Human pangenome: far-reaching implications in precision medicine

Yingyan Yu , Hongzhuan Chen

Front. Med. ›› 2024, Vol. 18 ›› Issue (2) : 403 -409.

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Front. Med. ›› 2024, Vol. 18 ›› Issue (2) : 403 -409. DOI: 10.1007/s11684-023-1039-1
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Human pangenome: far-reaching implications in precision medicine

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Yingyan Yu, Hongzhuan Chen. Human pangenome: far-reaching implications in precision medicine. Front. Med., 2024, 18(2): 403-409 DOI:10.1007/s11684-023-1039-1

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References

[1]

Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B. A draft human pangenome reference. Nature 2023; 617(7960): 312–324

[2]

Gao Y, Yang X, Chen H, Tan X, Yang Z, Deng L, Wang B, Kong S, Li S, Cui Y, Lei C, Wang Y, Pan Y, Ma S, Sun H, Zhao X, Shi Y, Yang Z, Wu D, Wu S, Zhao X, Shi B, Jin L, Hu Z, Lu Y, Chu J, Ye K, Xu S. A pangenome reference of 36 Chinese populations. Nature 2023; 619(7968): 112–121

[3]

Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q, Qian W, Ren Y, Tian G, Li J, Zhou G, Zhu X, Wu H, Qin J, Jin X, Li D, Cao H, Hu X, Blanche H, Cann H, Zhang X, Li S, Bolund L, Kristiansen K, Yang H, Wang J, Wang J. Building the sequence map of the human pan-genome. Nat Biotechnol 2010; 28(1): 57–63

[4]

Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953; 171(4356): 737–738

[5]

Wilkins MH, Stokes AR, Wilson HR. Molecular structure of deoxypentose nucleic acids. Nature 1953; 171(4356): 738–740

[6]

Franklin RE, Gosling RG. Molecular configuration in sodium thymonucleate. Nature 1953; 171(4356): 740–741

[7]

Attar N. Raymond Gosling: the man who crystallized genes. Genome Biol 2013; 14(4): 402

[8]

Edsall JT. Nobel Prize: two Britons, American share 1962 Award for Genetic Code Achievement. Science 1962; 138(3539): 498–500

[9]

Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74(12): 5463–5467

[10]

Olson MV. The human genome project. Proc Natl Acad Sci USA 1993; 90(10): 4338–4344

[11]

Chen Z, Zhang S. Chinese Human Genome Project-opportunity and challenge. Chin J Med Genet (Zhonghua YiXue YiChuanXue ZaZhi) 1998; 15(4): 195–197

[12]

Han ZG, Zhao GP, Chen Z. Transcriptome study in China. C R Biol 2003; 326(10–11): 949–957

[13]

Collins FS, Morgan M, Patrinos A. The Human Genome Project: lessons from large-scale biology. Science 2003; 300(5617): 286–290

[14]

Garver KL, Garver B. The Human Genome Project and eugenic concerns. Am J Hum Genet 1994; 54(1): 148–158

[15]

Jarvie T. Next generation sequencing technologies. Drug Discov Today Technol 2005; 2(3): 255–260

[16]

Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016; 17(6): 333–351

[17]

International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 2004; 431(7011): 931–945

[18]

Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res 2017; 27(5): 849–864

[19]

Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE. Characterizing the major structural variant alleles of the human genome. Cell 2019; 176(3): 663–675.e19

[20]

Yang X, Lee WP, Ye K, Lee C. One reference genome is not enough. Genome Biol 2019; 20(1): 104

[21]

Golicz AA, Bayer PE, Bhalla PL, Batley J, Edwards D. Pangenomics comes of age: from bacteria to plant and animal applications. Trends Genet 2020; 36(2): 132–145

[22]

Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 2005; 102(39): 13950–13955

[23]

Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann JC, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H. Genomic variation in 3010 diverse accessions of Asian cultivated rice. Nature 2018; 557(7703): 43–49

[24]

Gong Y, Li Y, Liu X, Ma Y, Jiang L. A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?. J Anim Sci Biotechnol 2023; 14(1): 73

[25]

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Deslattes Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. The sequence of the human genome. Science 2001; 291(5507): 1304–1351

[26]

Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B. A strategy for building and using a human reference pangenome. F1000 Res 2019; 8: 1751

[27]

Duan Z, Qiao Y, Lu J, Lu H, Zhang W, Yan F, Sun C, Hu Z, Zhang Z, Li G, Chen H, Xiang Z, Zhu Z, Zhao H, Yu Y, Wei C. HUPAN: a pan-genome analysis pipeline for human genomes. Genome Biol 2019; 20(1): 149

[28]

Li H, Feng X, Chu C. The design and construction of reference pangenome graphs with minigraph. Genome Biol 2020; 21(1): 265

[29]

Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, Garrison E. Pangenome graphs. Annu Rev Genomics Hum Genet 2020; 21(1): 139–162

[30]

Garg S, Balboa R, Kuja J. Chromosome-scale haplotype-resolved pangenomics. Trends Genet 2022; 38(11): 1103–1107

[31]

Massarat A, Gymrek M, McStay B, Jónsson H. Human pangenome supports analysis of complex genomic regions. Nature 2023; 617(7960): 256–258

[32]

Yu Y, Zhang Z, Dong X, Yang R, Duan Z, Xiang Z, Li J, Li G, Yan F, Xue H, Jiao D, Lu J, Lu H, Zhang W, Wei Y, Fan S, Li J, Jia J, Zhang J, Ji J, Liu P, Lu H, Zhao H, Chen S, Wei C, Chen H, Zhu Z. Pangenomic analysis of Chinese gastric cancer. Nat Commun 2022; 13(1): 5412

[33]

Yoshida T, Yatabe Y, Kato K, Ishii G, Hamada A, Mano H, Sunami K, Yamamoto N, Kohno T. The evolution of cancer genomic medicine in Japan and the role of the National Cancer Center Japan. Cancer Biol Med 2023; 3: j.issn.2095-3941.2023.0036

[34]

Stewart OA, Wu F, Chen Y. The role of gastric microbiota in gastric cancer. Gut Microbes 2020; 11(5): 1220–1230

[35]

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 2014; 513(7517): 202–209

[36]

Yu Y, Wei C. A powerful HUPAN on a pan-genome study: significance and perspectives. Cancer Biol Med 2020; 17(1): 1–5

[37]

Watson CM, Crinnion LA, Simmonds J, Camm N, Adlard J, Bonthron DT. Long-read nanopore sequencing enables accurate confirmation of a recurrent PMS2 insertion-deletion variant located in a region of complex genomic architecture. Cancer Genet 2021; 256–257: 122–126

[38]

Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011; 52(4): 413–435

[39]

Venkatesan BM, Bashir R. Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 2011; 6(10): 615–624

[40]

Ozsolak F. Third-generation sequencing techniques and applications to drug discovery. Expert Opin Drug Discov 2012; 7(3): 231–243

[41]

Tsai CM, Riestra AM, Ali SR, Fong JJ, Liu JZ, Hughes G, Varki A, Nizet V. Siglec-14 enhances NLRP3-inflammasome activation in macrophages. J Innate Immun 2020; 12(4): 333–343

[42]

Angata T, Hayakawa T, Yamanaka M, Varki A, Nakamura M. Discovery of Siglec-14, a novel sialic acid receptor undergoing concerted evolution with Siglec-5 in primates. FASEB J 2006; 20(12): 1964–1973

[43]

Yamanaka M, Kato Y, Angata T, Narimatsu H. Deletion polymorphism of SIGLEC14 and its functional implications. Glycobiology 2009; 19(8): 841–846

[44]

Varki A. Colloquium paper: uniquely human evolution of sialic acid genetics and biology. Proc Natl Acad Sci USA 2010; 107(Suppl 2): 8939–8946

[45]

Yu Y, Peng W. Recent progress in targeting the sialylated glycan-SIGLEC axis in cancer immunotherapy. Cancer Biol Med 2023; 20(5): 369–384

[46]

Lin YL, Pavlidis P, Karakoc E, Ajay J, Gokcumen O. The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol Biol Evol 2015; 32(4): 1008–1019

[47]

Cavalli M, Diamanti K, Dang Y, Xing P, Pan G, Chen X, Wadelius C. The thioesterase ACOT1 as a regulator of lipid metabolism in type 2 diabetes detected in a multi-omics study of human liver. OMICS 2021; 25(10): 652–659

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