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Allen-Brady K, Robison R, Cannon D, Varvil T, Villalobos M, Pingree C, Leppert MF, Miller J, McMahon WM, Coon H. Genome-wide linkage in Utah autism pedigrees. Mol Psychiatry 2010; 15:1006-15. [PMID: 19455147 PMCID: PMC4023913 DOI: 10.1038/mp.2009.42] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 03/25/2009] [Accepted: 04/13/2009] [Indexed: 01/04/2023]
Abstract
Genetic studies of autism over the past decade suggest a complex landscape of multiple genes. In the face of this heterogeneity, studies that include large extended pedigrees may offer valuable insights, as the relatively few susceptibility genes within single large families may be more easily discerned. This genome-wide screen of 70 families includes 20 large extended pedigrees of 6-9 generations, 6 moderate-sized families of 4-5 generations and 44 smaller families of 2-3 generations. The Center for Inherited Disease Research (CIDR) provided genotyping using the Illumina Linkage Panel 12, a 6K single-nucleotide polymorphism (SNP) platform. Results from 192 subjects with an autism spectrum disorder (ASD) and 461 of their relatives revealed genome-wide significance on chromosome 15q, with three possibly distinct peaks: 15q13.1-q14 (heterogeneity LOD (HLOD)=4.09 at 29 459 872 bp); 15q14-q21.1 (HLOD=3.59 at 36 837 208 bp); and 15q21.1-q22.2 (HLOD=5.31 at 55 629 733 bp). Two of these peaks replicate earlier findings. There were additional suggestive results on chromosomes 2p25.3-p24.1 (HLOD=1.87), 7q31.31-q32.3 (HLOD=1.97) and 13q12.11-q12.3 (HLOD=1.93). Affected subjects in families supporting the linkage peaks found in this study did not reveal strong evidence for distinct phenotypic subgroups.
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Affiliation(s)
- K Allen-Brady
- Utah Autism Research Project, Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA
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Coon H, Villalobos ME, Robison RJ, Camp NJ, Cannon DS, Allen-Brady K, Miller JS, McMahon WM. Genome-wide linkage using the Social Responsiveness Scale in Utah autism pedigrees. Mol Autism 2010; 1:8. [PMID: 20678250 PMCID: PMC2913945 DOI: 10.1186/2040-2392-1-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 04/08/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Autism Spectrum Disorders (ASD) are phenotypically heterogeneous, characterized by impairments in the development of communication and social behaviour and the presence of repetitive behaviour and restricted interests. Dissecting the genetic complexity of ASD may require phenotypic data reflecting more detail than is offered by a categorical clinical diagnosis. Such data are available from the Social Responsiveness Scale (SRS) which is a continuous, quantitative measure of social ability giving scores that range from significant impairment to above average ability. METHODS We present genome-wide results for 64 multiplex and extended families ranging from two to nine generations. SRS scores were available from 518 genotyped pedigree subjects, including affected and unaffected relatives. Genotypes from the Illumina 6 k single nucleotide polymorphism panel were provided by the Center for Inherited Disease Research. Quantitative and qualitative analyses were done using MCLINK, a software package that uses Markov chain Monte Carlo (MCMC) methods to perform multilocus linkage analysis on large extended pedigrees. RESULTS When analysed as a qualitative trait, linkage occurred in the same locations as in our previous affected-only genome scan of these families, with findings on chromosomes 7q31.1-q32.3 [heterogeneity logarithm of the odds (HLOD) = 2.91], 15q13.3 (HLOD = 3.64), and 13q12.3 (HLOD = 2.23). Additional positive qualitative results were seen on chromosomes 6 and 10 in regions that may be of interest for other neuropsychiatric disorders. When analysed as a quantitative trait, results replicated a peak found in an independent sample using quantitative SRS scores on chromosome 11p15.1-p15.4 (HLOD = 2.77). Additional positive quantitative results were seen on chromosomes 7, 9, and 19. CONCLUSIONS The SRS linkage peaks reported here substantially overlap with peaks found in our previous affected-only genome scan of clinical diagnosis. In addition, we replicated a previous SRS peak in an independent sample. These results suggest the SRS is a robust and useful phenotype measure for genetic linkage studies of ASD. Finally, analyses of SRS scores revealed linkage peaks overlapping with evidence from other studies of neuropsychiatric diseases. The information available from the SRS itself may, therefore, reveal locations for autism susceptibility genes that would not otherwise be detected.
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Affiliation(s)
- Hilary Coon
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
| | - Michele E Villalobos
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
| | - Reid J Robison
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
| | - Nicola J Camp
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
| | - Dale S Cannon
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
| | - Kristina Allen-Brady
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
| | - Judith S Miller
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
| | - William M McMahon
- Utah Autism Research Project, Department of Psychiatry and Division of Genetic Epidemiology, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT 84108, USA
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Ghosh S, Babron MC, Amos CI, Briollais L, Chen P, Chen WV, Chiu WF, Drigalenko E, Etzel CJ, Hamshere ML, Holmans PA, Margaritte-Jeannin P, Lebrec JJP, Lin S, Lin WY, Mandhyan DD, Nishchenko I, Schaid DJ, Seguardo R, Shete S, Taylor K, Tayo BO, Wan S, Wei LY, Wu CO, Yang XR. Linkage analyses of rheumatoid arthritis and related quantitative phenotypes: the GAW15 experience. Genet Epidemiol 2007; 31 Suppl 1:S86-95. [PMID: 18046767 DOI: 10.1002/gepi.20284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The group that formed on the theme of linkage analyses of rheumatoid arthritis RA and related phenotypes (Group 10) in the Genetic Analysis Workshop 15 comprised 18 sets of investigators. Two data sets were available: one was a real set provided by the North American Rheumatoid Arthritis Consortium and collaborators in Canada, France (European Consortium Of Rheumatoid Arthritis Families) and the UK; the other was a simulated data set modelled after the real data set. Whereas a majority of the investigators analyzed the RA affection status as a binary phenotype, a few contributions considered data on correlated quantitative traits such as anti-cyclic citrullinated peptide and rheumatoid factor-immunoglobulin M. The different investigators applied a wide spectrum of linkage methods. As expected, most methods could identify the human leukocyfeantigen region on chromosome 6 as a major genetic factor for RA. In addition, some novel chromosomal regions provided significant evidence of linkage in multiple contributions in the group. In this report, we discuss the different strategies explored by the different investigators with the common goal of improving the power to detect linkage.
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Affiliation(s)
- Saurabh Ghosh
- Human Genetics Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700-108, India.
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