A high-density SNP genome-wide linkage scan in a large autism extended pedigree

被引:64
|
作者
Allen-Brady, K. [1 ]
Miller, J. [1 ]
Matsunami, N. [2 ]
Stevens, J. [1 ]
Block, H. [1 ]
Farley, M. [1 ]
Krasny, L. [1 ]
Pingree, C. [1 ]
Lainhart, J. [1 ]
Leppert, M. [1 ]
McMahon, W. M. [1 ]
Coon, H. [1 ]
机构
[1] Univ Utah, Dept Psychiat, Salt Lake City, UT USA
[2] Univ Utah, Dept Human Genet, Salt Lake City, UT USA
关键词
autism spectrum disorder; genome-wide scan; chromosome; 3; 20; 7; 9; SINGLE-NUCLEOTIDE POLYMORPHISMS; GENETIC-LINKAGE; SPECTRUM DISORDERS; MAJOR DEPRESSION; FAMILY-HISTORY; ERROR RATES; SUSCEPTIBILITY; LOCI; SCREEN; ASSOCIATION;
D O I
10.1038/mp.2008.14
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We performed a high-density, single nucleotide polymorphism (SNP), genome-wide scan on a six-generation pedigree from Utah with seven affected males, diagnosed with autism spectrum disorder. Using a two-stage linkage design, we first performed a nonparametric analysis on the entire genome using a 10K SNP chip to identify potential regions of interest. To confirm potentially interesting regions, we eliminated SNPs in high linkage disequilibrium (LD) using a principal components analysis (PCA) method and repeated the linkage results. Three regions met genome-wide significance criteria after controlling for LD: 3q13.2-q13.31 (nonparametric linkage (NPL), 5.58), 3q26.31-q27.3 (NPL, 4.85) and 20q11.21-q13.12 (NPL, 5.56). Two regions met suggestive criteria for significance 7p14.1-p11.22 (NPL, 3.18) and 9p24.3 (NPL, 3.44). All five chromosomal regions are consistent with other published findings. Haplotype sharing results showed that five of the affected subjects shared more than a single chromosomal region of interest with other affected subjects. Although no common autism susceptibility genes were found for all seven autism cases, these results suggest that multiple genetic loci within these regions may contribute to the autism phenotype in this family, and further follow-up of these chromosomal regions is warranted. Molecular Psychiatry (2009) 14, 590-600; doi:10.1038/mp.2008.14; published online 19 February 2008
引用
收藏
页码:590 / 600
页数:11
相关论文
共 50 条
  • [31] Genome-wide linkage in Utah autism pedigrees
    K Allen-Brady
    R Robison
    D Cannon
    T Varvil
    M Villalobos
    C Pingree
    M F Leppert
    J Miller
    W M McMahon
    H Coon
    Molecular Psychiatry, 2010, 15 : 1006 - 1015
  • [32] Genome-wide linkage in Utah autism pedigrees
    Allen-Brady, K.
    Robison, R.
    Cannon, D.
    Varvil, T.
    Villalobos, M.
    Pingree, C.
    Leppert, M. F.
    Miller, J.
    McMahon, W. M.
    Coon, H.
    MOLECULAR PSYCHIATRY, 2010, 15 (10) : 1006 - 1015
  • [33] A genome-wide linkage study in autism.
    Buxbaum, JD
    Silveman, D
    Smith, CJ
    Kilifarski, MA
    Reichert, JG
    Lawlor, BA
    Fizgerald, M
    Greenberg, DA
    Davis, KL
    AMERICAN JOURNAL OF HUMAN GENETICS, 2000, 67 (04) : 49 - 49
  • [34] A genome-wide linkage study in autism.
    Buxbaum, JD
    Silverman, JM
    Smith, CJ
    Kilifarski, MA
    Reichert, JG
    Song, CY
    Zhou, G
    Lawlor, BA
    Fitzgerald, M
    Galvin, P
    Whiting, K
    Greenberg, DA
    Davis, KL
    MOLECULAR PSYCHIATRY, 1999, 4 : S13 - S13
  • [35] Genome-wide Linkage Analysis with Clustered SNP Markers
    Selmero, Kaja K.
    Brandal, Kristin
    Olstad, Ole K.
    Birkenes, Bard
    Undlien, Dag E.
    Egeland, Thore
    JOURNAL OF BIOMOLECULAR SCREENING, 2009, 14 (01) : 92 - 96
  • [36] Genome-wide linkage scan on a large Icelandik cohort with hip and knee osteoarthritis
    Ingvarsson, T.
    Jonsson, H.
    Hauksson, V.
    Kristjansson, K.
    Petursson, H.
    Lohmander, L.
    Stefansson, K.
    ANNALS OF THE RHEUMATIC DISEASES, 2007, 66 : 131 - 131
  • [37] A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer
    Middeldorp, Anneke
    Jagmohan-Changur, Shantie
    Helmer, Quinta
    van der Klift, Heleen M.
    Tops, Carli M. J.
    Vasen, Hans F. A.
    Devilee, Peter
    Morreau, Hans
    Houwing-Duistermaat, Jeanine J.
    Wijnen, Juul T.
    van Wezel, Tom
    BMC CANCER, 2007, 7 (1)
  • [38] A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer
    Anneke Middeldorp
    Shantie Jagmohan-Changur
    Quinta Helmer
    Heleen M van der Klift
    Carli MJ Tops
    Hans FA Vasen
    Peter Devilee
    Hans Morreau
    Jeanine J Houwing-Duistermaat
    Juul T Wijnen
    Tom van Wezel
    BMC Cancer, 7
  • [39] Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers
    Faji Li
    Weie Wen
    Zhonghu He
    Jindong Liu
    Hui Jin
    Shuanghe Cao
    Hongwei Geng
    Jun Yan
    Pingzhi Zhang
    Yingxiu Wan
    Xianchun Xia
    Theoretical and Applied Genetics, 2018, 131 : 1903 - 1924
  • [40] Genome-wide SNP linkage scan for high-velocity knee strength: The leuven genes for muscular strength study
    De Mars, Gunther
    Windelinckx, An
    Peeters, Maarten
    Huygens, Wim
    Aerssens, Jeroen
    Vlietinck, Robert
    Beunen, Gaston
    Thomis, Martine
    BEHAVIOR GENETICS, 2007, 37 (06) : 746 - 746