Archived | Autism Speaks: Autism Genome Project (AGP) | Circa 2004 #NotAnAutisticAlly

Autism Genome Project

Launched in 2004, the Autism Genome Project, or AGP, is the largest study ever conducted to find the genes associated with inherited risk for autism.

Many of the world’s leading genetics researchers pooled their resources and used a promising new technology, the DNA microarray, to scan the human genome in the search for the genetic causes of this devastating disorder, which continue to elude the medical field as prevalence rises.

The project is a public/private research partnership involving approximately 50 academic and research institutions that have pooled their DNA samples in a collaborative effort.

It is designed to enable doctors to biologically diagnose autism and enable researchers to develop universal medical treatments and a cure.

The first phase of the project, a research partnership with the National Institutes of Health, consist ed of two scans of the human genome searching for autism susceptibility genes.

The scans analyzed DNA samples from nearly 1, 200 families.

Phase 2 will expand on the results of the first phase and allow researchers to confirm or deny the role of genes previously identified as possibly harboring autism susceptibility genes.

Click here to learn about results from the first phase of the project.

Click here for a guide to understanding the initial findings of the project.

Click here to find out about phase two of the project.

Click here to read a 2004 release about the launch of the project.



Visit the Autism Genome Project site here. (Below)

Notes: Links from this point on link to the web archives on way back machine.

Home >


AGP
The Autism Genome Project
“Investigating the genetic basis of autism”

The Autism Genome Project (AGP)

1. Background

The AGP is a large-scale, collaborative genetics research project that aims to identify the genetic factors underlying autism.

The AGP consortium brings together researchers from over 50 centres in the USAEurope, and Canada.

AGP members have published more than 200 peer-reviewed manuscripts on autism since 2003.

An initial AGP research project (AGP Phase 1) was completed in 2007 (see: media reports and publications).

A second AGP project (AGP Phase 2) is currently ongoing and will be finalised in 2010. Initial results will be published in late 2009.

Initiated by the National Alliance for Autism Research, NAAR – now Autism Speaks – the AGP is funded by international, private and public partners (see funders).

2. Investigating the genetics of autism

Autism is a complex genetic disorder

This means that the identification of autism risk factors requires large samples of well characterised individuals, and strong scientific cooperation between clinical and laboratory researchers.

The AGP was initiated to pool resources, and clinical and scientific expertise. 

The clinicians and scientists participating in the AGP embody the phenotypic, statistical, molecular, and functional expertise needed to define the genetic architecture of autism.

3. Acknowledgement

The AGP would like to acknowledge and thank all the individuals with autism, and their families, who have contributed to this project. 

NEW!! We recommend: Books on autism for the general public



About the AGP:

1. Background

The Autism Genome Project (AGP) is a large-scale, collaborative genetics research project that aims to identify autism susceptibility genes.

The genetic architecture of autism is undoubtedly complex

This means that the identification of autism risk factors requires large samples of well characterised individuals, and strong scientific cooperation between clinical and laboratory researchers. 

The AGP consortium was initiated to pool resources, and clinical and scientific expertise. 

The clinicians and scientists participating in the AGP embody the phenotypic, statistical, molecular, and functional expertise needed to define the genetic architecture of autism. 

AGP members have published more than 200 peer-reviewed manuscripts on autism since 2003. 

An initial project – AGP Phase 1 – was completed in 2007. A second research project – AGP Phase 2 – was finalised in 2010. The AGP is currently seeking funding for a third project – AGP Phase 3.

Initiated by the National Alliance for Autism Research, NAAR – nowAutism Speaks – the AGP is funded by international, private and public partners. (See: AGP Funders). 

The AGP brings together researchers from centres in Europe, Canada and the USA. (See: AGP members).

2. The AGP Phase 1 project (2004-7):

The first phase of the Autism Genome Project – AGP Phase 1 – was successfully concluded in early 2007. (See: Times article, other media reports and publications.)

AGP Phase 1 was jointly led by two centres at the University of Oxford: Professor Anthony Monaco, from the Wellcome Trust Centre for Human Genetics, and Professor Anthony Bailey, from theDepartment of Psychiatry.

Scientists from over 50 research centres worked together on the project. (See: AGP Phase 1 members)

The main funder for AGP Phase 1 was Autism Speaks (formerly the National Alliance for Autism Research, NAAR).

In this first phase, the AGP achieved its initial goal of assembling the world’s largest gene bank for autism.

This was the most comprehensive database of autism families at the time, including both multiplex families (families with at least two affected individuals) and simplex families (one affected individual plus both parents). 

The AGP also achieved its goal of carrying out the world’s mostcomprehensive genome scan into the genetics of autism (further details below).

The main research findings were published in 2007. (See AGP publications).

Further details on this research HERE

See also: More on our research techniques

3. The AGP Phase 2 project (2007-2010):

The second phase of the Autism Genome Project (AGP Phase 2) was launched in April 2007. The project funding period ended in December 2010.

The AGP Phase 2 project was led by Professor Anthony Monaco from Oxford University. It received funding of $16 million over three years – from international, private and public partners. (See AGP Funders).

This project aimed to identify meaningful common and rare genetic variants that are associated with Autism Spectrum Disorders (ASD) including copy number variations. (see above). 

It benefited from the extensive and growing gene bank of autism families established by the AGP, which includes both multiplex and simplex families (see above)

The initial research findings were published in leading journals in 2010. (See AGP publications). Further findings will be published in 2011.

For further details on this research, see: Phase 2 research plan

See also: More on our research techniques

4. The AGP Phase 3 project (2011-):

In January 2011, the AGP received further funding to support its core Consortium activities only.

The AGP is currently seeking funding for a new Phase 3 project (ongoing).

5. Further details:

For more information about the work of the AGP, please contact:

Penny Farrar, AGP Project Manager: penny.farrar@gmail.com

Note: if you are seeking information on how to be included in an AGP study, please include details of your location, so that we can refer you to the nearest AGP site. Please note, however, that the AGP, as a Consortium, currently does not have funding to recruit any new families or carry out any further autism studies. 


AGP Research: Current Project

1. AGP Phase 2 project (2007-):

Publications:

CLICK HERE

Project research plan

The main aim of this three-year project was to genotype a new sample of over 3,000 AGP families (simplex and multiplex families) on the Illumina 1M beadchip, which enables the genotyping of over one million SNPs in each sample. 

In the first stage of the Phase 2 project – Stage 1

  • Over 1,500 AGP families were genotyped 
  • Subsequently, association, linkage and CNV analyses were performed.
  • The results from this study were published in 2010.

In the second project stage – Stage 2

  • A second sample of over 1,500 AGP families weregenotyped.
  • Subsequently, association, linkage and CNV analyses were performed for the complete Phase 2 sample-set (over 3,000 trios)..
  • The results from this study are now being finalised and will be submitted for publication in 2010.

In addition, analyses of AGP phenotypic data were also completed:

  • AGP sites uploaded phenotype data for the complete AGP sample-set (over 7,500 families). This includes the following data: ADI, ADOS, IQ, Vinelands, Body Measurements and Family Type.
  • Collaborating AGP sites conducted a number of analyses of this data.
  • A number of new publications are published / anticipated, based on these findings

See also:

2. AGP Phase 1 project (2004-2007):

CLICK HERE


AGP Research: Phase 1 Project

1. Current project: AGP Phase 2 (2007-):

CLICK HERE

2. AGP Phase 1 project (2004-2007):

2.1 Background

The first AGP project (Phase 1) was successfully concluded in early 2007.

In this first phase, the AGP achieved its initial goal of assembling the world’s largest gene bank for autism at this time.

This was also most comprehensive database of autism families, including both multiplex families (families with at least two affected individuals) and simplex families (one affected individual plus both parents). 

The AGP also achieved its goal of carrying out the world’s most comprehensive genome scan into the genetics of autism at this time (see AGP publications).

2.2 Who did we study?

The AGP assembled a sample of over 1,400 multiplex families, with two or more individuals affected by Autism Spectrum Disorders (ASDs).

Extensive phenotypic information was gathered on the individuals in each family, including the following data:

DNA and phenotypic information from the families included in the AGP sample was collected by researchers from a large number of centres collaborating in the project.

2.3 How did we work?

Autism susceptibility loci have been identified on a number of chromosomal regions (including 2q, 7q and 17q). 

Moreover, substantial evidence suggests that chromosomal abnormalities also contribute to autism risk.

According to the AGP model, autism risk is influenced by combinations of multiple loci that possibly interact, as well as microscopic or sub-microscopic chromosomal abnormalities.

This complicates the detection of individual autism risk loci and means that multiple strategies are required to localise autism susceptibility loci.

The AGP study was the first to attempt to merge linkage analysiswith studies of fine-level chromosomal variation. (See: research techniques).

The AGP also developed an approach to identify sub-microscopiccopy number variations (CNVs) as potential risk loci and as a tool to stratify the samples, in order to reduce genetic heterogeneity for linkage analyses.

A large sample of multiplex families was necessary to increase the likelihood of detecting susceptibility loci.

First, a complete-genome scan was carried out for the sample of over 1,400 multiplex families, using Affymetrix 10K v2 SNP arrays (10,000 SNPs). 

linkage analysis was then performed. This was the largest linkage scan to date for individuals with ASD.

Finally, a CNV analysis was performed to assess the CNV content of the samples. An algorithm was used to infer copy number from signal intensity of a SNP genotype, relative to intensity from other samples.

2.4 Our main research findings

See: AGP publications

Of the chromosomal regions that have been featured prominently in previous linkage analyses, the AGP study found only modest linkage support for regions 2q and 7q, and did not find support for region 17q. 

However, the study did find evidence for linkage in the chromosomal region 11p12–p13, which had not previously been a major focus for discovery of autism risk loci. The linkage analyses also found support for linkage on regions 5p and 9p.

It is known that risk for ASD can in small part be attributed to chromosomal copy number abnormalities (CNAs). 

The families in the AGP study were pre-screened for CNAs. However, the CNV analyses revealed evidence that relevant CNVs may also be a risk factor for autism.

Among a number of interesting discoveries, of particular note was the mizygous deletion of coding exons from the NRXN1 gene (2p16.3), whwhich was detected for a pair of affected siblings. 

Other studies have also found rare variants of this gene in individuals with ASD. Moreover, this gene interacts with neuroligins, for which rare mutations appear to generate risk for ASDs and mental retardation.

There seems, therefore, to be accumulating evidence for a role for neurexins and neuroligins in ASDs. [See: neuroligin-3 (NLGN3) and neuroligin-4 (NLGN4) ].


AGP Research: Publications

1. Main AGP Publications:

Phase 1 Project:

  1. Mapping autism risk loci using genetic linkage and chromosomal rearrangements. 
    The Autism Genome Project Consortium. 
    Nature Genetics 39319 – 328. Published online: 18 February 2007.
    [PubMed record] [abstract]
     
  2. Genome-wide Linkage Analyses of Quantitative and Categorical Autism Subphenotypes. 
    Liu X.Q., Paterson A.D., Szatmari P., The Autism Genome Project Consortium.
    Biological Psychiatry 2008 Jul 15. Epub ahead of print.[PubMed record] [Full article (pdf)] 

Phase 2 Project:

  1. Functional impact of global rare copy number variation in autism spectrum disorders.
    Dalila Pinto, Alistair T. Pagnamenta, Lambertus Klei, Richard Anney, et al.
    Nature, 466, pp.368-372, 15 July 2010. [PubMed record] [Full article (pdf)]
  2. A genome-wide scan for common alleles affecting risk for autism.
    Anney R, Klei L, Pinto D, Regan R, Conroy J, Magalhaes TR, et al.
    Human Molecular Genetics, 2010 Aug 16. [PubMed record][Full article (pdf)]

2. Publications acknowledging the AGP:

CLICK HERE

3. AGP Presentations and posters:

CLICK HERE


AGP Research: Research Techniques

On this page:

  1. Genome sequencing
  2. Complete genome scans
  3. Linkage analyses
  4. Association analyses
  5. CNV analyses

1. Genome sequencing

The DNA that is in each our cells is a double-stranded molecule arranged in a “double helix” structure. It is made up of an estimated 3.2 billion base pairs.

DNA is usually obtained from an individual by drawing a blood sample or by rubbing a cotton swab along the inside of the mouth to harvest cells.

Genome sequencing is the process whereby researchers “read” the specific order of DNA bases (nucleotides) that make up the individual’s DNA.  (More here: on genome sequencing)

An entire human genome was sequenced for the first time in 2003. (More here:on the Human Genome Project).

However, to sequence an individual’s entire genome is extremely costly and time-consuming. 

More often, researchers use genome sequencing to “read” smaller sections of an individual’s DNA, such as individual genes or parts of a gene (also referred to as gene mapping).

See also:

2. Complete genome scans

For complex genetic disorders such as autism, complete genome scans are an invaluable tool for researchers seeking out susceptibility genes – namely, genes that increase the likelihood of an individual being affected by that disorder.

It is now estimated that, for two unrelated, healthy individuals, about 99.8% of their DNA will be the same. 

Of the remaining genetic differences between individuals:  

Single base-pair changes in the DNA – are also known as single nucleotide polymorphisms, or SNPs – are estimated to contribute ~84%.

Structural variations of the genome – including CNVs (see section 5 below) – are estimated to contribute ~16%

There are an estimated 10 million SNPs that occur commonly in the human genome. (More here: on SNPs). The International HapMap Project aims to to identify and catalogue most of these SNPs. 

SNPs can be used as genetic markers, to indicate which version of a gene (allele) an individual carries on his or her DNA, at a given location along a chromosome.

These genetic markers can be thought of as signposts, each ‘marking’ a particular section of a chromosome, and providing clues to the section of chromosome where a susceptibility gene may possibly reside.

The testing of which specific alleles have been inherited by an individual is called genotyping. 

Rather than sequencing entire sections of a genome, genotyping can be carried out by testing selected SNPs at points along the genome. 

This is because groups of SNPs that are located near to each other on a chromosome are inherited in blocks (haplotypes). (More here: on tag SNPs.)

In a given sample of human DNA, it is now feasible for researchers to genotype many thousands of SNPs, across all 23 pairs of chromosomes a process referred to as a complete genome scan(or whole-genome scan).

In recent years, significant technological advances have allowed researchers to carry out genotyping ever more rapidly and cheaply. (More here: on Microarray Technology).

For example, the AGP is currently using the Illumina 1M beadchip to genotype over 1 million SNPs in samples of DNA from children affected with autism.

Complete-genome scans are used by researchers to track down the specific locations (loci) on the chromosome where there are differences between individuals affected by a certain disease or disorder and those who are unaffected.

DNA samples are collected from two groups of participants: people affected by the disorder being studied and similar people who are unaffected. The samples are then genotyped for selected genetic markers (SNPs).

Genome-wide association analyses and/or linkage analysescan then be carried out (see below).

3. Linkage analyses

Linkage can be defined as the tendency for genes or sections of DNA positioned near to each other on a chromosome to be inherited together.

Linkage analyses aim to discover the regions in which the DNA from the relatives of people affected by a particular disease or disorder is more similar than would be expected by chance.

The idea behind this is that, if affected individuals from the same family share identical versions of genes leading to the disorder, then these genes are located in regions of increased similarity – in other words, they are linked to the disorder.

By testing a set of genetic markers (or haplotype), researchers can infer the gene(s) that may be linked to the disorder. (More here: onlinkage analyses.)

Researchers will typically use a large number of genetic markers to test a sample of families consisting of two or more siblings affected with the disorder (sib pairs), plus both parents.

Statistical analysis will be used to identify haplotypes (or markers),of interest. If particular haplotypes are found to be inherited more often that would be expected by chance, then these loci are said to be in linkage disequilibrium.

Usually, a calculated LOD score (LOD = log of the odds) is used to evaluate whether a particular chromosomal region is linked with the disorder. Typically, a LOD score of more than 3 will be taken as proof of strong linkage.

Researchers often conduct a whole-genome linkage scan as a first step to identifying susceptibility genes for complex diseases.

Once linkage regions have been identified, a fine-mapping can then be carried out to narrow down the search and identify potential susceptibility genes.

Finally, candidate-gene evaluation can be used to identify the specific gene(s) associated with the disorder. (A candidate gene is a gene that encodes a protein that is thought might be responsible for the disorder).

TThere are two main kinds of linkage analysis:

Parametric linkage analysis is used to investigate single-gene disorders, where the parameters of the analysis (for example, mode of inheritance, penetrance) are clear.

Non-parametric linkage analysis is used for complex genetic disorders, where a number of different genes are implicated and the parameters of the analysis are therefore much less clear. Quantitative trait locus (QTL) mapping is one type of non-parametric linkage analysis.

4. Association Analyses

If certain genetic variations are found to be significantly more frequent in people affected by a certain disease or disorder than in those who are unaffected (controls), the variations are said to be associated with the disorder.For complex genetic disorders, such as autism, where a large number of different genes confer risk, association analyses have more power than linkage analyses. 

Association analyses are now typically performed using a large sample of affected individuals and controls, and testing with a significant number of genetic markers (SNPs). 

Association studies may compare either affected and non-affected members within a family (family-based association studies), or affected individuals with unaffected individuals who are not family members (case-control association studies).

An advantage of association analyses over linkage analyses is that it can be used for families where only one child is affected with the disorder in question.

Once identified, associated genetic variations can serve as powerful pointers to the region of the human genome where the disease-causing problem resides. 

However, the associated variants themselves may not directly cause the disease. They may just be ‘tagging along’ with the actual causal variants. 

For this reason, researchers often need to take additional steps to identify the exact genetic change involved in the disease, such as genotyping that particular region of the genome with additional markers, or carrying out sequencing (see abve)

5. CNV analyses

In addition to single base-pair changes in the DNA (see section 2 above), structural genetic variations are also important for understanding complex disorders.

One source of structural genetic variation that researchers are increasingly focusing on is Copy Number Variations (CNVs)

CNVs involve deletions or duplications of large chunks of DNA: from thousands to millions of DNA bases. CNVs in a DNA sample can be calculated from the results of complete-genome scans (see above) using microarray technology.

The Wellcome Trust Sanger Institute has recently established a CNV Project database, with the aim to gain a better understanding of the role of CNVs in genetic disorders.


AGP Research: Genetic disorders

1. Basic Genetics

Every cell in our body contains over 6 metres of a molecule known as DeoxyriboNucleic Acid (DNA)

DNA is packaged into small structures known as chromosomes. Our chromosomes are arranged within the cell as 22 pairs (called autosomes) and two sex chromosomes (X and Y). Males have one X and one Y sex chromosome, whereas females have two X chromosomes.

Together these 46 chromosomes carry all of the information necessary for you to live, grow and function. They are often referred to as the genetic blueprint. (See also: Figure 1 Word document).

In total our chromosomes contain approximately 30,000 genespasted together end to end. A gene is defined as a small length of a chromosome which contains all the instructions needed to make a single protein.

Everybody’s genes are slightly different and it is this genetic variation that makes you the way you are. For example, some people have genes for brown eyes, some for blue eyes; some people have genes which make them tall, some people have genes which make them short. 

Your individual combination of genes determines what you will look like and, to a certain extent, your chances of developing common illnesses, such as heart disease.

The DNA in our cells is a double-stranded molecule arranged in the well-known “double helix” structure. Each of the two DNA strands is made up of four chemical bases (or nucleotides): adenine (A) and guanine (G), cytosine (C) and thymine (T). 

The two DNA strands are connected to each other by chemical pairing of each base on one strand, to a specific partner on the other strand: adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C). These A-T and G-C pairings are referred to as base pairs. The DNA in each our cells is made up of an estimated 3.2 billion base pairs.

2. Inheritance

Of our 46 chromosomes, we inherit 23 from our mother and 23 from our father. The chromosome which is passed on from each parent is randomly chosen and this is what generates differences in our children. 

With 23 pairs of chromosomes, the number of possible combinations of chromosomes which can be passed onto our children is 223 –which is 8,388,608. So the chances of our children being genetically identical would therefore be 1 in 8,388,608.

But the variation does not stop there. During the production of eggs and sperm, our chromosomes become entangled with each other and can cross over, swapping parts of genetic material between chromosome pairs. This means that even cells with the same array of chromosomes will vary slightly, and that children actually inherit a mixture of both of your chromosomes from each pair. 

Because this crossing over of chromosomes occurs in a random manner the number of combinations of chromosomes in sperms and eggs is infinite and the chances of any child inheriting exactly the same chromosomes is therefore billions to one. 

The one exception to this is identical twins. These arise from the division of a fertilised egg early during pregnancy to form two genetically identical babies.

3. Single gene (Mendelian) disorders

Some diseases are caused by mutations in a single gene. For these disorders the pattern of genetic inheritance is clear and we are able to predict the chances of having another child with the same disorder. 

If you inherit one or two copies of the mutated gene then you develop the disorder. If you inherit two good copies of a gene you do not develop the disorder.

There are different patterns of inheritance depending on whether the gene with the mutations lies on an autosome (one of the 22 pairs of chromosomes) or one of the sex chromosomes (X and Y).

For genes found on an autosome

If only one copy of the mutated gene is required for an individual to be affected, inheritance is termed autosomal dominant.

If both copies of the mutated gene are required, then inheritance is termed autosomal recessive. Huntington’s disease is an example of an autosomal dominant disorder. (See Figure 3 , Word document)

For genes found on a sex chromosome

If only one copy of the mutated gene is required for an individual to be affected, inheritance is termed X-linked dominant (if on the X chromosome) or Y-linked recessive (if on the Y chromosome).

If both copies of the mutated gene are required for an individual to be affected, inheritance is termed X-linked recessive or Y-linked recessive

4. Complex genetic disorders

Other disorders do not appear to be inherited as a single gene disorder. Instead they may be caused by a number of different genes which combine and interact with environmental factors to produce an overall risk factor for developing the disorder. This is known as a complex disorder. 

Autism is one example of a complex disorder. 

A trait is complex at the genetic level if it does not display a classical Mendelian inheritance pattern that can be attributed to a single locus.

Unlike single-gene disorders, complex diseases are often not caused by mutations that disrupt genes, but rather by normal variations within genes

Everybody’s genes are slightly different and it is this variation which determines what you will look like and to a certain extent, your chances of developing heart disease or other common illnesses.


AGP Funders: current project

The AGP is currently supported by the following main funders:


AGP Links: More on autism

On this page:
1. Further information on autism: 
1.1 Books on autism 
1.2 General autism websites

 

1. Further information on autism – for the general public:

1.1 Books on autism

Autism Speaks recommendations:

Autism Speaks USA recently, asked their Facebook community, “What books about autism do you think are most helpful for newly diagnosed families?”. They received nearly 300 responses. For further details: CLICK HERE

AGP recommendations:

Our researchers recommend the following books on autism (listed in alphabetical order):

In English:

  • Atwood, T.  Asperger’s Syndrome: A Guide for Parents and Professionals.  Jessica Kingsley, 1998.
  • Bellini, S. Building social relationships: A systematic approach to teaching social interaction skills to children and adolescents with autism spectrum disorders and other social difficulties. Autism Asperger, 2008.
  • Faherty, C. Asperger’s… What Does it Mean to Me?  Future Horizons, Inc., 2005
  • Grandin, T.  Thinking in Pictures and Other Reports from My Life with Autism.  Doublday, 1995.
  • Harris, S.  Right from the Start: Behavioral Intervention for Young People with Autism.  A Guide for Parents and Professionals. Woodbine House, 1998
  • Gillberg, Christopher. A Guide to Asperger  Syndrome. Cambridge, CUP.
  • Gillberg, Christopher and Coleman, Mary. The Biology of the Autistic  Syndromes. Cambridge, CUP. 
  • Jacobson, J.,  Foxx, R., & Mulick, J. (2005). Controversial therapies for developmental disabilities: Fad, fashion and science in professional practice. Lawrence Erlbaum Associates, 2005
  • McClannahan, L. Activity Schedules for Children with Autism.  Woodbine House, 1999.
  • Ozonoff, S., Dawson, G., & McPartland, J. A parent’s guide to Asperger syndrome and high-functioning autism: How to meet the challenges and help your child thrive. Guilford Press, 2002
  • Powers, Michael D.  Children with Autism.  A Parent’s Guide.  Woodbine House, 2000.
  • Quill, K. Do-Watch-Listen-Say: Social and Communication Intervention for Children with Autism. Paul H. Brookes, 2000.
  • Siegel, B.  The World of the Autistic Child.  Oxford Press, 1996.  
  • Szatmari, Peter. A Mind Apart: Understanding Children with Autism and Asperger Syndrome. Guilford Press; ISBN-10: 1572305444; ISBN-13: 978-1572305441 [Link to Amazon]
  • Volkmar, Fred R. and Wiesner, Lisa A. A Practical Guide to Autism: What Every Parent, Family Member, and Teacher Needs to Know. August 2009. [Link to Barnes and Noble]

In Swedish:

  • Gillberg, Christopher. Aspergers syndrome. Stockhom, Cura.
  • Gillberg, Christopher. Autism. Stockholm, Natur och Kultur.

In German:

  • Freitag, Christine. Autismus-Spektrum-Störungen. Reinhardt-Verlag, 2008.
  • Poustka, Fritz; Bölte, Sven; Schmötzer, Gabriele; and Feineis-Matthews, Sabine , Autistische Störungen, Göttingen: Hogrefe, 2008.
1.2 General autism websites

In the UK:

In the USA:

  • Autism Speaks: the world’s largest autism advocacy organisation. Merged with the National Alliance for Autism Research (NAAR) in 2006.
  • Cure Autism Now: an organisation of parents, clinicians and leading scientists committed to accelerating the pace of biomedical research in autism through raising money for research projects, education and outreach. (To merge with Autism Speaks by 2008).
  • The Nancy Lurie Marks NLM) Family Foundation: aims to help people with autism lead fulfilling and rewarding lives.
  • Interactive Autism network (IAN): aims to facilitate research that will lead to advancements in the prevention, treatment, and cure of autism spectrum disorders.
  • Autism Today: the largest online autism resource.
  • ICARE4autism: international centre for autism and research.

In Canada:

  • CAIRN: Canadian Autism intervention Research Network.

2. Other useful links – autism research:

CLICK HERE


AGP Links: Autism research

On this page:
2. Information on autism research
3. Resources on understanding genetics
4. Information for scientists

 

1. General information on autism:

CLICK HERE

2. Information on autism research:

Autism research consortia:

  • International Molecular Genetic Study of Autism Consortium (IMGSAC): is an international autism consortium that includes scientific researchers and clinicians from a number of European countries, as well as from Canada and the United States. IMGSAC aims to identify the genes involved in susceptibility to autism, and to understand the relationship of these genes to clinical outcome, in order to provide better intervention for autistic individuals and their families. 
  • The Autism Genetic Resource Exchange Consortium (AGRE): is a DNA repository and family registry, housing a database of genotypic and phenotypic information for ASD that is available to the entire scientific community. The collection currently includes more than 800 multiplex and simplex families. 
  • Autism Genetics Cooperative: includes researchers on autism from institutions in the USA, Canada, France, Ireland and Sweden.
  • The Collaborative Programs of Excellence in Autism (CPEA): conducts research to learn about the possible causes of autism, including genetics, immunological, and environmental factors, as well as diagnosis, early detection, behavioral and communications characteristics, and treatment of autism. Established in 1997 by the National Institute of Child Health and Human Development (NICHD) and the National Institute on Deafness and Other Communications Disorders (NIDCD) , the CPEAs are part of the international Network on the Neurobiology and Genetics of Autism. 

Autism research projects

  • TASC project: the Autism Simplex Collection: is a project related to the AGP and running concurrently. It is funded byAutism Speaks (AS) and aims to gather medical information and genetic material, or DNA, from individuals who seem to have autism, as well as from their parents, and if available and willing, their brothers and sisters.
  • Simons Simplex Collection: The primary goal of the SSC is to establish a permanent repository of genetic samples from 2000 families, each of which has one child affected with an Autism Spectrum Disorder (ASD) and parents unaffected with ASD. Each genetic sample will have an associated collection of data that provides a precise characterization of the individual (phenotype). Rigorous phenotyping will maximize the value of the resource for a wide variety of future research projects into the causes and mechanisms of autism.
  • The Autism Tissue Program The Autism Tissue Program (ATP) was established: 1) to promote national awareness of the importance of brain tissue donation for the purpose of autism biomedical research; 2) to maintain a central database of registrants and available tissue; 3) to review requests for tissue and distribute tissue through its Tissue Advisory Board (TAB); 4) to promote information exchange among researchers through the TAB; and 5) to inform the autism community of research progress and findings. 
  • The Collaborative Linkage Study of Autism (CLSA)Project: aims to identify autism susceptibility genes for the purpose of improving diagnosis and treatment for ASD. Funded by the National Institute of Mental Health (NIMH). Principal Investigator: Susan Folstein, MD, Tufts University.
  • The Autism Language Project: aims to identify autism susceptibility genes. Also focuses on the study of language characteristics in individuals with ASD and their family members. Project conducted in collaboration with researchers from the University of Iowa and Boston University, and funded by the National Institute of Neurological Disorders and Stroke (NINDS). Principal Investigators: Susan Folstein, MD, Helen Tager-Flusberg, PhD, J. Bruce Tomblin, PhD.
  • The Discordant Sibling Project: seeks to identify potential autism susceptibility genes by studying individuals with autism and their unaffected siblings. Funded by the March of Dimes. Principal Investigator: Susan Santangelo, ScD.

3. Resources on understanding genetics:

The below table provides links for selected external websites on understanding genetics:

WebsiteArticle / Resource
Wellcome TrustInteractive sites:
(1) Chromosome browser: Find out more about the genes within each chromosome in the human genome, and; (2) Zoom in on your genome: Journey into the body to see where the genome is found
Glossary
National Center for Biotechnology Information (NCBI)What is a cell?
What is a genome?
Molecular Genetics: Piecing it together
Genome News Network (GNN)What’s a genome?
Gene ReviewsIllustrated Glossary
National Human Genome Research Institute (NHGRI)Talking glossary of genetic terms
List of other glossaries of genome / human genetics terms
Human Genome ProjectHuman Genome Project: Information

The below table lists relevant articles from scientific publications, (accessible free of charge) on understanding genetics:

JournalTitle
Nature GeneticsArticle on CNVs:
Major changes in our DNA lead to major changes in our thinking

The following are useful reference books on understanding genetics: 

  • A Dictionary of Genetics, Seventh Edition, R. King, W. D Stansfield, P. K. Mulligan, OUP, 2006.
  • Medical Genetics, I.D. Young, OUP, 2005.

4. Information for scientists:

Information on autism:

For a useful overview of genetic strategies in the search for autism susceptibility genes: 

For useful overviews on the genetics of autism and the current state of genetic research (journal articles: not open access):

  • Lamb, Parr, Bailey and Monaco (2002). “Autism: In search of susceptibility genes”. Neuromolecular Medicine 2: 55-72.[PubMed record]
  • Folstein and Rosen-Sheidley (2001). Genetics of autism: complex aetiology for a heterogeneous disorder”. Nat Rev Genet 2(12):943-955. [Med record] (not open access).
  • Muhle R, Trentacoste SV, Rapin I. “The genetics of autism. Pediatrics”. 2004 May;113(5) [Med record]
  • “Autism’s cause may reside in abnormalities at the Synapse”[News Focus in Science]

Research websites:

Diagnostic protocols:


AGP Members:

The AGP is a “consortium of consortia”. It brings together researchers from over 50 centres in the USAEurope, and Canada.

1. AGP Consortia

The AGP brings together the following four international research consortia on autism: 

2. Current AGP members – Phase 2 project (2007-):

The AGP Phase 2 project brings together over 100 researchers, including 32 Principal Investigators, from over 50 research centres across the USA, Europe and Canada:

3. Members of the AGP Phase 1 project (2004-7):


AGP Members: Current project (Phase 2)

The AGP is a “consortium of consortia”. It brings together researchers from over 50 centres in the USAEurope, and Canada.

1. List of current AGP Members (Phase 2 project): 

1.1 AGP Principal Investigators

CLICK HERE

1.2 COMPLETE LIST of All AGP members

CLICK HERE

1.3 List of AGP sites:
CountryInstitutionDepartment
a)USA
USAAutism SpeaksThe Autism Genetic Resource Exchange Consortium (AGRE)
University of California – Los Angeles (UCLA), School of Medicine, Los Angeles, California.Department of Human Genetics
Department of Neurology
The Children’s Hospital of Philadelphia (CHOP).The Center for Applied Genomics, Division of Human Genetics 
University of Illinois at Chicago (UIC), Chicago, Illinois.Institute for Juvenile Research,Department of Psychiatry
Indiana University School of Medicine, Indianapolis.Department of Psychiatry
University of Iowa, Iowa City, Iowa.Carver College of Medicine, Department of Pediatrics and Howard Hughes Medical Institute 
Carver College of Medicine, Department of Psychiatry
The Research Institute at Nationwide Children’s Hospitaland The Ohio State University, Columbus, Ohio.Battelle Center for Mathematical Medicine
University of Miami, Miami, Florida.John P. Hussman Institute for Human Genomics, Miami Institute for Human Genomics (MIHG)
University of Michigan, Ann Arbor, Michigan.Autism and Communicative Disorders Centre
Mount Sinai School of Medicine (MSSM), New York.The Seaver Autism Center for Research and Treatment, Department of Psychiatry
University of North Carolina (UNC), Chapel Hill, North Carolina.Department of. Psychiatry
University of Pennsylvania, Pennsylvania.Pathology and Laboratory Medicine
School of Medicine, Department of Pediatrics
University of Pittsburgh, Pittsburgh, Pennsylvania.School of Medicine
Stanford University School of Medicine, Stanford, California.Child and Adolescent Psychiatry and Child Development
University of Utah, Salt Lake City, Utah. Department of Psychiatry, University of Utah Medical School
Vanderbilt University, Nashville, Tennessee.Vanderbilt University Medical Centre, Center for Human Genetics Research (CHGR)
Department of Molecular Physiology and Biophysics
Vanderbilt Kennedy Center
 Centers for Human Genetics Research and Molecular Neuroscience
Yale University, New Haven, Connecticut.Child Study Centre
University of Washington, Seattle, Washington.Depts. of Psychology and Psychiatry
Department of Biostatistics and Medicine
Department of Medicine
b)Canada
CANADAUniversity of Alberta, Edmonton, Alberta.Department of Pediatrics
Dalhousie University, Halifax, Nova Scotia.Department of Pediatrics and Psychology
McGill University, Montreal, Quebec.Division of Psychiatry
McMaster University, Hamilton, Ontario.Department of Pediatrics
Department of Psychiatry and Behavioural Neurosciences
Memorial University of Newfoundland, St. John’s Newfoundland.Discipline of Genetics
Discipline of Medicine
University of Toronto, Toronto.The Hospital for Sick Children (CHOP) and Department of Molecular Genetics, The Centre for Applied Genomics (TCAG)and Program in Genetics and Genomic Biology
The Hospital for Sick Children (CHOP) and Bloorview Kids Rehabilitation, Autism Research Unit
c)Europe
FRANCEGroupe hospitalier Henri Mondor-Albert Chenevier, AP-HP, Créteil.INSERM U9595, Department of Psychiatry
Université Pierre et Marie Curie, ParisINSERM U952
University de Toulouse Le Miral, Toulouse.Centre d’Eudes et de Recherches en Psychopathologie
GERMANYGerman Cancer Research Center (DKFZ), Heidelberg.Division of Molecular Genome Analysis
J. W. Goethe University Frankfurt, Frankfurt.Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
GREECEAgia Sophia Children’s Hospital, Athens.University Department of Child Psychiatry, Athens University, Medical School
IRELANDTrinity College Dublin (TCD),Dublin.Autism Genetics Group, Department of Psychiatry, School of Medicine
University College Dublin (TCD), Dublin.School of Medicine Medical Science
ITALYUniversity of Bologna, BolognaDepartment of Biology
Stella Maris Institute for Child and Adolescent Neuropsychiatry, Pisa.   
SWEDENGoteborg University, Goteborg.Department of Child and Adolescent Psychiatry
THE NETHERLANDSUniversity Medical Center, Utrecht, The NetherlandsDepartment of Child Psychiatry
PORTUGALInstituto Nacional de Saude Dr Ricardo Jorge and Instituto Gulbenkian de Cîencia Lisbon, Lisbon 
Hospital Pediatrico de Coimbra, Coimbra 
UKBooth Hall of Children’s Hospital, Blackley, Manchester.Academic Department of Child Psychiatry
Guy’s Hospital, LondonNewcomen Centre
Institute of Psychiatry (IoP), London.Department of Child and Adolescent Psychiatry
Social, Genetic and Developmental Psychiatry Centre, 
University of Manchester, Manchester.Centre for Integrated Genomic Medical Research,
Department of Medicine, School of Epidemiology and Health Science.
Centre for Integrated Genomic Medical Research (CIGMR)
University of Newcastle, Sir James Spence Institute, Newcastle upon Tyne.Child and Adolescent Mental Health,
University of Oxford, OxfordThe Autism research team, Wellcome Trust Centre for Human Genetics (WTCHG)
University Department of Psychiatry, Warneford Hospital

2. Members of the AGP Phase 1 project (2004-7):


Contact Us:

For further information about the AGP, please contact:

    Penny Farrar, AGP Project Manager:

    penny.farrar@well.ox.ac.uk

Thank you for your interest in our work!


AGP Members Area

Sorry, but this section of the website is only accessible to AGP members:



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.


3 Replies to “Archived | Autism Speaks: Autism Genome Project (AGP) | Circa 2004 #NotAnAutisticAlly”

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.