Literature DB >> 23250814

Detecting rare variants for psychiatric disorders using next generation sequencing: a methods primer.

Andre Altmann1, Carina Quast, Peter Weber.   

Abstract

Recent advances in massively parallel sequencing (MPS) have had an extensive impact on research in medical genomics. In particular, the analysis of rare variants using MPS promises to lead to a better understanding of complex disorders. Nevertheless, for meaningful studies that address the genetic basis for neuropsychiatric disorders, at least hundreds of patient samples have to be analyzed. This undertaking is still not feasible for single research groups on a whole-genome scale and in individual samples. Thus, researchers increasingly employ strategies for reducing the amount of sequencing efforts, such as target enrichment and non-barcoded sample pooling. This review provides an overview of current technologies, discusses options for reduced experimental designs, and illustrates the successful application of the presented methodologies in a recent study of panic disorder patients. Thereby, it aims to introduce the emerging field of MPS into neuropsychiatric research and might serve as a guide for further studies.

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Year:  2013        PMID: 23250814     DOI: 10.1007/s11920-012-0333-4

Source DB:  PubMed          Journal:  Curr Psychiatry Rep        ISSN: 1523-3812            Impact factor:   5.285


  34 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

Review 2.  Target-enrichment strategies for next-generation sequencing.

Authors:  Lira Mamanova; Alison J Coffey; Carol E Scott; Iwanka Kozarewa; Emily H Turner; Akash Kumar; Eleanor Howard; Jay Shendure; Daniel J Turner
Journal:  Nat Methods       Date:  2010-02       Impact factor: 28.547

3.  Personal genomes: The case of the missing heritability.

Authors:  Brendan Maher
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962

Review 4.  Sequencing technologies - the next generation.

Authors:  Michael L Metzker
Journal:  Nat Rev Genet       Date:  2009-12-08       Impact factor: 53.242

5.  Sequencing of 50 human exomes reveals adaptation to high altitude.

Authors:  Xin Yi; Yu Liang; Emilia Huerta-Sanchez; Xin Jin; Zha Xi Ping Cuo; John E Pool; Xun Xu; Hui Jiang; Nicolas Vinckenbosch; Thorfinn Sand Korneliussen; Hancheng Zheng; Tao Liu; Weiming He; Kui Li; Ruibang Luo; Xifang Nie; Honglong Wu; Meiru Zhao; Hongzhi Cao; Jing Zou; Ying Shan; Shuzheng Li; Qi Yang; Peixiang Ni; Geng Tian; Junming Xu; Xiao Liu; Tao Jiang; Renhua Wu; Guangyu Zhou; Meifang Tang; Junjie Qin; Tong Wang; Shuijian Feng; Guohong Li; Jiangbai Luosang; Wei Wang; Fang Chen; Yading Wang; Xiaoguang Zheng; Zhuo Li; Zhuoma Bianba; Ge Yang; Xinping Wang; Shuhui Tang; Guoyi Gao; Yong Chen; Zhen Luo; Lamu Gusang; Zheng Cao; Qinghui Zhang; Weihan Ouyang; Xiaoli Ren; Huiqing Liang; Huisong Zheng; Yebo Huang; Jingxiang Li; Lars Bolund; Karsten Kristiansen; Yingrui Li; Yong Zhang; Xiuqing Zhang; Ruiqiang Li; Songgang Li; Huanming Yang; Rasmus Nielsen; Jun Wang; Jian Wang
Journal:  Science       Date:  2010-07-02       Impact factor: 47.728

6.  TMEM132D, a new candidate for anxiety phenotypes: evidence from human and mouse studies.

Authors:  A Erhardt; L Czibere; D Roeske; S Lucae; P G Unschuld; S Ripke; M Specht; M A Kohli; S Kloiber; M Ising; A Heck; H Pfister; P Zimmermann; R Lieb; B Pütz; M Uhr; P Weber; J M Deussing; M Gonik; M Bunck; M S Kebler; E Frank; C Hohoff; K Domschke; P Krakowitzky; W Maier; B Bandelow; C Jacob; J Deckert; S Schreiber; J Strohmaier; M Nöthen; S Cichon; M Rietschel; T Bettecken; M E Keck; R Landgraf; B Müller-Myhsok; F Holsboer; E B Binder
Journal:  Mol Psychiatry       Date:  2010-04-06       Impact factor: 15.992

7.  Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia.

Authors:  Christopher T Johansen; Jian Wang; Matthew B Lanktree; Henian Cao; Adam D McIntyre; Matthew R Ban; Rebecca A Martins; Brooke A Kennedy; Reina G Hassell; Maartje E Visser; Stephen M Schwartz; Benjamin F Voight; Roberto Elosua; Veikko Salomaa; Christopher J O'Donnell; Geesje M Dallinga-Thie; Sonia S Anand; Salim Yusuf; Murray W Huff; Sekar Kathiresan; Robert A Hegele
Journal:  Nat Genet       Date:  2010-07-25       Impact factor: 38.330

8.  A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST).

Authors:  Stephan Morgenthaler; William G Thilly
Journal:  Mutat Res       Date:  2006-11-13       Impact factor: 2.433

9.  A statistical method for the detection of variants from next-generation resequencing of DNA pools.

Authors:  Vikas Bansal
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

10.  vipR: variant identification in pooled DNA using R.

Authors:  Andre Altmann; Peter Weber; Carina Quast; Monika Rex-Haffner; Elisabeth B Binder; Bertram Müller-Myhsok
Journal:  Bioinformatics       Date:  2011-07-01       Impact factor: 6.937

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