About: Clustering by phenotype and genome-wide association study in autism

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Clustering by phenotype and genome-wide association study in autism
Creator	Kobayashi, Tomoko Hozawa, Atsushi Ishikuro, Mami Kikuya, Masahiro Kobayashi, Mika Kuniyoshi, Yasutaka Kure, Shigeo Kuriyama, Shinichi Makino, Satoshi Matsubara, Hiroko Metoki, Hirohito Mizuno, Satoshi Murakami, Keiko Nagai, Masato Narita, Akira Noda, Aoi Obara, Taku Ogishima, Soichi Ohseto, Hisashi Sakurai, Rieko Tamiya, Gen Ueki, Masao Ueno, Fumihiko Usuzaki, Takuma Yamanaka, Chizuru
source	BioRxiv
abstract	Background Autism spectrum disorder (ASD) has phenotypically and genetically heterogeneous characteristics. A simulation study demonstrated that attempts to categorize patients with a complex disease into more homogeneous subgroups could have more power to elucidate hidden heritability. Methods We conducted cluster analyses using the k-means algorithm with a cluster number of 15 based on phenotypic variables from the Simons Simplex Collection (SSC). As a preliminary study, we conducted a conventional genome-wide association study (GWAS) with a dataset of 597 ASD cases and 370 controls. In the second step, we divided cases based on the clustering results and conducted GWAS in each of the subgroups vs controls (cluster-based GWAS). We also conducted cluster-based GWAS on another SSC dataset of 712 probands and 354 controls in the replication stage. Results In the preliminary study, we observed no significant associations. In the second step of cluster-based GWASs, we identified 65 chromosomal loci, which included 30 intragenic loci located in 21 genes and 35 intergenic loci that satisfied the threshold of P<5.0×10−8. Some of these loci were located within or near previously reported candidate genes for ASD: CDH5, CNTN5, CNTNAP5, DNAH17, DPP10, DSCAM, FOXK1, GABBR2, GRIN2A5, ITPR1, NTM, SDK1, SNCA and SRRM4. Of these 65 significant chromosomal loci, rs11064685 located within the SRRM4 gene had a significantly different distribution in the cases vs. controls in the replication cohort. Conclusions These findings suggest that clustering may successfully identify subgroups with relatively homogeneous disease etiologies. Further cluster validation and replication studies are warranted in larger cohorts.
has issue date	2020-03-24(xsd:dateTime)
bibo:doi	10.1101/614958
has license	biorxiv
sha1sum (hex)	e54151b0a9e2bf85ef4f44324269c2d10f4eb787
schema:url	https://doi.org/10.1101/614958
resource representing a document's title	Clustering by phenotype and genome-wide association study in autism
schema:publication	bioRxiv
resource representing a document's body	covid:e54151b0a9e2bf85ef4f44324269c2d10f4eb787#body_text
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