Performance of case-control rare copy number variation annotation in classification of autism

บทความในวารสาร

ผู้เขียน/บรรณาธิการ

กลุ่มสาขาการวิจัยเชิงกลยุทธ์

ไม่พบข้อมูลที่เกี่ยวข้อง

รายละเอียดสำหรับงานพิมพ์

รายชื่อผู้แต่ง: Engchuan W., Dhindsa K., Lionel A.C., Scherer S.W., Chan J.H., Merico D.

ผู้เผยแพร่: BioMed Central

ปีที่เผยแพร่ (ค.ศ.): 2015

วารสาร: Journal Title BMC Medical Genomics (1755-8794)

Volume number: 8

Issue number: 1

นอก: 1755-8794

eISSN: 1755-8794

URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964502119&doi=10.1186%2f1755-8794-8-S1-S7&partnerID=40&md5=895643de2e33dcf431d7ab24db276711

ภาษา: English-Great Britain (EN-GB)

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บทคัดย่อ

Background: A substantial proportion of Autism Spectrum Disorder (ASD) risk resides in de novo germline and rare inherited genetic variation. In particular, rare copy number variation (CNV) contributes to ASD risk in up to 10% of ASD subjects. Despite the striking degree of genetic heterogeneity, case-control studies have detected specific burden of rare disruptive CNV for neuronal and neurodevelopmental pathways. Here, we used machine learning methods to classify ASD subjects and controls, based on rare CNV data and comprehensive gene annotations. We investigated performance of different methods and estimated the percentage of ASD subjects that could be reliably classified based on presumed etiologic CNV they carry. Results: We analyzed 1,892 Caucasian ASD subjects and 2,342 matched controls. Rare CNVs (frequency 1% or less) were detected using Illumina 1M and 1M-Duo BeadChips. Conditional Inference Forest (CF) typically performed as well as or better than other classification methods. We found a maximum AUC (area under the ROC curve) of 0.533 when considering all ASD subjects with rare genic CNVs, corresponding to 7.9% correctly classified ASD subjects and less than 3% incorrectly classified controls; performance was significantly higher when considering only subjects harboring de novo or pathogenic CNVs. We also found rare losses to be more predictive than gains and that curated neurally-relevant annotations (brain expression, synaptic components and neurodevelopmental phenotypes) outperform Gene Ontology and pathway-based annotations. Conclusions: CF is an optimal classification approach for case-control rare CNV data and it can be used to prioritize subjects with variants potentially contributing to ASD risk not yet recognized. The neurally-relevant annotations used in this study could be successfully applied to rare CNV case-control data-sets for other neuropsychiatric disorders. ฉ 2015 Engchuan et al; licensee BioMed Central Ltd.

คำสำคัญ

Autism Spectrum Disorders (ASD), Copy number variation (CNV), machine learning classification, Random Forest (RF), rare genetic variants