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Ukuhlaziywa Kobudlelwano Bomhlaba Wonke be-Genome
Inhloso ye-Genome-Wide Association Studies (GWAS) ukuhlonza izinhlobo zezakhi zofuzo (izinhlobo zezakhi zofuzo) ezixhunyaniswe nezici ezithile (izinhlobo ze-phenotype). Ngokuhlola izimpawu zezakhi zofuzo kulo lonke i-genome kubantu abaningi, i-GWAS ikhipha izinhlangano ze-genotype-phenotype ngokusebenzisa ukuhlaziywa kwezibalo ezingeni labantu. Le ndlela ithola ukusetshenziswa okubanzi ekucwaningeni izifo zabantu nasekuhloleni izakhi zofuzo ezisebenzayo ezihlobene nezici eziyinkimbinkimbi ezilwaneni noma ezitshalweni.
Kwa-BMKGENE, sinikeza izindlela ezimbili zokwenza i-GWAS kubantu abaningi: ukusebenzisa i-Whole-Genome Sequencing (WGS) noma ukukhetha indlela yokulandelela i-genome encishisiwe, i-Specific-Locus Amplified Fragment (SLAF) ethuthukiswe ngaphakathi endlini. Ngenkathi i-WGS ifanela ama-genome amancane, i-SLAF ivela njengendlela engcono kakhulu yokufunda abantu abaningi abanama-genome amade, inciphisa ngempumelelo izindleko zokulandelela, ngenkathi iqinisekisa ukusebenza kahle kokuthola uphawu lwezakhi zofuzo.
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Ukulandelana Kwezakhi Zofuzo Zezitshalo/Zezilwane
I-Whole Genome Sequencing (WGS) inqubo esetshenziswa ukunquma ngokuphelele ukulandelana kwe-DNA ye-genome yesidalwa ngesikhathi esisodwa.
Ngokuvamile, le nsizakalo ihlukaniswe ngamaqembu amabili ahlukene kuye ngokuthi kukhona i-genome ebhekisela kuyo:
- De novoukulandelana kwe-genome ephelele.Kulesi simo, i-genome ezolandelaniswa ayinayo i-genome yokubhekisela etholakalayo, futhi ngenxa yaleso sizathu, inhloso yalokhu kulandelana ukuyikhiqiza (noma ukuthuthukisa ekhona). Le ndlela idinga ukusebenzisa kokubili, idatha ye-Illumina kanye nokulandelana kokufunda isikhathi eside ukuthuthukisa ukuhlanganiswa kwe-genome ngokudala ukufana phakathi kokufundwa.
- Ukulandelanisa kabusha.Kubhekisela ekulandeleni konke kwezakhi zofuzo zabantu abahlukene bezinhlobo ngezinhlobo zofuzo ezaziwa ngokuthi ama-genome. Ngalesi sisekelo, umehluko wezakhi zofuzo wabantu noma abantu ungabonakala kabanzi.
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Izakhi Zofuzo Ezivela Emvelweni
I-Evolutionary Genetics iyisevisi ephelele yokulandelana eyenzelwe ukunikeza incazelo eqondakalayo yokuvela kwezakhi zofuzo ngaphakathi kweqembu elikhulu labantu, ngokusekelwe ekuhlukeni kwezakhi zofuzo, okuhlanganisa ama-SNP, ama-InDels, ama-SV, nama-CNV. Le nsizakalo ihlanganisa konke ukuhlaziya okubalulekile okudingekayo ukuze kucaciswe ukushintsha kokuvela kwezakhi zofuzo kanye nezici zezakhi zofuzo zabantu, okuhlanganisa ukuhlolwa kwesakhiwo sabantu, ukuhlukahluka kwezakhi zofuzo, kanye nobudlelwano be-phylogenetic. Ngaphezu kwalokho, ihlola izifundo ngokugeleza kwezakhi zofuzo, okwenza kube lula ukulinganisa ubukhulu benani labantu kanye nesikhathi sokwehlukana. Izifundo zezakhi zofuzo eziguqukayo ziveza ukuqonda okubalulekile ngemvelaphi kanye nokuzivumelanisa kwezinhlobo.
Kwa-BMKGENE, sinikeza izindlela ezimbili zokwenza izifundo zezakhi zofuzo eziziphendukela kwemvelo kubantu abaningi: ukusebenzisa ukulandelana kwezakhi zofuzo eziphelele (i-WGS) noma ukukhetha indlela yokulandelelana kwezakhi zofuzo encishisiwe, i-Specific-Locus Amplified Fragment (SLAF) ethuthukiswe ngaphakathi endlini. Nakuba i-WGS ifanelana nama-genome amancane, i-SLAF ivela njengendlela engcono kakhulu yokufunda abantu abaningi abanama-genome amade, okunciphisa ngempumelelo izindleko zokulandelana.
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I-Genomics Eqhathanisayo
I-genomics yokuqhathanisa ihilela ukuhlolwa nokuqhathanisa ukulandelana kwezakhi zofuzo kanye nezakhiwo phakathi kwezinhlobo ezahlukene. Lo mkhakha ufuna ukwembula ukuvela kwezinhlobo, ukucacisa imisebenzi yezakhi zofuzo, nokucacisa izindlela zokulawula izakhi zofuzo ngokuhlonza izakhiwo zokulandelana ezigciniwe noma ezihlukene nezinto eziphilayo ezihlukahlukene. Ucwaningo oluphelele lwe-genomics lokuqhathanisa luhlanganisa ukuhlaziywa okufana nemindeni yezakhi zofuzo, intuthuko yokuziphendukela kwemvelo, imicimbi yokuphindaphindwa kwezakhi zofuzo eziphelele, kanye nomthelela wezingcindezi ezikhethiwe.
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Ukuhlanganiswa Kwe-Genome Okusekelwe ku-Hi-C
I-Hi-C iyindlela eklanyelwe ukubamba ukumiswa kwe-chromosome ngokuhlanganisa ukusebenzisana okusekelwe ekuhloleni ukusondelana kanye nokulandelana okuphezulu. Ukuqina kwalokhu kusebenzisana kukholakala ukuthi kuhlobene kabi nebanga elingokoqobo kuma-chromosome. Ngakho-ke, idatha ye-Hi-C isetshenziselwa ukuqondisa ukuhlanganiswa, ukuhleleka, kanye nokuqondiswa kokulandelana okuhlanganisiwe ku-genome ehleliwe kanye nokunamathela kunani elithile lama-chromosome. Lobu buchwepheshe bunika amandla ukuhlanganiswa kwe-genome yezinga le-chromosome lapho kungekho imephu yezakhi zofuzo esekelwe kubantu. I-genome ngayinye idinga i-Hi-C.
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Ukulandelanisa Kwezitshalo/Isilwane Se-De Novo Genome
I-De NovoUkulandelana kubhekisela ekwakhiweni kwe-genome yonke yohlobo kusetshenziswa ubuchwepheshe bokulandelana ngaphandle kwe-genome yokubhekisela. Ukwethulwa kanye nokwamukelwa kabanzi kokulandelana kwesizukulwane sesithathu, okuhlanganisa ukufunda okude, kuye kwathuthukisa kakhulu ukuhlanganiswa kwe-genome ngokwandisa ukuhlangana phakathi kokufundwa. Lokhu kuthuthukiswa kubaluleke kakhulu lapho kubhekene nama-genome ayinselele, njengalawo abonisa i-heterozygosity ephezulu, isilinganiso esiphezulu sezifunda eziphindaphindayo, ama-polyploid, kanye nezifunda ezinezici eziphindaphindayo, okuqukethwe kwe-GC okungavamile, noma ubunzima obukhulu obuvame ukuhlanganiswa kabi kusetshenziswa ukulandelana kokufunda okufushane kuphela.
Isixazululo sethu esisodwa sinikeza izinsizakalo zokulandelana ezihlanganisiwe kanye nokuhlaziywa kwe-bioinformatic okuletha i-genome ehlanganisiwe yekhwalithi ephezulu. Ucwaningo lokuqala lwe-genome ne-Illumina lunikeza izilinganiso zobukhulu be-genome kanye nobunzima, futhi lolu lwazi lusetshenziselwa ukuqondisa isinyathelo esilandelayo sokulandelana okufundwa isikhathi eside nge-PacBio HiFi, kulandelwe yide novoukuhlanganiswa kwama-contig. Ukusetshenziswa okulandelayo kwe-HiC assembly kwenza kube lula ukunamathela kwama-contig ku-genome, kutholakale i-chromosome-level assembly. Okokugcina, i-genome ichazwa ngokubikezela izakhi zofuzo nangokulandelanisa izakhi zofuzo eziveziwe, kusetshenziswe ama-transcriptome anokufundwa okufushane nokude.
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Ukulandelana Kwe-Exome Yabantu Bonke
Ukulandelana kwe-Human Whole exome (hWES) kwamukelwa kabanzi njengendlela yokulandelana engabizi kakhulu futhi enamandla yokuthola izinguquko ezibangela izifo. Naphezu kokuthi yakha cishe u-1.7% we-genome yonke, ama-exons adlala indima ebalulekile ngokubonakalisa ngqo iphrofayili yemisebenzi yeprotheni iyonke. Okuphawulekayo ukuthi, ku-genome yomuntu, ngaphezu kuka-85% wezinguquko ezihlobene nezifo ezibonakala ezindaweni zokubhala ikhodi yamaprotheni. I-BMKGENE inikeza insizakalo ephelele futhi eguquguqukayo yokulandelana kwe-human whole exome enamasu amabili ahlukene okubamba ama-exon atholakalayo ukuze kuhlangatshezwane nemigomo eyahlukene yocwaningo.
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Ukulandelana Kwezingcezu Ezihlanganisiwe Zendawo Ethile (SLAF-Seq)
Le ndlela eyasungulwa ngokuzimela yi-BMKGene, ingahlukaniswa ngaphakathi kokulandelana kwe-genome okuncishisiwe. Ithuthukisa isethi ye-enzyme yokukhawulela yonke iphrojekthi. Lokhu kuqinisekisa ukukhiqizwa kwenani elikhulu lamathegi e-SLAF (izifunda ezingu-400-500 bps ze-genome ezilandelanayo) ezisatshalaliswa ngokulinganayo kulo lonke i-genome ngenkathi zigwema ngempumelelo izifunda eziphindaphindayo, ngaleyo ndlela ziqinisekisa ukutholakala kwezimpawu zofuzo ezinhle kakhulu.
Ihlinzeka nge-genotyping esheshayo futhi ibeka isisekelo sokutholakala kwezakhi zofuzo ezisebenzayo noma ukuhlaziywa kokuziphendukela kwemvelo okunciphisa izindleko ngesampula ngayinye ngenkathi kugcinwa ukusebenza kahle ekutholakaleni kwezimpawu zezakhi zofuzo. I-RRGS ifinyelela lokhu ngokugaya i-DNA ngama-enzyme okukhawulela nokugxila ebangeni elithile losayizi wezingcezu, ngaleyo ndlela ilandelela ingxenye encane kuphela ye-genome. Phakathi kwezindlela ezahlukene ze-RRGS, i-Specific-Locus Amplified Fragment Sequencing (SLAF) iyindlela engenziwa ngokwezifiso futhi esezingeni eliphezulu.
