KA GENOME RESEQUENCING
ʻO nā ʻano like ʻole i ka heluna Kina a me kā lākou hopena i nā phenotypes, nā maʻi a me ka hoʻololi ʻana o ka heluna kanaka
Nanopore |PacBio |Hoʻopili hou ʻia ka genome holoʻokoʻa |Kāhea ʻano hoʻololi hale
Ma kēia noiʻi ʻana, ua hāʻawi ʻia ka sequencing Nanopore PromethION e Biomarker Technologies.
Nā mea nui
Ma kēia noiʻi ʻana, ua hōʻike ʻia kahi ʻāina holoʻokoʻa o nā ʻano like ʻole (SVs) i ka genome kanaka me ke kōkua o ke kaʻina heluhelu lōʻihi ma Nanopore PromethION platfrom, kahi e hoʻonui ai i ka ʻike o nā SV i nā phenotypes, nā maʻi a me ka evolution.
Hoʻolālā hoʻokolohua
Nā Laʻana: Nā leukocytes koko ʻaoʻao o 405 mau kānaka Pākē pili ʻole (206 kāne a me 199 wahine) me 68 phenotypic a me nā ana lapaʻau.Ma waena o nā kānaka a pau, ʻo nā ʻāpana kupuna o 124 mau kānaka he mau panalāʻau ma ʻĀkau, ʻo ka poʻe o 198 mau kānaka he Hema, 53 ʻo SouthWest a ʻo 30 ʻaʻole i ʻike ʻia.
Hoʻolālā Sequencing: Whole genome long-read sequencing (LRS) me Nanopore 1D heluhelu a me PacBio HiFi heluhelu.
Ke kahua hoʻonohonoho: Nanopore PromethION;PacBio Sequel II
Kāhea ʻano like ʻole
Kiʻi 1. Ka holo o ka SV kelepona a me kāna kānana
Nā Hana Nui
ʻO ka ʻike ʻana a me ka hōʻoia ʻana i ka hoʻololi ʻana o ka hale
Nanopore dateset: Ma ka huina o 20.7 Tb maʻemaʻe heluhelu i hana ʻia ma ka PromethION sequencing platform, e loaʻa ana ka awelika o 51 Gb data no kēlā me kēia laʻana, kokoke.17-fold ka hohonu.
Kuhikuhi genome alignment (GRCh38): Awelika ka helu palapala ʻāina o 94.1% i loaʻa.Ua like ka mean error rate (12.6%) me kahi haʻawina benchmarking ma mua (12.6%) (Figure 2b a me 2c)
Kāhea ʻano hoʻololi (SV): ʻO nā mea kelepona SV i hoʻohana ʻia i kēia haʻawina ʻo Sniffles, NanoVar a me NanoSV.Ua wehewehe ʻia nā SV hilinaʻi kiʻekiʻe ma ke ʻano he SV i ʻike ʻia e nā mea kelepona ʻelua ma lalo o ʻelua a hala nā kānana ma ka hohonu, ka lōʻihi a me ka ʻāpana.
ʻO ka awelika o 18,489 (mai ka 15,439 a hiki i ka 22,505) nā SV hilinaʻi kiʻekiʻe i ʻike ʻia i kēlā me kēia laʻana.(Kiʻi 2d, 2e a me 2f)
Kiʻi 2. ʻO ka ʻāina holoʻokoʻa o nā SV i ʻike ʻia e Nanopore dataset
Hōʻoia ʻia e PacBio: Ua hōʻoia ʻia nā SV i hoʻokahi laʻana (HG002, keiki) e kahi ʻikepili PacBio HiFi.ʻO 3.2% ka helu ʻike hoʻopunipuni holoʻokoʻa (FDR), e hōʻike ana i kahi ʻike SV hilinaʻi ʻia e Nanopore heluhelu.
ʻO nā SV hoʻonui ʻole a me nā hiʻohiʻona genomic
Nā SV hoʻopau ʻole: Ua loaʻa kahi pūʻulu o 132,312 mau SV hoʻopau ʻole ma o ka hoʻohui ʻana i nā SV i nā laʻana a pau, ʻo ia hoʻi he 67,405 DEL, 60,182 INS, 3,956 DUP a me 769 INV.(Kiʻi 3a)
Hoʻohālikelike me nā pūʻulu SV i loaʻa: Ua hoʻohālikelike ʻia kēia ʻikepili i paʻi ʻia me TGS a i ʻole NGS dataset.I loko o nā waihona ʻehā i hoʻohālikelike ʻia, ʻo LRS15, ʻo ia wale nō ka hōʻiliʻili ʻikepili mai ka papa kuhikuhi kaʻina heluhelu lōʻihi (PacBio) i kaʻana like i nā overlaps nui loa me kēia waihona.Eia kekahi, ʻo 53.3%(70,471) o nā SV i kēia ʻikepili i hōʻike ʻia no ka manawa mua.Ma ka nānā ʻana i kēlā me kēia ʻano SV, ʻoi aku ka nui o ka helu o nā INS i hoʻihoʻi ʻia me ka helu helu helu heluhelu lōʻihi ma mua o nā mea heluhelu pōkole ʻē aʻe, e hōʻike ana he maikaʻi loa ke kaʻina heluhelu lōʻihi i ka ʻike INS.(Kiʻi 3b a me 3c)
Kiʻi 3. Nā waiwai o nā SV hoʻonui ʻole no kēlā me kēia ʻano SV
Nā hiʻohiʻona Genomic: Ua ʻike ʻia ka nui o nā SV i pili nui me ka lōʻihi o ka chromosome.Ua hōʻike ʻia ka māhele ʻana o nā genes, nā hana hou, nā DEL ('ōmaʻomaʻo), INS (uliuli), DUP (melemele) a me INV (ʻalani) ma kahi kiʻi Circos, kahi i ʻike ʻia ai ka piʻi nui o ka SV ma ka hopena o nā lima chromosome.(Kiʻi 3d a me 3e)
Ka lōʻihi o nā SV: Ua ʻike ʻia nā lōʻihi o nā INS a me nā DEL he ʻoi aku ka pōkole ma mua o nā DUPs a me nā INV, i ʻae like me nā mea i ʻike ʻia e PacBio HiFi dataset.Hoʻohui ʻia ka lōʻihi o nā SV āpau i ʻike ʻia a hiki i 395.6 Mb, kahi i noho ai i 13.2% o ka genome kanaka holoʻokoʻa.Ua pili nā SV i ka 23.0 Mb (kokoke. 0.8%) o ka genome no kēlā me kēia kanaka ma ka awelika.(Kiʻi 3f a me 3g)
Nā hopena hana, phenotypical a me nā hopena lapaʻau o nā SV
Kuhi ʻia ka nalowale o ka hana (pLoF) SVs: Ua wehewehe ʻia nā pLoF SV e like me nā SV i launa pū me CDS, kahi i hoʻopau ʻia ai nā nucleotides coding a i hoʻololi ʻia nā ORF.Ma ka huina o 1,929 pLoF SV e pili ana i ka CDS o 1,681 genes i hōʻike ʻia.I loko o ia mau mea, ua hōʻike ʻia nā genes 38 i ka "immunoglobulin receptor binding" i ka loiloi hoʻonui GO.Ua hōʻike hou ʻia kēia mau pLoF SV e GWAS, OMIM a me COSMIC.(Kiʻi 4a a me 4b)
Phenotypically a clinically pili SVs: Ua hōʻike 'ia kekahi helu o SV i nanopore dataset i phenotypically a clinically pili.Ua ʻike ʻia kahi DEL heterozygous kakaikahi o 19.3 kb, i ʻike ʻia ke kumu o ka alpha-thalassemia, i ʻekolu mau kānaka, nāna i hoʻopau i nā genes o Hemoglobin Subunit Alpha 1 a me 2 (HBA1 a me HBA2).ʻO kekahi DEL o 27.4 kb ma ka gene coding Hemoglobin Subunit Beta (HBB) i ʻike ʻia i kekahi kanaka ʻē aʻe.Ua ʻike ʻia kēia SV i ke kumu o ka hemoglobinopathies koʻikoʻi.(Kiʻi 4c)
Kiʻi 4. Nā pLoF SV pili i nā phenotypes a me nā maʻi
Ua ʻike ʻia kahi DEL maʻamau o 2.4 kb i 35 homozygous a me 67 heterozygous carriers, e uhi ana i ka ʻāpana piha o ka exon 3 o Growth Homone Receptor (GHR).Ua ʻike ʻia nā mea lawe homozygous ʻoi aku ka pōkole ma mua o nā heterzygous (p=0.033).(Kiʻi 4d)
Eia kekahi, ua hana ʻia kēia mau SV no nā haʻawina evolutionary heluna kanaka ma waena o ʻelua pūʻulu kūloko: ʻĀkau a me Kina Hema.Ua ʻike ʻia nā SV ʻokoʻa koʻikoʻi ma Chr 1, 2, 3, 6,10,12,14 a me 19, i loko o ia mea, ua pili nā mea kiʻekiʻe me nā ʻāpana palekana, e like me IGH, MHC, a pēlā aku. ʻO ka hoʻokaʻawale ʻana i kēia mau SV ma muli o ka genetic drift a me ka lōʻihi o ka hōʻike ʻana i nā ʻāpana like ʻole no nā sub-populations ma Kina.
Kuhikuhi
Wu, Zhikun, et al."ʻO nā ʻano like ʻole i ka heluna Kina a me kā lākou hopena i nā phenotypes, nā maʻi a me ka hoʻololi ʻana o ka heluna kanaka."bioRxiv(2021).
Nūhou a me nā mea nui manaʻo e kaʻana like i nā hihia kūleʻa hou loa me Biomarker Technologies, ka hopu ʻana i nā hoʻokō ʻepekema hou a me nā ʻenehana kaulana i hoʻohana ʻia i ka wā o ke aʻo ʻana.
Ka manawa hoʻouna: Jan-06-2022