaborator. 2. A letter from an Institutional Review Board (IRB). Each SFARI project led by a PI must be governed by a protocol approved or exempted by an IRB. A protocol specifies the regulatory issues pertaining to the research, and may include co-investigators at multiple institutions. You will need to obtain a PDF copy of the letter from your IRB approving or exempting your protocol. Prerequisite Application Instructions 1. sdownload, sign, and mail all RDAs to the Simons Foundation: ATTN: Research Liaison Simons Foundation 160 Fifth Avenue, 7th Floor New York, NY Obtain a PDF version of the letter(s) from your IRB approving or exempting your protocol(s). SFARI Researcher Welcome Packet Page 18

19 Online SFARI Application Instructions Note: These instructions are always available online at Step 1 : Sign Up for SFARI Base 1.1 Log into SFARI Base Direct your browser to Your screen will display the form shown below. If you already have a SFARI Base OpenID, enter your Username (or ) and password in the designated fields to sign in. If you do not have an SFARI Base Open ID, move on to step 1.2 to learn how to obtain one. Note: Firefox browser is required. Click here for the free download. 1.2 Create a SFARI Base Account OpenID is a popular emerging standard for user authentication, which is quickly replacing conventional Usernames and Passwords. With your new SFARI Base OpenID, you will be able to access all SFARI resources. To get started, follow the steps outlined below. 1. Click "Create Account" (The link resides on the tab adjacent to Sign In). 2. Create a Username and password. Make sure to check the box at the bottom of page to confirm that you will comply with Simons Policty. SFARI Researcher Welcome Packet Page 19

20 If you are unable to duplicate the CAPTCHA, use the refresh icon, (available in the CAPTCHA dialog box) to generate a new set of words. 3. Click the "Create Account button at the bottom of the form. A confirmation will be sent to the address you have provided. 4. Click continue to proceed to SFARI Base. If you received an invitation to SFARI Base, and you were subsequently redirected to obtain a SFARI Base account, return to the original link to proceed. Copy and paste the link from the original into your browser. Otherwise, you will be directed to the SFARI Base Lab Management Wizard Homescreen. SFARI Researcher Welcome Packet Page 20

21 Step 2 : Declare your Institutional Affiliation 2.1. Navigating SFARI Base If you have successfully completed each of these steps, you are now logged into SFARI Base. Use the links on the Home Screen to navigate SFARI Base. For additional resources and information, click the Help Resources button. Click on Get Started to start your Application for Data and Biospecimens Join or Create A Lab 1. If you don t currently have a lab affiliation you will be redirected to Join or Create a Lab. You can also navigate to this screen using the Join or Create Lab button on the Lab Management Home Page. 2. Review the list of institutions available in the left-hand pane. If someone has already created an account for your lab, then select the lab and and click Join Lab. An will automatically be sent to current lab members to approve your request to join the lab. SFARI Researcher Welcome Packet Page 21

22 3. If you do not see your institutional affiliation, click Create New Lab. A form will appear. 4. Enter your Lab s information, including the address of the Principal Investigator. An will be sent to your PI with instructions to confirm their position in the newly created Lab. Upload a PDF version of your RDA. If it is not readily available at the lab s creation, you may select to Edit Lab Info and upload the agreement at your next visit to SFARI Base. 5. Click Save to store your Lab s Information. A Simons Reviewer will be notified once the PI has confirmed your Lab Manage Lab Membership 6. You may invite additional lab members at this time. Click on the link to affiliate other researchers with your lab. All invitees will have access to Research Projects and Requests submitted for your Lab Return to the Lab Membership screen by clicking on the Manage Lab Membership button available on the Lab Management Home. You can accept pending member requests, as well as remove current members. SFARI Researcher Welcome Packet Page 22

23 7. When the Affiliate Researchers with this Lab dialog box appears, enter the addresses for researchers that you would like to have access to all projects for your lab. Use commas to separate the addresses. 8. Click Send Invites to send notifications to future lab members. Once a member has an accepted an invite to affiliate with your lab, they will be listed in the Current Members pane on the Lab Membership screen. Step 3 : Submit Applications for Data and Biospecimens SFARI Researcher Welcome Packet Page 23

24 3.1. Create A Project 1. Navigate to your Lab Management home and click on the Request SFARI Data or Biospecimens button. For your first login,your Project List will contain no projects. Once you have created a project, it will be displayed here. 2. To add a project, simply click the Create New Project button. 3. Enter the title of your project, the abstract, and your IRB status. Upload a copy of your IRB letter for review by the Simons Foundation. (You will be notified when it is time to renew your IRB.) 4. Click Save View/Edit A Project 1. You may wish to view or edit project details. From the Project List, hi-light and click on the project that you wish to view. You will arrive at the Phenotype and Biospecimen Request List for the project you selected. 2. The "View/Edit Project" button is In the top right-hand corner. Click on it. The Project form will appear. SFARI Researcher Welcome Packet Page 24

25 3. Update your Project information, and click Save to store your changes. You may choose to log out if you do not wish to immediately add collaborators or requests. Your project will remain saved, and will appear on the Project List upon your next login. For instructions about how to Log out of SFARI Base, move on to Step Add Project Collaborators You can invite researchers outside of your Lab to view a single project and its related data and biospecimen requests. If you have been invited to collaborate on a project, you can see it by clicking on the Collaboration button, available on the Homescreen. 1. From the Project List, hi-light and click on the project that you wish to view. You will arrive at the Phenotype and Biospecimen Request List for the project you selected. 2. The "Manage Collaborators for this Project" button is In the top right-hand corner. Click on it. The Project Collaborator Management screen will appear. 3. Click Invite to add collaborators to the project. notifications will be sent Add Requests SFARI Researcher Welcome Packet Page 25

26 1. To submit a new request for a project, simply select a Project from your Project List. You will arrive at the Phenotype and Biospecimen Request List for the project you selected. 2. Click "Create New Request". A Request form will appear 3. Select your Request Type When you make a choice, the form will expand with further questions, specific to the type of request that you ve chosen. 4. Click Save. A dialog box will appear, giving you the option to either submit your Request for Simons Review immediately, or store the details for edits to be made at a later visit. 5. Click Yes to submit the request to the SSC now, or click No, Save and Keep Working. You can repeat the Add a Request process as many times as needed. Each will remain saved in your account until you choose to remove them What if I want both Phenotype Data and Biospecimens? You can request biospecimen and phenotype data for the same project. Simply add a separate request for each. 1. If you would like to request more than one type of biospecimen, please fill out a separate request for each type; phenotype requests can be combined. Complete the request form (refer to the example images below) SFARI Researcher Welcome Packet Page 26

27 Phenotype Example: SFARI Researcher Welcome Packet Page 27

28 Biospecimen Example: SFARI Researcher Welcome Packet Page 28

29 Step 4 : Logging Out of SFARI Base 4.1. Ending Your Session Once you've finished adding your project and requests, you must logout of SFARI Base. To log out, click the Logout button, indicated by the red arrow in the screenshot below. For specific questions not addressed in the Help documentation, support-ordering@prometheusresearch.com SFARI Researcher Welcome Packet Page 29

30 Appendix A : Researcher Distribution Agreement Researcher Distribution Agreement

31 Appendix B : Simons Simplex Collection IRB Simons Simplex Collection IRB

32 Appendix C : Sample SSC Consent Form Sample SSC Consent Form