Literature DB >> 23752795

Sequencing studies in human genetics: design and interpretation.

David B Goldstein1, Andrew Allen, Jonathan Keebler, Elliott H Margulies, Steven Petrou, Slavé Petrovski, Shamil Sunyaev.   

Abstract

Next-generation sequencing is becoming the primary discovery tool in human genetics. There have been many clear successes in identifying genes that are responsible for Mendelian diseases, and sequencing approaches are now poised to identify the mutations that cause undiagnosed childhood genetic diseases and those that predispose individuals to more common complex diseases. There are, however, growing concerns that the complexity and magnitude of complete sequence data could lead to an explosion of weakly justified claims of association between genetic variants and disease. Here, we provide an overview of the basic workflow in next-generation sequencing studies and emphasize, where possible, measures and considerations that facilitate accurate inferences from human sequencing studies.

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Year:  2013        PMID: 23752795      PMCID: PMC4117319          DOI: 10.1038/nrg3455

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  85 in total

1.  Pooled association tests for rare variants in exon-resequencing studies.

Authors:  Alkes L Price; Gregory V Kryukov; Paul I W de Bakker; Shaun M Purcell; Jeff Staples; Lee-Jen Wei; Shamil R Sunyaev
Journal:  Am J Hum Genet       Date:  2010-05-13       Impact factor: 11.025

Review 2.  Uncovering the roles of rare variants in common disease through whole-genome sequencing.

Authors:  Elizabeth T Cirulli; David B Goldstein
Journal:  Nat Rev Genet       Date:  2010-06       Impact factor: 53.242

3.  Diabetes mellitus in long-term survivors of childhood cancer. Increased risk associated with radiation therapy: a report for the childhood cancer survivor study.

Authors:  Lillian R Meacham; Charles A Sklar; Suwen Li; Qi Liu; Nora Gimpel; Yutaka Yasui; John A Whitton; Marilyn Stovall; Leslie L Robison; Kevin C Oeffinger
Journal:  Arch Intern Med       Date:  2009-08-10

Review 4.  Sense from sequence reads: methods for alignment and assembly.

Authors:  Paul Flicek; Ewan Birney
Journal:  Nat Methods       Date:  2009-11       Impact factor: 28.547

5.  De novo gene disruptions in children on the autistic spectrum.

Authors:  Ivan Iossifov; Michael Ronemus; Dan Levy; Zihua Wang; Inessa Hakker; Julie Rosenbaum; Boris Yamrom; Yoon-Ha Lee; Giuseppe Narzisi; Anthony Leotta; Jude Kendall; Ewa Grabowska; Beicong Ma; Steven Marks; Linda Rodgers; Asya Stepansky; Jennifer Troge; Peter Andrews; Mitchell Bekritsky; Kith Pradhan; Elena Ghiban; Melissa Kramer; Jennifer Parla; Ryan Demeter; Lucinda L Fulton; Robert S Fulton; Vincent J Magrini; Kenny Ye; Jennifer C Darnell; Robert B Darnell; Elaine R Mardis; Richard K Wilson; Michael C Schatz; W Richard McCombie; Michael Wigler
Journal:  Neuron       Date:  2012-04-26       Impact factor: 17.173

6.  De novo mutations revealed by whole-exome sequencing are strongly associated with autism.

Authors:  Stephan J Sanders; Michael T Murtha; Abha R Gupta; John D Murdoch; Melanie J Raubeson; A Jeremy Willsey; A Gulhan Ercan-Sencicek; Nicholas M DiLullo; Neelroop N Parikshak; Jason L Stein; Michael F Walker; Gordon T Ober; Nicole A Teran; Youeun Song; Paul El-Fishawy; Ryan C Murtha; Murim Choi; John D Overton; Robert D Bjornson; Nicholas J Carriero; Kyle A Meyer; Kaya Bilguvar; Shrikant M Mane; Nenad Sestan; Richard P Lifton; Murat Günel; Kathryn Roeder; Daniel H Geschwind; Bernie Devlin; Matthew W State
Journal:  Nature       Date:  2012-04-04       Impact factor: 49.962

7.  A method and server for predicting damaging missense mutations.

Authors:  Ivan A Adzhubei; Steffen Schmidt; Leonid Peshkin; Vasily E Ramensky; Anna Gerasimova; Peer Bork; Alexey S Kondrashov; Shamil R Sunyaev
Journal:  Nat Methods       Date:  2010-04       Impact factor: 28.547

8.  Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations.

Authors:  Heather A Bruce; Nancy Sachs; Dobrila D Rudnicki; Stephanie G Lin; Virginia L Willour; John K Cowell; Jeffrey Conroy; Devin E McQuaid; Michael Rossi; Daniel P Gaile; Norma J Nowak; Susan E Holmes; Pamela Sklar; Christopher A Ross; Lynn E Delisi; Russell L Margolis
Journal:  Psychiatr Genet       Date:  2009-04       Impact factor: 2.458

9.  Personalized copy number and segmental duplication maps using next-generation sequencing.

Authors:  Can Alkan; Jeffrey M Kidd; Tomas Marques-Bonet; Gozde Aksay; Francesca Antonacci; Fereydoun Hormozdiari; Jacob O Kitzman; Carl Baker; Maika Malig; Onur Mutlu; S Cenk Sahinalp; Richard A Gibbs; Evan E Eichler
Journal:  Nat Genet       Date:  2009-08-30       Impact factor: 38.330

10.  The theory of discovering rare variants via DNA sequencing.

Authors:  Michael C Wendl; Richard K Wilson
Journal:  BMC Genomics       Date:  2009-10-20       Impact factor: 3.969

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  111 in total

Review 1.  Genetic basis of adult-onset nephrotic syndrome and focal segmental glomerulosclerosis.

Authors:  Jian Liu; Weiming Wang
Journal:  Front Med       Date:  2017-08-03       Impact factor: 4.592

2.  Comparison of haplotype-based statistical tests for disease association with rare and common variants.

Authors:  Ananda S Datta; Swati Biswas
Journal:  Brief Bioinform       Date:  2015-09-02       Impact factor: 11.622

Review 3.  Nanotechnologies for biomedical science and translational medicine.

Authors:  James R Heath
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-24       Impact factor: 11.205

4.  Can the impact of human genetic variations be predicted?

Authors:  Yuval Itan; Jean-Laurent Casanova
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-08       Impact factor: 11.205

5.  Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database.

Authors:  Jinchen Li; Tao Cai; Yi Jiang; Huiqian Chen; Xin He; Chao Chen; Xianfeng Li; Qianzhi Shao; Xia Ran; Zhongshan Li; Kun Xia; Chunyu Liu; Zhong Sheng Sun; Jinyu Wu
Journal:  Mol Psychiatry       Date:  2015-04-07       Impact factor: 15.992

6.  Likelihood-based complex trait association testing for arbitrary depth sequencing data.

Authors:  Song Yan; Shuai Yuan; Zheng Xu; Baqun Zhang; Bo Zhang; Guolian Kang; Andrea Byrnes; Yun Li
Journal:  Bioinformatics       Date:  2015-05-14       Impact factor: 6.937

Review 7.  Genetic testing for kidney disease of unknown etiology.

Authors:  Thomas Hays; Emily E Groopman; Ali G Gharavi
Journal:  Kidney Int       Date:  2020-04-24       Impact factor: 10.612

Review 8.  Genetic variants at the IFNL3 locus and their association with hepatitis C virus infections reveal novel insights into host-virus interactions.

Authors:  Sreedhar Chinnaswamy
Journal:  J Interferon Cytokine Res       Date:  2014-02-20       Impact factor: 2.607

Review 9.  Genetic influences on the development of alcoholism.

Authors:  Mary-Anne Enoch
Journal:  Curr Psychiatry Rep       Date:  2013-11       Impact factor: 5.285

10.  Bivariate logistic Bayesian LASSO for detecting rare haplotype association with two correlated phenotypes.

Authors:  Xiaochen Yuan; Swati Biswas
Journal:  Genet Epidemiol       Date:  2019-09-23       Impact factor: 2.135

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