Literature DB >> 25548800

Whole genome sequencing as a means to assess pathogenic mutations in medical genetics and cancer.

Beryl Royer-Bertrand1, Carlo Rivolta.   

Abstract

The past decade has seen the emergence of next-generation sequencing (NGS) technologies, which have revolutionized the field of human molecular genetics. With NGS, significant portions of the human genome can now be assessed by direct sequence analysis, highlighting normal and pathological variants of our DNA. Recent advances have also allowed the sequencing of complete genomes, by a method referred to as whole genome sequencing (WGS). In this work, we review the use of WGS in medical genetics, with specific emphasis on the benefits and the disadvantages of this technique for detecting genomic alterations leading to Mendelian human diseases and to cancer.

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Year:  2014        PMID: 25548800     DOI: 10.1007/s00018-014-1807-9

Source DB:  PubMed          Journal:  Cell Mol Life Sci        ISSN: 1420-682X            Impact factor:   9.261


  50 in total

1.  Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.

Authors:  Sanchit Misra; Ankit Agrawal; Wei-keng Liao; Alok Choudhary
Journal:  Bioinformatics       Date:  2010-11-18       Impact factor: 6.937

2.  De novo loss-of-function mutations in SETD5, encoding a methyltransferase in a 3p25 microdeletion syndrome critical region, cause intellectual disability.

Authors:  Detelina Grozeva; Keren Carss; Olivera Spasic-Boskovic; Michael J Parker; Hayley Archer; Helen V Firth; Soo-Mi Park; Natalie Canham; Susan E Holder; Meredith Wilson; Anna Hackett; Michael Field; James A B Floyd; Matthew Hurles; F Lucy Raymond
Journal:  Am J Hum Genet       Date:  2014-03-27       Impact factor: 11.025

3.  Genome sequencing identifies major causes of severe intellectual disability.

Authors:  Christian Gilissen; Jayne Y Hehir-Kwa; Djie Tjwan Thung; Maartje van de Vorst; Bregje W M van Bon; Marjolein H Willemsen; Michael Kwint; Irene M Janssen; Alexander Hoischen; Annette Schenck; Richard Leach; Robert Klein; Rick Tearle; Tan Bo; Rolph Pfundt; Helger G Yntema; Bert B A de Vries; Tjitske Kleefstra; Han G Brunner; Lisenka E L M Vissers; Joris A Veltman
Journal:  Nature       Date:  2014-06-04       Impact factor: 49.962

4.  Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study.

Authors:  Anita Rauch; Dagmar Wieczorek; Elisabeth Graf; Thomas Wieland; Sabine Endele; Thomas Schwarzmayr; Beate Albrecht; Deborah Bartholdi; Jasmin Beygo; Nataliya Di Donato; Andreas Dufke; Kirsten Cremer; Maja Hempel; Denise Horn; Juliane Hoyer; Pascal Joset; Albrecht Röpke; Ute Moog; Angelika Riess; Christian T Thiel; Andreas Tzschach; Antje Wiesener; Eva Wohlleber; Christiane Zweier; Arif B Ekici; Alexander M Zink; Andreas Rump; Christa Meisinger; Harald Grallert; Heinrich Sticht; Annette Schenck; Hartmut Engels; Gudrun Rappold; Evelin Schröck; Peter Wieacker; Olaf Riess; Thomas Meitinger; André Reis; Tim M Strom
Journal:  Lancet       Date:  2012-09-27       Impact factor: 79.321

5.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.

Authors:  Xose S Puente; Magda Pinyol; Víctor Quesada; Laura Conde; Gonzalo R Ordóñez; Neus Villamor; Georgia Escaramis; Pedro Jares; Sílvia Beà; Marcos González-Díaz; Laia Bassaganyas; Tycho Baumann; Manel Juan; Mónica López-Guerra; Dolors Colomer; José M C Tubío; Cristina López; Alba Navarro; Cristian Tornador; Marta Aymerich; María Rozman; Jesús M Hernández; Diana A Puente; José M P Freije; Gloria Velasco; Ana Gutiérrez-Fernández; Dolors Costa; Anna Carrió; Sara Guijarro; Anna Enjuanes; Lluís Hernández; Jordi Yagüe; Pilar Nicolás; Carlos M Romeo-Casabona; Heinz Himmelbauer; Ester Castillo; Juliane C Dohm; Silvia de Sanjosé; Miguel A Piris; Enrique de Alava; Jesús San Miguel; Romina Royo; Josep L Gelpí; David Torrents; Modesto Orozco; David G Pisano; Alfonso Valencia; Roderic Guigó; Mónica Bayés; Simon Heath; Marta Gut; Peter Klatt; John Marshall; Keiran Raine; Lucy A Stebbings; P Andrew Futreal; Michael R Stratton; Peter J Campbell; Ivo Gut; Armando López-Guillermo; Xavier Estivill; Emili Montserrat; Carlos López-Otín; Elías Campo
Journal:  Nature       Date:  2011-06-05       Impact factor: 49.962

6.  Landscape of genomic alterations in cervical carcinomas.

Authors:  Akinyemi I Ojesina; Lee Lichtenstein; Samuel S Freeman; Chandra Sekhar Pedamallu; Ivan Imaz-Rosshandler; Trevor J Pugh; Andrew D Cherniack; Lauren Ambrogio; Kristian Cibulskis; Bjørn Bertelsen; Sandra Romero-Cordoba; Victor Treviño; Karla Vazquez-Santillan; Alberto Salido Guadarrama; Alexi A Wright; Mara W Rosenberg; Fujiko Duke; Bethany Kaplan; Rui Wang; Elizabeth Nickerson; Heather M Walline; Michael S Lawrence; Chip Stewart; Scott L Carter; Aaron McKenna; Iram P Rodriguez-Sanchez; Magali Espinosa-Castilla; Kathrine Woie; Line Bjorge; Elisabeth Wik; Mari K Halle; Erling A Hoivik; Camilla Krakstad; Nayeli Belem Gabiño; Gabriela Sofia Gómez-Macías; Lezmes D Valdez-Chapa; María Lourdes Garza-Rodríguez; German Maytorena; Jorge Vazquez; Carlos Rodea; Adrian Cravioto; Maria L Cortes; Heidi Greulich; Christopher P Crum; Donna S Neuberg; Alfredo Hidalgo-Miranda; Claudia Rangel Escareno; Lars A Akslen; Thomas E Carey; Olav K Vintermyr; Stacey B Gabriel; Hugo A Barrera-Saldaña; Jorge Melendez-Zajgla; Gad Getz; Helga B Salvesen; Matthew Meyerson
Journal:  Nature       Date:  2013-12-25       Impact factor: 49.962

7.  Predicting functional effect of human missense mutations using PolyPhen-2.

Authors:  Ivan Adzhubei; Daniel M Jordan; Shamil R Sunyaev
Journal:  Curr Protoc Hum Genet       Date:  2013-01

8.  A practical method to detect SNVs and indels from whole genome and exome sequencing data.

Authors:  Daichi Shigemizu; Akihiro Fujimoto; Shintaro Akiyama; Tetsuo Abe; Kaoru Nakano; Keith A Boroevich; Yujiro Yamamoto; Mayuko Furuta; Michiaki Kubo; Hidewaki Nakagawa; Tatsuhiko Tsunoda
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

Review 9.  The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

Authors:  Peter D Stenson; Matthew Mort; Edward V Ball; Katy Shaw; Andrew Phillips; David N Cooper
Journal:  Hum Genet       Date:  2014-01       Impact factor: 4.132

10.  Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events.

Authors:  Jinfeng Liu; William Lee; Zhaoshi Jiang; Zhongqiang Chen; Suchit Jhunjhunwala; Peter M Haverty; Florian Gnad; Yinghui Guan; Houston N Gilbert; Jeremy Stinson; Christiaan Klijn; Joseph Guillory; Deepali Bhatt; Steffan Vartanian; Kimberly Walter; Jocelyn Chan; Thomas Holcomb; Peter Dijkgraaf; Stephanie Johnson; Julie Koeman; John D Minna; Adi F Gazdar; Howard M Stern; Klaus P Hoeflich; Thomas D Wu; Jeff Settleman; Frederic J de Sauvage; Robert C Gentleman; Richard M Neve; David Stokoe; Zora Modrusan; Somasekar Seshagiri; David S Shames; Zemin Zhang
Journal:  Genome Res       Date:  2012-10-02       Impact factor: 9.043

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  8 in total

Review 1.  Applications of Next-generation Sequencing in Systemic Autoimmune Diseases.

Authors:  Yiyangzi Ma; Na Shi; Mengtao Li; Fei Chen; Haitao Niu
Journal:  Genomics Proteomics Bioinformatics       Date:  2015-10-15       Impact factor: 7.691

2.  Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.

Authors:  Qian Zhang; Se-Ran Jun; Michael Leuze; David Ussery; Intawat Nookaew
Journal:  Sci Rep       Date:  2017-01-19       Impact factor: 4.379

3.  Comparative mutational landscape analysis of patient-derived tumour xenografts.

Authors:  Mariana Brait; Evgeny Izumchenko; Luciane T Kagohara; Samuel Long; Piotr T Wysocki; Brian Faherty; Elana J Fertig; Tin Oo Khor; Elizabeth Bruckheimer; Gilson Baia; Daniel Ciznadija; Ido Sloma; Ido Ben-Zvi; Keren Paz; David Sidransky
Journal:  Br J Cancer       Date:  2017-01-24       Impact factor: 7.640

Review 4.  Uses of Next-Generation Sequencing Technologies for the Diagnosis of Primary Immunodeficiencies.

Authors:  Michael Seleman; Rodrigo Hoyos-Bachiloglu; Raif S Geha; Janet Chou
Journal:  Front Immunol       Date:  2017-07-24       Impact factor: 7.561

5.  Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution.

Authors:  Daniil Nikitin; Andrew Garazha; Maxim Sorokin; Dmitry Penzar; Victor Tkachev; Alexander Markov; Nurshat Gaifullin; Pieter Borger; Alexander Poltorak; Anton Buzdin
Journal:  Cells       Date:  2019-02-06       Impact factor: 6.600

6.  Molecular characterization of PRKN structural variations identified through whole-genome sequencing.

Authors:  Paloma Bravo; Hossein Darvish; Abbas Tafakhori; Luis J Azcona; Amir Hossein Johari; Faezeh Jamali; Coro Paisán-Ruiz
Journal:  Mol Genet Genomic Med       Date:  2018-10-16       Impact factor: 2.183

7.  Improved High-Throughput Sequencing of the Human Oral Microbiome: From Illumina to PacBio.

Authors:  Jie Zhang; Lingkai Su; Yuan Wang; Shuli Deng
Journal:  Can J Infect Dis Med Microbiol       Date:  2020-12-11       Impact factor: 2.471

Review 8.  Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives.

Authors:  Vincenza Precone; Valentina Del Monaco; Maria Valeria Esposito; Fatima Domenica Elisa De Palma; Anna Ruocco; Francesco Salvatore; Valeria D'Argenio
Journal:  Biomed Res Int       Date:  2015-11-19       Impact factor: 3.411

  8 in total

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