Literature DB >> 32504078

Long-read human genome sequencing and its applications.

Glennis A Logsdon1, Mitchell R Vollger1, Evan E Eichler2,3.   

Abstract

Over the past decade, long-read, single-molecule DNA sequencing technologies have emerged as powerful players in genomics. With the ability to generate reads tens to thousands of kilobases in length with an accuracy approaching that of short-read sequencing technologies, these platforms have proven their ability to resolve some of the most challenging regions of the human genome, detect previously inaccessible structural variants and generate some of the first telomere-to-telomere assemblies of whole chromosomes. Long-read sequencing technologies will soon permit the routine assembly of diploid genomes, which will revolutionize genomics by revealing the full spectrum of human genetic variation, resolving some of the missing heritability and leading to the discovery of novel mechanisms of disease.

Entities:  

Mesh:

Year:  2020        PMID: 32504078      PMCID: PMC7877196          DOI: 10.1038/s41576-020-0236-x

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


  136 in total

1.  Segmental duplications: organization and impact within the current human genome project assembly.

Authors:  J A Bailey; A M Yavor; H F Massa; B J Trask; E E Eichler
Journal:  Genome Res       Date:  2001-06       Impact factor: 9.043

2.  Genetic evidence for high-altitude adaptation in Tibet.

Authors:  Tatum S Simonson; Yingzhong Yang; Chad D Huff; Haixia Yun; Ga Qin; David J Witherspoon; Zhenzhong Bai; Felipe R Lorenzo; Jinchuan Xing; Lynn B Jorde; Josef T Prchal; RiLi Ge
Journal:  Science       Date:  2010-05-13       Impact factor: 47.728

3.  The large-scale distribution of somatic mutations in cancer genomes.

Authors:  Alan Hodgkinson; Ying Chen; Adam Eyre-Walker
Journal:  Hum Mutat       Date:  2011-10-20       Impact factor: 4.878

Review 4.  The Third Revolution in Sequencing Technology.

Authors:  Erwin L van Dijk; Yan Jaszczyszyn; Delphine Naquin; Claude Thermes
Journal:  Trends Genet       Date:  2018-06-22       Impact factor: 11.639

5.  Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome.

Authors:  Sarah B Ng; Abigail W Bigham; Kati J Buckingham; Mark C Hannibal; Margaret J McMillin; Heidi I Gildersleeve; Anita E Beck; Holly K Tabor; Gregory M Cooper; Heather C Mefford; Choli Lee; Emily H Turner; Joshua D Smith; Mark J Rieder; Koh-Ichiro Yoshiura; Naomichi Matsumoto; Tohru Ohta; Norio Niikawa; Deborah A Nickerson; Michael J Bamshad; Jay Shendure
Journal:  Nat Genet       Date:  2010-08-15       Impact factor: 38.330

6.  Diversity of human copy number variation and multicopy genes.

Authors:  Peter H Sudmant; Jacob O Kitzman; Francesca Antonacci; Can Alkan; Maika Malig; Anya Tsalenko; Nick Sampas; Laurakay Bruhn; Jay Shendure; Evan E Eichler
Journal:  Science       Date:  2010-10-29       Impact factor: 47.728

7.  A general framework for estimating the relative pathogenicity of human genetic variants.

Authors:  Martin Kircher; Daniela M Witten; Preti Jain; Brian J O'Roak; Gregory M Cooper; Jay Shendure
Journal:  Nat Genet       Date:  2014-02-02       Impact factor: 38.330

8.  An integrated map of structural variation in 2,504 human genomes.

Authors:  Peter H Sudmant; Tobias Rausch; Eugene J Gardner; Robert E Handsaker; Alexej Abyzov; John Huddleston; Yan Zhang; Kai Ye; Goo Jun; Markus Hsi-Yang Fritz; Miriam K Konkel; Ankit Malhotra; Adrian M Stütz; Xinghua Shi; Francesco Paolo Casale; Jieming Chen; Fereydoun Hormozdiari; Gargi Dayama; Ken Chen; Maika Malig; Mark J P Chaisson; Klaudia Walter; Sascha Meiers; Seva Kashin; Erik Garrison; Adam Auton; Hugo Y K Lam; Xinmeng Jasmine Mu; Can Alkan; Danny Antaki; Taejeong Bae; Eliza Cerveira; Peter Chines; Zechen Chong; Laura Clarke; Elif Dal; Li Ding; Sarah Emery; Xian Fan; Madhusudan Gujral; Fatma Kahveci; Jeffrey M Kidd; Yu Kong; Eric-Wubbo Lameijer; Shane McCarthy; Paul Flicek; Richard A Gibbs; Gabor Marth; Christopher E Mason; Androniki Menelaou; Donna M Muzny; Bradley J Nelson; Amina Noor; Nicholas F Parrish; Matthew Pendleton; Andrew Quitadamo; Benjamin Raeder; Eric E Schadt; Mallory Romanovitch; Andreas Schlattl; Robert Sebra; Andrey A Shabalin; Andreas Untergasser; Jerilyn A Walker; Min Wang; Fuli Yu; Chengsheng Zhang; Jing Zhang; Xiangqun Zheng-Bradley; Wanding Zhou; Thomas Zichner; Jonathan Sebat; Mark A Batzer; Steven A McCarroll; Ryan E Mills; Mark B Gerstein; Ali Bashir; Oliver Stegle; Scott E Devine; Charles Lee; Evan E Eichler; Jan O Korbel
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

9.  Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Authors:  Mark J P Chaisson; Ashley D Sanders; Xuefang Zhao; Ankit Malhotra; David Porubsky; Tobias Rausch; Eugene J Gardner; Oscar L Rodriguez; Li Guo; Ryan L Collins; Xian Fan; Jia Wen; Robert E Handsaker; Susan Fairley; Zev N Kronenberg; Xiangmeng Kong; Fereydoun Hormozdiari; Dillon Lee; Aaron M Wenger; Alex R Hastie; Danny Antaki; Thomas Anantharaman; Peter A Audano; Harrison Brand; Stuart Cantsilieris; Han Cao; Eliza Cerveira; Chong Chen; Xintong Chen; Chen-Shan Chin; Zechen Chong; Nelson T Chuang; Christine C Lambert; Deanna M Church; Laura Clarke; Andrew Farrell; Joey Flores; Timur Galeev; David U Gorkin; Madhusudan Gujral; Victor Guryev; William Haynes Heaton; Jonas Korlach; Sushant Kumar; Jee Young Kwon; Ernest T Lam; Jong Eun Lee; Joyce Lee; Wan-Ping Lee; Sau Peng Lee; Shantao Li; Patrick Marks; Karine Viaud-Martinez; Sascha Meiers; Katherine M Munson; Fabio C P Navarro; Bradley J Nelson; Conor Nodzak; Amina Noor; Sofia Kyriazopoulou-Panagiotopoulou; Andy W C Pang; Yunjiang Qiu; Gabriel Rosanio; Mallory Ryan; Adrian Stütz; Diana C J Spierings; Alistair Ward; AnneMarie E Welch; Ming Xiao; Wei Xu; Chengsheng Zhang; Qihui Zhu; Xiangqun Zheng-Bradley; Ernesto Lowy; Sergei Yakneen; Steven McCarroll; Goo Jun; Li Ding; Chong Lek Koh; Bing Ren; Paul Flicek; Ken Chen; Mark B Gerstein; Pui-Yan Kwok; Peter M Lansdorp; Gabor T Marth; Jonathan Sebat; Xinghua Shi; Ali Bashir; Kai Ye; Scott E Devine; Michael E Talkowski; Ryan E Mills; Tobias Marschall; Jan O Korbel; Evan E Eichler; Charles Lee
Journal:  Nat Commun       Date:  2019-04-16       Impact factor: 17.694

10.  Global diversity, population stratification, and selection of human copy-number variation.

Authors:  Peter H Sudmant; Swapan Mallick; Bradley J Nelson; Fereydoun Hormozdiari; Niklas Krumm; John Huddleston; Bradley P Coe; Carl Baker; Susanne Nordenfelt; Michael Bamshad; Lynn B Jorde; Olga L Posukh; Hovhannes Sahakyan; W Scott Watkins; Levon Yepiskoposyan; M Syafiq Abdullah; Claudio M Bravi; Cristian Capelli; Tor Hervig; Joseph T S Wee; Chris Tyler-Smith; George van Driem; Irene Gallego Romero; Aashish R Jha; Sena Karachanak-Yankova; Draga Toncheva; David Comas; Brenna Henn; Toomas Kivisild; Andres Ruiz-Linares; Antti Sajantila; Ene Metspalu; Jüri Parik; Richard Villems; Elena B Starikovskaya; George Ayodo; Cynthia M Beall; Anna Di Rienzo; Michael F Hammer; Rita Khusainova; Elza Khusnutdinova; William Klitz; Cheryl Winkler; Damian Labuda; Mait Metspalu; Sarah A Tishkoff; Stanislav Dryomov; Rem Sukernik; Nick Patterson; David Reich; Evan E Eichler
Journal:  Science       Date:  2015-08-06       Impact factor: 47.728

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  120 in total

Review 1.  Prokaryotic DNA methylation and its functional roles.

Authors:  Hoon Je Seong; Sang-Wook Han; Woo Jun Sul
Journal:  J Microbiol       Date:  2021-02-23       Impact factor: 3.422

2.  Mining the gaps of chromosome 8.

Authors:  Glennis A Logsdon; Evan E Eichler
Journal:  Nature       Date:  2021-05-14       Impact factor: 49.962

3.  A long read of the human genome.

Authors:  Katharine H Wrighton
Journal:  Nat Rev Genet       Date:  2020-10       Impact factor: 53.242

4.  Global Repeat Map (GRM): Advantageous Method for Discovery of Largest Higher-Order Repeats (HORs) in Neuroblastoma Breakpoint Family (NBPF) Genes, in Hornerin Exon and in Chromosome 21 Centromere.

Authors:  Vladimir Paar; Ines Vlahović; Marija Rosandić; Matko Glunčić
Journal:  Prog Mol Subcell Biol       Date:  2021

5.  A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics.

Authors:  Yafei Mao; Guojie Zhang
Journal:  Nat Methods       Date:  2022-06       Impact factor: 28.547

6.  Assessing the utility of long-read nanopore sequencing for rapid and efficient characterization of mobile element insertions.

Authors:  Christopher M Watson; Laura A Crinnion; Helen Lindsay; Rowena Mitchell; Nick Camm; Rachel Robinson; Caroline Joyce; George A Tanteles; Domhnall J O' Halloran; Sergio D J Pena; Ian M Carr; David T Bonthron
Journal:  Lab Invest       Date:  2020-09-28       Impact factor: 5.662

7.  Targeted long-read sequencing identifies missing disease-causing variation.

Authors:  Danny E Miller; Arvis Sulovari; Tianyun Wang; Hailey Loucks; Kendra Hoekzema; Katherine M Munson; Alexandra P Lewis; Edith P Almanza Fuerte; Catherine R Paschal; Tom Walsh; Jenny Thies; James T Bennett; Ian Glass; Katrina M Dipple; Karynne Patterson; Emily S Bonkowski; Zoe Nelson; Audrey Squire; Megan Sikes; Erika Beckman; Robin L Bennett; Dawn Earl; Winston Lee; Rando Allikmets; Seth J Perlman; Penny Chow; Anne V Hing; Tara L Wenger; Margaret P Adam; Angela Sun; Christina Lam; Irene Chang; Xue Zou; Stephanie L Austin; Erin Huggins; Alexias Safi; Apoorva K Iyengar; Timothy E Reddy; William H Majoros; Andrew S Allen; Gregory E Crawford; Priya S Kishnani; Mary-Claire King; Tim Cherry; Jessica X Chong; Michael J Bamshad; Deborah A Nickerson; Heather C Mefford; Dan Doherty; Evan E Eichler
Journal:  Am J Hum Genet       Date:  2021-07-02       Impact factor: 11.025

Review 8.  Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology.

Authors:  Leho Tedersoo; Mads Albertsen; Sten Anslan; Benjamin Callahan
Journal:  Appl Environ Microbiol       Date:  2021-08-11       Impact factor: 4.792

Review 9.  Advancing crop genomics from lab to field.

Authors:  Michael D Purugganan; Scott A Jackson
Journal:  Nat Genet       Date:  2021-05-06       Impact factor: 38.330

10.  Exome variant discrepancies due to reference-genome differences.

Authors:  He Li; Moez Dawood; Michael M Khayat; Jesse R Farek; Shalini N Jhangiani; Ziad M Khan; Tadahiro Mitani; Zeynep Coban-Akdemir; James R Lupski; Eric Venner; Jennifer E Posey; Aniko Sabo; Richard A Gibbs
Journal:  Am J Hum Genet       Date:  2021-06-14       Impact factor: 11.025

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