Archived | The AGRE Program FAQs | Circa April 2004 #NotAnAutisticAlly #AutisticHistory


AGRE Frequently Asked Questions

What is AGRE?

How do I gain access to AGRE?

How do I order biomaterials from AGRE?

How do I select biomaterials

Are AGRE samples free?

What kinds of Biomaterials does AGRE distribute?

What kind of data does AGRE collect and distribute?

Is AGRE affiliated with the NIMH?

How do I download phenotypic data?

Iím lost! Who do I contact for help?


Q: What is AGRE?


A: The Autism Genetic Resource Exchange (AGRE) was created by Cure Autism Now (CAN) to advance genetic research in autism spectrum disorders. Genetic biomaterials and clinical data are obtained from families that have more than one family member diagnosed with an Autism Spectrum Disorder. The biological samples, along with the accompanying clinical data, are made available to AGRE-approved researchers.

Q: How do I gain access to AGRE?


A: There are three critical steps required to gain access to the AGRE database:

1) Complete the online AGRE Access Application. 
2) Print, complete, and sign the AGRE Researcher Distribution Agreement. 
3) Mail or FAX the AGRE Researcher Distribution Agreement along with a copy of the Principal Investigator’s IRB approval or exemption to AGRE at the address or FAX number below. 

Vlad Kustanovich, Ph.D.
Researcher Liaison 
Autism Genetic Resource Exchange 
Cure Autism Now 
5455 Wilshire Blvd., Suite 715,
Los Angeles, CA 90036-4234
FAX: 323-931-1977

Once your application has been received at our office, the AGRE researcher review committee will review your application. All applications are reviewed no more than 2 weeks from the date submitted. If your application is approved, you will receive a letter welcoming you to AGRE and providing you with a username and password. This will allow you to access the data posted on the AGRE website immediately. 

Q: How do I order biomaterials from AGRE?


A: After your application has been approved and you have been granted your username and password, you may download a pedigree catalog file (in Excel format) containing a listing of families, their relationships and their sample identification numbers. 

Please download the AGRE Biomaterials Online Order Form from the AGRE website. Then fill out the Form according to the instructions given within, save a copy to your computer and email it to the AGRE Researcher Liaison. Please call the Researcher Liaison for pricing information (based on Academic or Commercial Pricing). Please FAX an approved purchase order for the samples.

Q: How do I select biomaterials?


A: It is important to look through the data and make sure that all the data that you are interested in can be found in the pedigrees of interest.

AGRE collects phenotypic data in a tier-wise fashion, based on the availability of the family to be scheduled for an appointment. While AGRE will only distribute pedigrees with validated ADI-R diagnoses, sample distribution may precede collection of other data. 

AGRE has created a Flags list which identifies families in the collection with atypical characteristics that may make them questionable for certain genetic studies (ex. Families with a known Fragile X mutation). Therefore, it is important to identify selection criteria before purchasing biomaterials.

Q: Are AGRE samples free?


A: No. Sample acquisition, processing, and distribution are expensive processes, and we pass on a fraction of these costs to researchers.

AGRE charges researchers a per sample fee for the acquisition of samples. Our prices are very competitive with other gene banks. For pricing information, please contact the Researcher Liaison.

Q: What kinds of Biomaterials does AGRE distribute?

A: AGRE distributes DNA, Cell line and Serum samples. Please note that serum samples are NOT available for every family in the AGRE repository. Please contact the Researcher Liaison for sample availability.

Q: What kind of data does AGRE collect and distribute?


A: AGRE collects the Autism Diagnostic Interview Ė Revised (ADI-R) on each of the reported affected individuals.

In addition, affected individuals are assessed with the Autism Diagnostic Observational Scales (ADOS). Over time, we aim to collect a set of cognitive exams including the Raven Progressive Matrices, the Vineland and the PPVT. Many families are also scheduled for physician visits during which time we collect medical histories on the parents, affected, and unaffected children. In addition, Physical and Neurological Exam data is also collected during the physician visit.

While AGRE aims to eventually collect all data for all subjects in the study, pedigrees are distributed before the entire process of data collection has been completed. Therefore, it is important to choose pedigrees for your study based on the specific criteria of your study as well as the availability of the necessary data. 

Q: Is AGRE affiliated with the NIMH?

A: Yes. AGRE is serving as a collection site for the NIMH Genetics Initiative.

All samples collected by AGRE are placed in the NIMH repository. Samples contributed by AGRE can be found by referencing Site numbers 72 and 74.

Q: How do I download phenotypic data?


A: We have a step-by-step instructional guide on our website to walk researchers through the process that can be accessed by clicking here

Q: Iím lost! Who do I contact for help?


A: Please contact the Researcher Liaison toll free at 866-612-2473 x31 for assistance.


Screenshot of Order form page.

Biomaterials Order Application

BIOMATERIALS ORDER APPLICATION
Please fill out the contact information below.
Then click on the AGRE Order Worksheet tab and fill
out the worksheet according to the example below.
Save the file and email the completed file to the Researcher Liaison,
vlad@agre.org.
In addition, please FAX a copy of your Purchase Order.
Customer (Shipping Address)
Name
Company
Address
City
Country
Phone
FAX
Email
Customer (Billing Address)
Name
Company
Address
City
Country
Phone
FAX
Email
Purchase Order #
Sample Order Worksheet:
Family CodeIndividual CodeBlood IDResearcher NameCellsDNASerumDate
AU0005AU000501HI0576Gregor Mendel1112/4/03
AU0005AU000502HI0577Gregor Mendel1112/4/03
AU0005AU000503HI0578Gregor Mendel11212/4/03
AU0005AU000504HI0579Gregor Mendel11212/4/03

Autism Genetic Resource Exchange
5455 Wilshire Blvd., Suite 2250
Los Angeles, CA  90036
Phone: 323-931-6577
Fax: 323-931-1977
Email: vlad@agre.org


Screenshot of AGRE webpage. 2004

Researcher Liason

Please take the AGRE Researcher Survey

AGRE provides biomaterials and an unprecedented resource of phenotype and genotype information that is freely available for analysis by members of the scientific community.
obtain access

AGRE Frequently Asked Questions
Answers to commmon questions about AGRE.

ISAAC User Guide:
A step-by-step guide for downloading phenotype data from ISAAC.

GENOTYPE DATA:
Whole Genome Scan data and Finemapping data on 356families.

PHENOTYPE DATA: 
ADI-R, ADOS, Raven, and Handedness testing results with all interview data points and computer scored algorithm results are available for download.
Medical histories, Physical Neurological exam data, Peabody scores, and Vineland scores are also available. 

PAPERS CITING AGRE CONSORTIUM 
AGRE participants may also be interested in the Autism Tissue Program.


AGRE Researcher Survey


APPLYING FOR ACCESS TO AGRE DATA AND BIOMATERIALS


In order to gain access to online AGRE phenotypic and genotypic data, as well as to order biomaterials (DNA, cell lines and serum*), please complete the following steps:

1) Fill out the AGRE Access Application online 
2) Print, fill out and sign the AGRE Researcher Distribution Agreement.
3) Mail or FAX the AGRE Researcher Distribution Agreement along with a copy of the Principal Investigator’s IRB approval or exemption to AGRE at the address or FAX number below.

Please note that AGRE requires that the Principal Investigator obtain IRB approval or exemption and sign the AGRE Researcher Agreement in order to gain access to the AGRE sample set. 

Access the Biomaterials Online Order Form or the Data Download Area if you have already submitted your AGRE Access Application and Biomaterials Application and have received your user code. 

* Please Note: Serum samples are NOT available for every family in the AGRE repository. Please contact the Researcher Liaison for sample availability.


Screenshot of sign-in page to AGRE

Download Data Area

Access to AGRE Genotypic and Phenotypic data requires a user name and password. Please use the AGRE Access Application to obtain your account.

Authentication Required 

This area is accessible only to registered users



ISAAC User Guide

GUIDE FOR DOWNLOADING PHENOTYPIC DATA

  1. Access the AGRE website by going to http://www.agre.org using a web browser.
  2. Click on the link for “Phenotype Data.”
  3. You will be directed to the AGRE data center and prompted to enter your username and password.
    After these have been entered, click on the submit button.
  4. Once
    a. PHENOTYPIC DATA DOWNLOAD AND ANALYSES
    b. DESCRIPTION OF ASSESSMENTS
    c. FAMILY PEDIGREE STRUCTURES
    d. GENOTYPIC DATA DOWNLOAD, INFORMATION AND ANALYSES
    e. CANDIDATE GENES, LOCI AND SPECIAL ANALYSES
    f. AGRE RESEARCHER NEWS, REPORTS, DATA ANALYSES
    g. AGRE DATA KEYS
  5. To access ISAAC, either:
    a. Click on the “P” , or
    b. Click on the “Go” link next to PHENOTYPIC DATA DOWNLOAD, AND ANALYSES
    You will be redirected to the “PHENOTYPIC DATA DOWNLOAD AND INFORMATION.”page.
    c. Scroll down and click on the ISAAC icon. A new web browser window will be launched, which serves as the ISAAC portal and Maximize window.
  6. Click on “View Download List” and this will display a listing of all data available for download from ISAAC.
    in the AGRE Data Center, you will be presented with the following options:
  7. On the right hand side of the webpage, a list of the phenotype exams will be displayed. You may alter the default setting for the number of columns included in a single table at this time. The default setting will divide a large exam table, such as the ADIR, into two smaller tables so that programs such as Microsoft Excel which have limitations on the number of columns allowed may open the tables.
    In order to have all the date exported into a single file, change the maximum number of columns to include in each file from 250 to 999. In order to download the data for a particular exam, click on the “Download This Data” link. Another small browser window will be launched to initialize the data set. Once the dataset has been compiled, the window will display a hyperlink describing the specific data set. Click on the hyperlink (i.e. the name of exam), and you will be prompted to “Open” or “Save” the data set to a local place on your computer.
  8. Open the file, which is in tab delimited text format (but appended with .XLS to make the file opened by Microsoft Excel). Each record in the Excel spreadsheet represents data for one subject, and each column is an item on a questionnaire or other exam. Each record is indexed by the Individual Code of the subject, which consists of the AU family ID and the pedigree ID.
  9. In case the number of maximum columns was not adjusted a second spreadsheet for a given exam indicates that there were too many columns (data points) per subject. In this case, the second Excel spreadsheet (ex. ADIR2.xls) will not contain the Individual Code of the patient but will contain a linking number called PatientRecordID which links it to the first table. This allows one to put the tables side by side.
  10. Exam and item descriptions are provided in the codebooks for each individual exam. You can click on “View This Form’s Codebook” from the main ISAAC page. A new web browser window will be launched with ISAAC at the top, and it will show the Variable Name (e.g. the name at the top of the column for that form’s data), the Question Text (e.g. the question asked or the exam done), the Response Type (ex. Text, Dropdown, Numeric Range), and the Selection List (e.g. value definitions).
  11. While many of the column headings will be self-explanatory, some data sets will require a detailed understanding of the instruments. A starter with hyperlinks for further information is available on the AGRE website by entering the AGRE Data Center and clicking on the “Go” link next to “DESCRIPTION OF ASSESSMENTS”.


[Note: links to to Internet Archive of PMID]

PAPERS CITING AGRE CONSORTIUM

Gharani N, Benayed R, Mancuso V, Brzustowicz LM, Millonig JH.
Association of the homeobox transcription factor, ENGRAILED 2, 3, with autism spectrum disorder. 
Mol Psychiatry. 2004 Mar 16 :1-11 [Epub ahead of print]
PMID:15024396

Conciatori M, Stodgell CJ, Hyman SL, O’Bara M, Militerni R, Bravaccio C, Trillo S, Montecchi F, Schneider C, Melmed R, Elia M, Crawford L, Spence SJ, Muscarella L, Guarnieri V, D’Agruma L, Quattrone A, Zelante L, Rabinowitz D, Pascucci T, Puglisi-Allegra S, Reichelt KL, Rodier PM, Persico AM. 
Association between the HOXA1 A218G polymorphism and increased head circumference in patients with autism. 
Biol Psychiatry. 2004 Feb 15;55(4):413-9. 
PMID:14960295

Nabi R, Serajee FJ, Chugani DC, Zhong H, Huq AH. 
Association of tryptophan 2,3 dioxygenase gene polymorphism with autism. 
Am J Med Genet. 2004 Feb 15;125B(1):63-8. 
PMID:14755447

Raiford KL, Shao Y, Allen IC, Martin ER, Menold MM, Wright HH, Abramson RK, Worley G, DeLong GR, Vance JM, Cuccaro ML, Gilbert JR, Pericak-Vance MA. 
No association between the APOE gene and autism.
Am J Med Genet. 2004 Feb 15;125B(1):57-60. 
PMID:14755445

Vincent JB, Thevarkunnel S, Kolozsvari D, Paterson AD, Roberts W, Scherer SW. 
Association and transmission analysis of the FMR1 IVS10 + 14C-T variant in autism.
Am J Med Genet. 2004 Feb 15;125B(1):54-6. 
PMID:14755444

Buxbaum JD, Silverman J, Keddache M, Smith CJ, Hollander E, Ramoz N, Reichert JG. 
Linkage analysis for autism in a subset families with obsessive-compulsive behaviors: Evidence for an autism susceptibility gene on chromosome 1 and further support for susceptibility genes on chromosome 6 and 19. 
Mol Psychiatry. 2004 Feb;9(2):144-150. 
PMID:14699429

Serajee FJ, Nabi R, Zhong H, Mahbubul Huq AH. 
Association of INPP1, PIK3CG, and TSC2 gene variants with autistic disorder: implications for phosphatidylinositol signalling in autism.
J Med Genet. 2003 Nov;40(11):e119. 
PMID:14627686

Yonan AL, Alarcon M, Cheng R, Magnusson PK, Spence SJ, Palmer AA, Grunn A, Juo SH, Terwilliger JD, Liu J, Cantor RM, Geschwind DH, Gilliam TC. 
A genomewide screen of 345 families for autism-susceptibility loci. Am J Hum Genet. 2003 Oct;73(4):886-97. Epub 2003 Sep 17. 
PMID:13680528

Yonan AL, Palmer AA, Smith KC, Feldman I, Lee HK, Yonan JM, Fischer SG, Pavlidis P, Gilliam TC.  Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction.
Genes Brain Behav. 2003 Oct;2(5):303-20. 
PMID:14606695

Nabi R, Zhong H, Serajee FJ, Huq AH. 
No association between single nucleotide polymorphisms in DLX6 and Piccolo genes at 7q21-q22 and autism. 
Am J Med Genet 2003 May 15;119B(1):98-101. 
PMID:12525552

Serajee FJ, Zhong H, Nabi R, Huq AH. 
The metabotropic glutamate receptor 8 gene at 7q31: partial duplication and possible association with autism. 
J Med Genet 2003 Apr;40(4):e42. 
PMID:12676915

Cisternas FA, Vincent JB, Scherer SW, Ray PN. 
Cloning and characterization of human CADPS and CADPS2, new members of the Ca(2+)-dependent activator for secretion protein family. 
Genomics 2003 Mar;81(3):279-91. 
PMID:12659812

Weiss LA, Escayg A, Kearney JA, Trudeau M, MacDonald BT, Mori M, Reichert J, Buxbaum JD, Meisler MH. Sodium channels SCN1A, SCN2A and SCN3A in familial autism.
Mol Psychiatry 2003 Feb;8(2):186-94. 
PMID:12610651

Zhong H, Serajee FJ, Nabi R, Huq AH. 
No association between the EN2 gene and autistic disorder. 
J Med Genet 2003 Jan;40(1):e4. 
PMID:12525552

Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M, Scherer SW. 
The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a complex multi-transcript system.
Genomics 2002 Sep;80(3):283-94. 
PMID:12213198

Yamagata T, Aradhya S, Mori M, Inoue K, Momoi MY, Nelson DL. 
The human secretin gene: fine structure in 11p15.5 and sequence variation in patients with autism. 
Genomics 2002 Aug;80(2):185-94. 
PMID:12160732

Torres AR, Maciulis A, Stubbs EG, Cutler A, Odell D. 
The transmission disequilibrium test suggests that HLA-DR4 and DR13 are linked to autism spectrum disorder.
Hum Immunol 2002 Apr;63(4):311-6. 
PMID:12039413

Fatemi SH. 
The role of Reelin in pathology of autism.
Mol Psychiatry 2002;7(9):919-20. PMID:12399938

Zhang H, Liu X, Zhang C, Mundo E, Macciardi F, Grayson DR, Guidotti AR, Holden JJ. 
Reelin gene alleles and susceptibility to autism spectrum disorders.
Mol Psychiatry 2002;7(9):1012-7. 
PMID:12399956

Xu ASL, Papadaes S, Knapp D, Gooch R, Walker SJ, Breese G. 
ProteinChip(r) SELDI-TOF MS technology: a novel proteomics tool for biomarker discovery. 


2002 North Carolina Tissue Engineering Meeting.Silverman JM, Smith CJ, Schmeidler J, Hollander E, Lawlor BA, Fitzgerald M, Buxbaum JD, Delaney K, Galvin P; Autism Genetic Research Exchange Consortium. 
Symptom domains in autism and related conditions: evidence for familiality. 
Am J Med Genet 2002 Jan 8;114(1):64-73 
PMID:11840508

Alarcon M, Cantor RM, Liu J, Gilliam TC, Geschwind DH; Autism Genetic Research Exchange Consortium. 
Evidence for a language quantitative trait locus on chromosome 7q in multiplex autism families. 
Am J Hum Genet 2002 Jan;70(1):60-71 
PMID:11741194

Greenberg DA, Hodge SE, Sowinski J, Nicoll D. 
Excess of twins among affected sibling pairs with autism: implications for the etiology of autism. 
Am J Hum Genet 2001 Nov;69(5):1062-7 
PMID:11590546

Cheung J, Petek E, Nakabayashi K, Tsui LC, Vincent JB, Scherer SW 
Identification of the human cortactin-binding protein-2 gene from the autism candidate region at 7q31. 
Genomics. 2001 Nov; 78(1-2):7-11. 
PMID:11707066

Asano E, Kuivaniemi H, Huq AH, Tromp G, Behen M, Rothermel R, Herron J, Chugani DC. 
A study of novel polymorphisms in the upstream region of vasoactive intestinal peptide receptor type 2 gene in autism.
J Child Neurol 2001 May;16(5):357-63 
PMID:11392521

Buxbaum JD, Silverman JM, Smith CJ, Kilifarski M, Reichert J, Hollander E, Lawlor BA, Fitzgerald M, Greenberg DA, Davis KL.  
Evidence for a susceptibility gene for autism on chromosome 2 and for genetic heterogeneity.
Am J Hum Genet 2001 Jun;68(6):1514-20. 
PMID:11353400

Zhong N, Ye L, Ju W, Brown WT, Tsiouris J, Cohen I. 
5-HTTLPR variants not associated with autistic spectrum disorders. Neurogenetics 1999 Apr;2(2):129-31. 
PMID:10369890

   

contact AGRE webmaster

   Autism Genetic Resource Exchange
   Cure Autism Now
   5455 Wilshire Blvd., Suite 715, 
   Los Angeles, CA 90036-4234 
   1-323-931-6577
   fax:1-323-549-0547

   email info@agre.org

   hosting by Accu-Find Internet Services
   made possible by a donation from Network Appliance, Inc.


More With AGRE



Note/Warning:

Autistic people have fought the inclusion of ABA in therapy for us since before Autism Speaks, and other non-Autistic-led autism organizations, started lobbying legislation to get it covered by insurances and Medicaid. 

ABA is a myth originally sold to parents that it would keep their Autistic child out of an institution. Today, parents are told that with early intervention therapy their child will either be less Autistic or no longer Autistic by elementary school, and can be mainstreamed in typical education classes. ABA is very expensive to pay out of pocket. Essentially, Autism Speaks has justified the big price tag up front will offset the overall burden on resources for an Autistic’s lifetime. The recommendation for this therapy is 40 hours a week for children and toddlers.

The original study that showed the success rate of ABA to be at 50% has never been replicated. In fact, the study of ABA by United States Department of Defense was denounced as a failure. Not just once, but multiple times. Simply stated: ABA doesn’t workIn study after repeated study: ABA (conversion therapy) doesn’t work. 

What more recent studies do show: Autistics who experienced ABA therapy are at high risk to develop PTSD and other lifelong trauma-related conditions. Historically, the autism organizations promoting ABA as a cure or solution have silenced Autistic advocates’ opposition. ABA is also known as gay conversion therapy.


The ‘cure’ for Autistics not born yet is the prevention of birth. 

The ‘cure’ is a choice to terminate a pregnancy based on ‘autism risk.’ The cure is abortion. This is the same ‘cure’ society has for Down Syndrome. 

This is eugenics 2021. Instead of killing Autistics and disabled children in gas chambers or ‘mercy killings’ like in Aktion T4, it’ll happen at the doctor’s office, quietly, one Autistic baby at a time. Different approaches yes, but still eugenics and the extinction of an entire minority group of people.


Fact: You can’t cure Autistics from being Autistic.

Fact: You can’t recover an Autistic from being Autistic.

Fact: You can groom an Autistic to mask and hide their traits. Somewhat. … however, this comes at the expense of the Autistic child, promotes Autistic Burnout (this should not be confused with typical burnout, Autistic Burnout can kill Autistics), and places the Autistic child at high risk for PTSD and other lifelong trauma-related conditions.


[Note: Autism is NOT a disease, but a neurodevelopmental difference and disability.]


Fact: Vaccines Do Not Cause Autism.


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