TAG NRHO GENOME RESEQUENCING
Cov qauv sib txawv hauv Suav cov pej xeem thiab lawv qhov cuam tshuam rau phenotypes, kab mob thiab kev hloov ntawm cov pejxeem
Nanopor |PacBio |Tag nrho genome re-sequencing |Tus qauv variation hu
Hauv txoj kev tshawb no, Nanopore PromethION sequencing yog muab los ntawm Biomarker Technologies.
Qhov tseem ceeb
Hauv txoj kev tshawb no, tag nrho cov toj roob hauv pes ntawm cov qauv kev hloov pauv (SVs) hauv tib neeg genome tau tshwm sim nrog kev pab los ntawm kev nyeem ntev ntev ntawm Nanopore PromethION platfrom, uas ua rau nkag siab tob txog SVs hauv phenotypes, kab mob thiab evolution.
Kev sim tsim
Cov Qauv: Peripheral ntshav leukocytes ntawm 405 tus neeg suav tsis txheeb (206 tus txiv neej thiab 199 tus poj niam) nrog 68 phenotypic thiab soj ntsuam kev ntsuas.Ntawm tag nrho cov tib neeg, thaj tsam yawg koob ntawm 124 tus neeg yog cov xeev nyob rau sab qaum teb, cov ntawm 198 tus neeg yog South, 53 yog SouthWest thiab 30 tsis paub.
Sequencing lub tswv yim: Tag nrho genome long-read sequencing (LRS) nrog Nanopore 1D nyeem thiab PacBio HiFi nyeem.
Sequencing platform: Nanopore PromethION;PacBio Sequel II
Qauv Variation Hu
Daim duab 1. Kev ua haujlwm ntawm SV hu thiab lim
Kev Ua Tau Zoo
Structure variation discovery thiab validation
Nanopore dateset: Nyob rau hauv tag nrho ntawm 20.7 Tb huv si nyeem generated ntawm PromethION sequencing platform, ua tiav qhov nruab nrab ntawm 51 Gb cov ntaub ntawv ib tug qauv, kwv yees li.17-fold hauv qhov tob.
Reference genome alignment (GRCh38): Qhov nruab nrab daim ntawv qhia tus nqi ntawm 94.1% tau ua tiav.Qhov nruab nrab qhov yuam kev (12.6%) zoo ib yam li kev tshawb fawb ua ntej (12.6%) (Daim duab 2b thiab 2c)
Structure variation(SV) hu: SV callers thov hauv txoj kev tshawb no suav nrog Sniffles, NanoVar thiab NanoSV.Kev ntseeg siab SVs tau txhais tias yog SVs txheeb xyuas los ntawm tsawg kawg ob tus neeg hu thiab dhau qhov pom ntawm qhov tob, ntev thiab thaj tsam.
Qhov nruab nrab ntawm 18,489 (xws li ntawm 15,439 txog 22,505) kev ntseeg siab SVs tau txheeb xyuas hauv txhua tus qauv.(Daim duab 2d, 2e thiab 2f)
Daim duab 2. Tag nrho cov toj roob hauv pes ntawm SVs txheeb xyuas los ntawm Nanopore dataset
Kev lees paub los ntawm PacBio: SVs txheeb xyuas hauv ib qho qauv (HG002, tus menyuam) tau lees paub los ntawm PacBio HiFi dataset.Qhov kev tshawb pom tsis tseeb tag nrho (FDR) yog 3.2%, qhia txog qhov kev txheeb xyuas qhov tseeb SV los ntawm Nanopore nyeem.
SVs uas tsis yog redundant thiab genomic nta
SVs tsis-redundant: Ib txheej ntawm 132,312 SVs uas tsis yog rov qab tau los ntawm kev sib koom ua ke SVs hauv txhua qhov qauv, uas suav nrog 67,405 DELs, 60,182 INSs, 3,956 DUPs thiab 769 INVs.(Daim duab 3a)
Kev sib piv nrog SV datasets: Cov ntaub ntawv no tau muab piv rau TGS lossis NGS cov ntaub ntawv luam tawm.Nyob rau hauv plaub datasets piv, LRS15, uas kuj yog tib dataset los ntawm ntev-nyeem sequencing platform (PacBio) qhia qhov loj tshaj overlaps nrog cov dataset no.Ntxiv mus, 53.3% (70,471) ntawm SVs hauv cov ntaub ntawv no tau tshaj tawm thawj zaug.Los ntawm kev saib rau hauv txhua hom SV, tus naj npawb ntawm cov INS tau zoo nrog cov ntaub ntawv nyeem ntev ntev tau ntau dua li cov ntawv nyeem luv luv, qhia tias kev nyeem ntev ntev yog qhov tshwj xeeb hauv kev tshawb nrhiav INSs.(Daim duab 3b thiab 3c)
Daim duab 3. Cov cuab yeej ntawm cov SV uas tsis yog rov qab rau txhua hom SV
Genomic nta: Tus naj npawb ntawm SVs tau pom muaj feem cuam tshuam nrog chromosome ntev.Kev faib tawm ntawm cov noob, rov ua dua, DELs (ntsuab), INS (xiav), DUP (daj) thiab INV (txiv kab ntxwv) tau tshwm sim rau ntawm daim duab Circos, qhov twg qhov kev nce hauv SV tau pom thaum kawg ntawm chromosome caj npab.(Daim duab 3d thiab 3e)
Ntev ntawm SVs: Ntev ntawm INSs thiab DELs tau pom tias luv dua li ntawm DUPs thiab INVs, uas pom zoo nrog cov txheeb xyuas los ntawm PacBio HiFi dataset.Ntev ntawm tag nrho cov txheeb cais SVs ntxiv txog 395.6 Mb, uas nyob 13.2% ntawm tag nrho tib neeg genome.SVs cuam tshuam 23.0 Mb (kwv yees 0.8%) ntawm genome rau ib tus neeg hauv qhov nruab nrab.(Daim duab 3f thiab 3g)
Kev ua haujlwm, phenotypical thiab kev kho mob cuam tshuam ntawm SVs
Kev kwv yees poob ntawm kev ua haujlwm (pLoF) SVs: pLoF SVs tau txhais tias yog SVs cuam tshuam nrog CDS, qhov twg coding nucleotides raug tshem tawm lossis ORFs tau hloov pauv.Hauv tag nrho ntawm 1,929 pLoF SVs cuam tshuam rau CDS ntawm 1,681 noob tau sau tseg.Hauv cov no, 38 cov noob tau hais txog "immunoglobulin receptor khi" hauv GO enrichment tsom xam.Cov pLoF SVs no tau piav qhia ntxiv los ntawm GWAS, OMIM thiab COSMIC, feem.(Daim duab 4a thiab 4b)
Phenotypically thiab kho mob ntsig txog SVs: Ntau tus SV hauv nanopore dataset tau pom tias yog phenotypically thiab kho mob cuam tshuam.Ib qho tsis tshua muaj heterozygous DEL ntawm 19.3 kb, paub tias ua rau alpha-thalassemia, tau txheeb xyuas nyob rau hauv peb tus neeg, uas ua rau cov noob tsis zoo ntawm Hemoglobin Subunit Alpha 1 thiab 2 (HBA1 thiab HBA2).Lwm DEL ntawm 27.4 kb ntawm noob coding Hemoglobin Subunit Beta (HBB) tau txheeb xyuas hauv lwm tus neeg.Qhov SV no tau paub tias ua rau mob hnyav hemoglobinopathies.(Daim duab 4c)
Daim duab 4. pLoF SVs txuam nrog phenotypes thiab kab mob
Ib qho DEL ntawm 2.4 kb tau pom nyob rau hauv 35 homozygous thiab 67 heterozygous carriers, uas npog tag nrho cheeb tsam ntawm 3rd exon ntawm Kev Loj Hlob Homone Receptor (GHR).Cov neeg nqa khoom homozygous tau pom luv luv dua li cov heterzygous (p = 0.033).(Daim duab 4d)
Tsis tas li ntawd, cov SVs no tau ua tiav rau cov pej xeem evolutionary kev tshawb fawb ntawm ob pawg hauv cheeb tsam: North thiab South China.Qhov tseem ceeb sib txawv SVs tau pom tau muab faib rau ntawm Chr 1, 2, 3, 6, 10, 12, 14 thiab 19, nyob rau hauv uas, cov saum toj kawg nkaus tau cuam tshuam nrog cov cheeb tsam tiv thaiv kab mob, xws li IGH, MHC, thiab lwm yam. Kev sib txawv ntawm cov SVs no tuaj yeem yog vim muaj caj ces thiab lub sijhawm ntev ua rau muaj kev sib txawv rau cov neeg nyob hauv Suav teb.
Kev siv
Wu, Zhikun, et al."Cov qauv sib txawv hauv Suav cov pej xeem thiab lawv qhov cuam tshuam rau phenotypes, kab mob thiab kev hloov ntawm cov pej xeem."bioRxiv(2021).
Xov xwm thiab qhov tseem ceeb Lub hom phiaj ntawm kev sib koom cov xwm txheej ua tiav tshiab nrog Biomarker Technologies, khaws cov kev tshawb fawb tshiab thiab cov txuj ci tseem ceeb siv thaum kawm.
Post lub sij hawm: Jan-06-2022