YESE GENOME RESEQUENCING
Zvimiro zvakasiyana muhuwandu hweChinese uye maitiro avo pane phenotypes, zvirwere uye kugadziriswa kwevanhu
Nanopore |PacBio |Yese genome re-sequencing |Structural variation calling
Muchidzidzo ichi, Nanopore PromethION kutevedzana kwakapihwa neBiomarker Technologies.
Pfungwa huru
Muchidzidzo ichi, nzvimbo yese yekusiyana kwechimiro (SVs) mugenome yemunhu yakaratidzwa nerubatsiro rwekuverenga kwenguva refu kutevedzana paNanopore PromethION platfrom, iyo inodzamisa kunzwisisa kweSV mune phenotypes, zvirwere uye shanduko.
Kuedza Dhizaini
Mienzaniso: Peripheral blood leukocytes ye405 vanhu vasina hukama hweChinese (206 varume uye 199 vakadzi) vane 68 phenotypic uye kliniki zviyero.Pakati pevanhu vese, matunhu emadzitateguru evanhu zana nemakumi maviri nemana aive mapurovhinzi kuNorth, avo vevanhu zana nemakumi mapfumbamwe nevasere vaive Maodzanyemba, makumi mashanu nenhatu vaive SouthWest uye makumi matatu vaisazivikanwa.
Sequencing zano: Yese genome yakareba-kuverenga kutevedzana (LRS) ine Nanopore 1D inoverenga uye PacBio HiFi inoverenga.
Sequencing platform: Nanopore PromethION;PacBio Sequel II
Chimiro Kusiyana Kufona
Mufananidzo 1. Kufamba kwebasa reSV kudana uye kusefa
Zvinangwa Zvikuru
Kuwanikwa kwekuchinja kwechimiro uye kusimbiswa
Nanopore dateset: Pakazara 20.7 Tb yakachena kuverenga yakagadzirwa paPromethION sequencing chikuva, kuwana avhareji ye51 Gb data pamuenzaniso, approx.17-peta pakadzika.
Reference genome alignment(GRCh38): Avhareji yemepu mwero we94.1% yakawanikwa.Kuremerwa kukanganisa mwero (12.6%) yaive yakafanana neyekutanga bhenjimarking kudzidza (12.6%) (Mufananidzo 2b uye 2c)
Musiyano wechimiro(SV) kufona: Vanofona veSV vakaiswa muchidzidzo ichi vaisanganisira Sniffles, NanoVar neNanoSV.High-confidence SVs dzakatsanangurwa seSV dzakaonekwa nevaviri vanofona uye dzakapfuura mafirita pakudzika, kureba uye dunhu.
Avhareji ye18,489 (kubva pa15,439 kusvika ku22,505) maSV akavimbika akaonekwa mumuenzaniso wega wega.(Mufananidzo 2d, 2e uye 2f)
Mufananidzo 2. Mamiriro ose eSVs akaonekwa neNanopore dataset
Kusimbiswa nePacBio: maSV akaonekwa mune imwe sampu (HG002, mwana) akasimbiswa nePacBio HiFi dataset.Huwandu hwekuwanikwa kwenhema hwese (FDR) hwaive 3.2%, zvichiratidza yakavimbika SV kuzivikanwa neNanopore inoverenga.
Zvisiri-zvisina basa maSV uye genomic maficha
MaSV asingadzoreki: Seti ye132,312 isiri-yedundundu SV yakawanikwa nekubatanidza maSV mumasampuli ese, ayo anosanganisira 67,405 DELs, 60,182 INSs, 3,956 DUPs uye 769 INVs.(Mufananidzo 3a)
Kuenzanisa neaive aripo eSV dataset: Iyi dataset yakaenzaniswa neyakaburitswa TGS kana NGS dataset.Mukati memaseti mana akaenzaniswa, LRS15, inova zvakare yega dhatabheti kubva kure-kurebera kuverenga kuteedzera papuratifomu (PacBio) yakagovanisa yakakura kudarika neiyi dataset.Zvakare, 53.3% (70,471) yeSVs mune iyi dataset yakashumwa kekutanga.Nekutarisa mumhando yega yega yeSV, huwandu hweakadzoserwa maINS ane dhata-yekuverenga-yekutevedzana dataset yaive yakakura kudarika mamwe mapfupi-kuverenga, zvichiratidza kuti kutevedzana kwekuverenga kwenguva refu kunonyanya kushanda mukuonekwa kweINS.(Mufananidzo 3b na3c)
Mufananidzo 3. Zvivako zvevasina-dundunt SVs kune imwe neimwe SV mhando
Genomic features: Nhamba yeSVs yakawanikwa yakabatana zvakanyanya nehurefu hwechromosome.Kugoverwa kwemajini, kudzokorora, DELs(girini), INS(blue), DUP(yero) uye INV(orenji) zvakaratidzwa paCircos diagram, apo kuwedzera kweSV kwakaonekwa pakupera kwemaoko echromosome.(Mufananidzo 3d uye 3e)
Kureba kweSVs: Kureba kweINSs uye DELs kwakawanikwa kupfupika kupfuura izvo zveDUPs uye INVs, izvo zvakabvumirana neavo vakaonekwa nePacBio HiFi dataset.Hurefu hwese maSV akaonekwa akawedzera kusvika 395.6 Mb, iyo yakatora 13.2% yegenome yemunhu.SVs dzakakanganisa 23.0 Mb(approx. 0.8%) ye genome pamunhu paavhareji.(Mufananidzo 3f uye 3g)
Inoshanda, phenotypical uye kiriniki zvinokonzerwa neSVs
Kufanotaurwa kurasikirwa kwebasa (pLoF) SVs: pLoF SVs yakatsanangurwa seSVs yakabatana neCDS, uko kukodha nucleotides kwakabviswa kana ORFs yakashandurwa.Pakazara 1,929 pLoF SVs inobata maCDS e1,681 majini akatsanangurwa.Mukati meavo, makumi matatu nemasere majini akasimbisa "immunoglobulin receptor binding" muGO kusimudzira ongororo.Aya pLoF SVs akatsanangurwa zvakare neGWAS, OMIM neCOSMIC, zvichiteerana.(Mufananidzo 4a na4b)
Phenotypically uye kliniki yakakosha SVs: Nhamba yeSV mune nanopore dataset yakaratidzwa kuva phenotypically uye kliniki yakakosha.Iyo isingawanzo heterozygous DEL ye19.3 kb, inozivikanwa kukonzera alpha-thalassemia, yakaonekwa muvanhu vatatu, iyo isingashande majini eHemoglobin Subunit Alpha 1 uye 2 (HBA1 neHBA2).Imwe DEL ye27.4 kb pane gene coding Hemoglobin Subunit Beta(HBB) yakaonekwa mune mumwe munhu.Iyi SV yaizivikanwa kuti inokonzera hemoglobinopathies yakakomba.(Mufananidzo 4c)
Mufananidzo 4. pLoF SVs yakabatana ne phenotypes uye zvirwere
DEL yakajairika ye2.4 kb yakaonekwa mu35 homozygous uye 67 heterozygous vatakuri, iyo inovhara nharaunda yakazara ye3rd exon yeGrowth Homone Receptor (GHR).Iwo homozygous vatakuri vakawanikwa vakapfupika kupfuura heterzygous avo (p = 0.033).(Mufananidzo 4d)
Uyezve, aya maSV akagadziriswa zvidzidzo zvekushanduka kwevanhu pakati pemapoka maviri ematunhu: Maodzanyemba neSouth China.MaSV akanyanya kusiyanisa akawanikwa akagoverwa paChr 1, 2, 3, 6, 10, 12, 14 uye 19, mukati mawo, epamusoro aisanganiswa nematunhu ekudzivirira, senge IGH, MHC, nezvimwewo. Zvine musoro kufungidzira kuti mutsauko mune idzi maSV unogona nekuda kwekudonha kwemajini uye kuratidzwa kwenguva refu kune dzakasiyana siyana kune vanhu vashoma muChina.
Reference
Wu, Zhikun, et al."Misiyano yezvimiro muhuwandu hweChinese uye maitiro avo pane phenotypes, zvirwere uye kuchinjika kwevanhu."bioRxiv(2021).
Nhau Nezvakakosha inovavarira kugovera nyaya dzichangoburwa dzakabudirira neBiomarker Technologies, kutora budiriro yesainzi pamwe nemaitiro ane mukurumbira akashandiswa panguva yekudzidza.
Nguva yekutumira: Jan-06-2022