LONKE I-GENOME RESEQUENCING
Ukuhlukahluka kwesakhiwo kubantu baseShayina kanye nomthelela wabo kuma-phenotypes, izifo kanye nokuguquguquka kwabantu
Nanopore |PacBio |Ukulandelana kabusha kwe-genome |Ubizo lokwehluka kwesakhiwo
Kulolu cwaningo, ukulandelana kwe-Nanopore PromethION kunikezwe yi-Biomarker Technologies.
Amaphuzu avelele
Kulolu cwaningo, indawo yonke yokuhluka kwesakhiwo(ama-SV) ku-genome yomuntu yembulwa ngosizo lokulandelana okufundwe isikhathi eside ku-Nanopore PromethION platfrom, ejulisa ukuqonda kwama-SVs kuma-phenotypes, izifo kanye nokuziphendukela kwemvelo.
Idizayini Yokuhlola
Amasampula: Ama-leukocyte egazi e-peripheral of 405 abantu baseShayina abangahlobene (abesilisa abangu-206 nabesifazane abangu-199) abanezilinganiso ze-phenotypic ezingu-68 nezomtholampilo.Kubo bonke abantu, izifunda zokhokho babantu abangu-124 kwakuyizifundazwe eziseNyakatho, ezabantu abangu-198 zaziseNingizimu, ezingama-53 zaziseNingizimu-ntshonalanga kanti ezingama-30 zazingaziwa.
Isu lokulandelanisa: I-Whole genome long-read sequencing(LRS) enokufundwa kwe-Nanopore 1D kanye ne-PacBio HiFi efundwayo.
Inkundla yokulandelanisa: I-Nanopore PromethION;I-PacBio Sequel II
Ukushaya Ukwehluka Kwesakhiwo
Umfanekiso 1. Ukuhamba komsebenzi kokushaya nokuhlunga kwe-SV
Izimpumelelo Eziyinhloko
Ukutholwa nokuqinisekiswa kokuhlukahluka kwesakhiwo
Idethi yedethi ye-Nanopore: Sekukonke okungu-20.7 Tb okufundwayo okuhlanzekile okukhiqizwe kuplathifomu yokulandelana ye-PromethION, kufinyelelwe isilinganiso sedatha engu-51 Gb isampula ngayinye, cishe.17-ukujula.
Ukuqondanisa i-genome eyireferensi(GRCh38): Izinga elimaphakathi lokudweba lama-94.1% lifinyelelwe.Isilinganiso sephutha esimaphakathi(12.6%) sasifana nocwaningo lokulinganisa lwangaphambilini(12.6%) (Umfanekiso 2b no-2c)
Ukushaya kwesakhiwo(SV): Abafonayo be-SV abasetshenziswe kulolu cwaningo bafaka i-Sniffles, i-NanoVar ne-NanoSV.Ama-SV okuzethemba okuphezulu achazwa njengama-SV akhonjwe okungenani ngabashayi ucingo ababili futhi adlulisa izihlungi ekujuleni, ubude nendawo.
Isilinganiso sama-SV angu-18,489 (okusukela ku-15,439 kuya ku-22,505) ama-SV okuzethemba okukhulu akhonjwe kusampula ngayinye.(Umfanekiso 2d, 2e kanye no-2f)
Umfanekiso 2. Ingqikithi yokuma kwezwe yama-SV akhonjwe isethi yedatha ye-Nanopore
Ukuqinisekiswa yi-PacBio: Ama-SV akhonjwe kusampula eyodwa(HG002, ingane) aqinisekiswa yidathasethi ye-PacBio HiFi.Isilinganiso sokutholwa okungamanga sisonke (i-FDR) sasingu-3.2%, okubonisa ukuhlonza okuthembekile kwe-SV ngokufundwa kwe-Nanopore.
Ama-SV angadideki nezici ze-genomic
Ama-SV angadideki: Isethi yama-SV angu-132,312 angadideki atholwe ngokuhlanganisa ama-SV kuwo wonke amasampula, ahlanganisa ama-DEL angu-67,405, 60,182 INS, 3,956 DUP kanye nama-INV angu-769.(Umfanekiso 3a)
Ukuqhathaniswa namasethi edatha e-SV akhona: Le dathasethi iqhathaniswe nedathasethi yedatha ye-TGS noma ye-NGS eshicilelwe.Kumadathasethi amane uma kuqhathaniswa, i-LRS15, okuwukuphela kwedathasethi evela kunkundla yokulandelana efunde isikhathi eside(i-PacBio) eyabelane ngokugqagqana okukhulu ngale dathasethi.Ngaphezu kwalokho, u-53.3% (70,471) wama-SVs kule dathasethi abikwe okokuqala ngqa.Ngokubheka uhlobo ngalunye lwe-SV, inani lama-INS atholiwe anedathasethi elandelanayo efunde isikhathi eside lalilikhulu kakhulu kunamanye afunde kafushane, okubonisa ukuthi ukulandelana okufunde isikhathi eside kusebenza kahle kakhulu ekutholweni kwe-INS.(Umfanekiso 3b no-3c)
Umfanekiso 3. Izakhiwo zama-SV angasadingeki ohlotsheni ngalunye lwe-SV
Izici ze-Genomic: Inombolo yama-SV itholwe ihlotshaniswa kakhulu nobude be-chromosome.Ukusatshalaliswa kwezakhi zofuzo, ukuphinda, ama-DEL(okuluhlaza), INS(okuluhlaza okwesibhakabhaka), i-DUP(ophuzi) kanye ne-INV(owolintshi) aboniswe kumdwebo we-Circos, lapho ukwanda okuvamile kwe-SV kubonwe ekupheleni kwezingalo zekhromosome.(Umfanekiso 3d no-3e)
Ubude bama-SV: Ubude bama-INS kanye nama-DEL butholakale bufushane kakhulu kunama-DUP nama-INV, obuvumelana nalawo ahlonzwe isethi yedatha ye-PacBio HiFi.Ubude bawo wonke ama-SV akhonjiwe angezwe afinyelela ku-395.6 Mb, athatha u-13.2% wayo yonke igenome yomuntu.Ama-SV athinte u-23.0 Mb(cishe. 0.8%) we-genome ngomuntu ngamunye ngokwesilinganiso.(Umfanekiso 3f no-3g)
Imithelela esebenzayo, ye-phenotypical kanye nemitholampilo yama-SV
Ukulahleka okubikezelwe kokusebenza(pLoF) SVs: ama-pLoF SV achazwa ngokuthi ama-SV asebenzisana ne-CDS, lapho ama-nucleotide ekhodi asuswa khona noma ama-ORF ashintshwa.Sekukonke ama-pLoF SV angu-1,929 athinta i-CDS yezakhi zofuzo eziyi-1,681 achazwa.Ngaphakathi kwalezo, izakhi zofuzo ezingama-38 zagqamisa “ukubopha i-immunoglobulin receptor” ekuhlaziyeni okunothisiwe kwe-GO.Lawa ma-pLoF SV aphinde achazwa yi-GWAS, i-OMIM ne-COSMIC, ngokulandelana.(Umfanekiso 4a no-4b)
I-Phenotypically and Clinical SVs ehambisanayo: Inani lama-SV kudathasethi ye-nanopore aboniswe ukuthi afaneleka ngokwedlulele nangokomtholampilo.I-heterozygous DEL eyivelakancane engu-19.3 kb, eyaziwa ngokubangela i-alpha-thalassemia, ikhonjwe kubantu abathathu, engasebenzi kahle izakhi zofuzo ze-Hemoglobin Subunit Alpha 1 kanye no-2(HBA1 kanye ne-HBA2).Enye i-DEL engu-27.4 kb ekufakweni ngekhodi kofuzo i-Hemoglobin Subunit Beta(HBB) ikhonjwe komunye umuntu.Le SV yaziwa ngokubangela i-hemoglobinopathies engathi sína.(Umfanekiso 4c)
Umfanekiso 4. PLoF SVs ehambisana nama-phenotypes kanye nezifo
I-DEL evamile engu-2.4 kb yabonwa ku-35 homozygous kanye nabathwali be-heterozygous abangu-67, ehlanganisa isifunda esiphelele se-exon yesi-3 ye-Growth Homone Receptor(GHR).Abathwali be-homozygous batholakala bebafushane kakhulu kune-heterzygous (p=0.033).(Umfanekiso 4d)
Ngaphezu kwalokho, lawa ma-SV acutshungulwa ezifundweni zokuguquguquka kwenani labantu phakathi kwamaqembu amabili esifunda: eNyakatho neNingizimu yeChina.Ama-SV ahluke kakhulu atholwe asatshalaliswa ku-Chr 1, 2, 3, 6,10,12,14 kanye no-19, lapho, aphezulu ahlotshaniswa nezifunda zokugomela, njenge-IGH, MHC, njll. Kunengqondo ukuqagela ukuthi ukuhlukaniswa kulawa ma-SV kungase kube ngenxa yokukhukhuleka kofuzo kanye nokuchayeka kwesikhathi eside ezindaweni ezihlukahlukene kubantu abancane e-China.
Ireferensi
Wu, Zhikun, et al."Izinhlobonhlobo zesakhiwo kubantu baseShayina kanye nomthelela wazo kuma-phenotypes, izifo kanye nokuguquguquka kwabantu."i-bioRxiv(2021).
Izindaba Namaphuzu Avelele ihlose ukwabelana ngamacala akamuva ayimpumelelo ne-Biomarker Technologies, ithwebula izimpumelelo zesayensi ezinoveli kanye nezindlela ezivelele ezisetshenziswe phakathi nocwaningo.
Isikhathi sokuthumela: Jan-06-2022