Literature DB >> 33929893

The Need for a Human Pangenome Reference Sequence.

Karen H Miga1, Ting Wang2.   

Abstract

The reference human genome sequence is inarguably the most important and widely used resource in the fields of human genetics and genomics. It has transformed the conduct of biomedical sciences and brought invaluable benefits to the understanding and improvement of human health. However, the commonly used reference sequence has profound limitations, because across much of its span, it represents the sequence of just one human haplotype. This single, monoploid reference structure presents a critical barrier to representing the broad genomic diversity in the human population. In this review, we discuss the modernization of the reference human genome sequence to a more complete reference of human genomic diversity, known as a human pangenome. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Entities:  

Year:  2021        PMID: 33929893     DOI: 10.1146/annurev-genom-120120-081921

Source DB:  PubMed          Journal:  Annu Rev Genomics Hum Genet        ISSN: 1527-8204            Impact factor:   8.929


  13 in total

1.  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

2.  Thousands of human mutation clusters are explained by short-range template switching.

Authors:  Ari Löytynoja
Journal:  Genome Res       Date:  2022-06-27       Impact factor: 9.438

Review 3.  Mammalian genome innovation through transposon domestication.

Authors:  Andrew J Modzelewski; Johnny Gan Chong; Ting Wang; Lin He
Journal:  Nat Cell Biol       Date:  2022-08-25       Impact factor: 28.213

4.  Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history.

Authors:  Yang Zhou; Lv Yang; Xiaotao Han; Jiazheng Han; Yan Hu; Fan Li; Han Xia; Lingwei Peng; Clarissa Boschiero; Benjamin D Rosen; Derek M Bickhart; Shujun Zhang; Aizhen Guo; Curtis P Van Tassell; Timothy P L Smith; Liguo Yang; George E Liu
Journal:  Genome Res       Date:  2022-08-17       Impact factor: 9.438

5.  Epigenetic patterns in a complete human genome.

Authors:  Ariel Gershman; Michael E G Sauria; Xavi Guitart; Mitchell R Vollger; Paul W Hook; Savannah J Hoyt; Miten Jain; Alaina Shumate; Roham Razaghi; Sergey Koren; Nicolas Altemose; Gina V Caldas; Glennis A Logsdon; Arang Rhie; Evan E Eichler; Michael C Schatz; Rachel J O'Neill; Adam M Phillippy; Karen H Miga; Winston Timp
Journal:  Science       Date:  2022-04-01       Impact factor: 63.714

6.  Complete genomic and epigenetic maps of human centromeres.

Authors:  Glennis A Logsdon; Andrey V Bzikadze; Pragya Sidhwani; Sasha A Langley; Gina V Caldas; Nicolas Altemose; Savannah J Hoyt; Lev Uralsky; Fedor D Ryabov; Colin J Shew; Michael E G Sauria; Matthew Borchers; Ariel Gershman; Alla Mikheenko; Valery A Shepelev; Tatiana Dvorkina; Olga Kunyavskaya; Mitchell R Vollger; Arang Rhie; Ann M McCartney; Mobin Asri; Ryan Lorig-Roach; Kishwar Shafin; Julian K Lucas; Sergey Aganezov; Daniel Olson; Leonardo Gomes de Lima; Tamara Potapova; Gabrielle A Hartley; Marina Haukness; Peter Kerpedjiev; Fedor Gusev; Kristof Tigyi; Shelise Brooks; Alice Young; Sergey Nurk; Sergey Koren; Sofie R Salama; Benedict Paten; Evgeny I Rogaev; Aaron Streets; Gary H Karpen; Abby F Dernburg; Beth A Sullivan; Aaron F Straight; Travis J Wheeler; Jennifer L Gerton; Evan E Eichler; Adam M Phillippy; Winston Timp; Megan Y Dennis; Rachel J O'Neill; Justin M Zook; Michael C Schatz; Pavel A Pevzner; Mark Diekhans; Charles H Langley; Ivan A Alexandrov; Karen H Miga
Journal:  Science       Date:  2022-04-01       Impact factor: 63.714

7.  A complete reference genome improves analysis of human genetic variation.

Authors:  Sergey Aganezov; Stephanie M Yan; Daniela C Soto; Melanie Kirsche; Samantha Zarate; Pavel Avdeyev; Dylan J Taylor; Kishwar Shafin; Alaina Shumate; Chunlin Xiao; Justin Wagner; Jennifer McDaniel; Nathan D Olson; Michael E G Sauria; Mitchell R Vollger; Arang Rhie; Melissa Meredith; Skylar Martin; Joyce Lee; Sergey Koren; Jeffrey A Rosenfeld; Benedict Paten; Ryan Layer; Chen-Shan Chin; Fritz J Sedlazeck; Nancy F Hansen; Danny E Miller; Adam M Phillippy; Karen H Miga; Rajiv C McCoy; Megan Y Dennis; Justin M Zook; Michael C Schatz
Journal:  Science       Date:  2022-04-01       Impact factor: 63.714

Review 8.  The Human Pangenome Project: a global resource to map genomic diversity.

Authors:  Ting Wang; Lucinda Antonacci-Fulton; Kerstin Howe; Heather A Lawson; Julian K Lucas; Adam M Phillippy; Alice B Popejoy; Mobin Asri; Caryn Carson; Mark J P Chaisson; Xian Chang; Robert Cook-Deegan; Adam L Felsenfeld; Robert S Fulton; Erik P Garrison; Nanibaa' A Garrison; Tina A Graves-Lindsay; Hanlee Ji; Eimear E Kenny; Barbara A Koenig; Daofeng Li; Tobias Marschall; Joshua F McMichael; Adam M Novak; Deepak Purushotham; Valerie A Schneider; Baergen I Schultz; Michael W Smith; Heidi J Sofia; Tsachy Weissman; Paul Flicek; Heng Li; Karen H Miga; Benedict Paten; Erich D Jarvis; Ira M Hall; Evan E Eichler; David Haussler
Journal:  Nature       Date:  2022-04-20       Impact factor: 69.504

9.  The complete sequence of a human genome.

Authors:  Sergey Nurk; Sergey Koren; Arang Rhie; Mikko Rautiainen; Andrey V Bzikadze; Alla Mikheenko; Mitchell R Vollger; Nicolas Altemose; Lev Uralsky; Ariel Gershman; Sergey Aganezov; Savannah J Hoyt; Mark Diekhans; Glennis A Logsdon; Michael Alonge; Stylianos E Antonarakis; Matthew Borchers; Gerard G Bouffard; Shelise Y Brooks; Gina V Caldas; Nae-Chyun Chen; Haoyu Cheng; Chen-Shan Chin; William Chow; Leonardo G de Lima; Philip C Dishuck; Richard Durbin; Tatiana Dvorkina; Ian T Fiddes; Giulio Formenti; Robert S Fulton; Arkarachai Fungtammasan; Erik Garrison; Patrick G S Grady; Tina A Graves-Lindsay; Ira M Hall; Nancy F Hansen; Gabrielle A Hartley; Marina Haukness; Kerstin Howe; Michael W Hunkapiller; Chirag Jain; Miten Jain; Erich D Jarvis; Peter Kerpedjiev; Melanie Kirsche; Mikhail Kolmogorov; Jonas Korlach; Milinn Kremitzki; Heng Li; Valerie V Maduro; Tobias Marschall; Ann M McCartney; Jennifer McDaniel; Danny E Miller; James C Mullikin; Eugene W Myers; Nathan D Olson; Benedict Paten; Paul Peluso; Pavel A Pevzner; David Porubsky; Tamara Potapova; Evgeny I Rogaev; Jeffrey A Rosenfeld; Steven L Salzberg; Valerie A Schneider; Fritz J Sedlazeck; Kishwar Shafin; Colin J Shew; Alaina Shumate; Ying Sims; Arian F A Smit; Daniela C Soto; Ivan Sović; Jessica M Storer; Aaron Streets; Beth A Sullivan; Françoise Thibaud-Nissen; James Torrance; Justin Wagner; Brian P Walenz; Aaron Wenger; Jonathan M D Wood; Chunlin Xiao; Stephanie M Yan; Alice C Young; Samantha Zarate; Urvashi Surti; Rajiv C McCoy; Megan Y Dennis; Ivan A Alexandrov; Jennifer L Gerton; Rachel J O'Neill; Winston Timp; Justin M Zook; Michael C Schatz; Evan E Eichler; Karen H Miga; Adam M Phillippy
Journal:  Science       Date:  2022-03-31       Impact factor: 63.714

10.  The European Variation Archive: a FAIR resource of genomic variation for all species.

Authors:  Timothe Cezard; Fiona Cunningham; Sarah E Hunt; Baron Koylass; Nitin Kumar; Gary Saunders; April Shen; Andres F Silva; Kirill Tsukanov; Sundararaman Venkataraman; Paul Flicek; Helen Parkinson; Thomas M Keane
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

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