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I-Genome-wide Association Analysis
Inhloso ye-Genome-Wide Association Studies (GWAS) ukukhomba okuhlukile kofuzo (ama-genotype) axhunywe nezici ezithile (phenotypes). Ngokuhlolisisa izimpawu zofuzo kulo lonke i-genome ngenani elikhulu labantu, i-GWAS ikhipha izinhlangano ze-genotype-phenotype ngokuhlaziywa kwezibalo zezinga labantu. Le ndlela yokwenza ithola ukusetshenziswa okubanzi ekucwaningeni izifo zabantu kanye nokuhlola izakhi zofuzo ezisebenzayo ezihlobene nezici eziyinkimbinkimbi ezilwaneni noma ezitshalweni.
Kwa-BMKGENE, sinikeza izindlela ezimbili zokuqhuba i-GWAS kubantu abaningi: ukusebenzisa i-Whole-Genome Sequencing (WGS) noma ukukhetha indlela encishisiwe yokumelela igenome yokulandelanisa, i-Specific-Locus Amplified Fragment (SLAF) ethuthukisiwe endlini. Nakuba i-WGS ifanele ama-genome amancane, i-SLAF ivela njengendlela engabizi kakhulu yokutadisha abantu abaningi abanama-genome amade, inciphisa ngempumelelo izindleko zokulandelana, kuyilapho iqinisekisa ukutholakala komaka okuphezulu kofuzo.
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Ukulandelana Kohlobo Lonke Lwezitshalo/Izilwane
I-Whole Genome Sequencing (WGS), eyaziwa nangokuthi i-requencing, ibhekisela kukho konke ukulandelana kofuzo lwabantu abahlukene bezinhlobo zofuzo ezaziwayo eziyireferensi. Ngalesi sisekelo, ukuhlukana kwe-genomic kwabantu noma imiphakathi kungabuye kukhonjwe. I-WGS inika amandla ukuhlonzwa kwe-Single Nucleotide Polymorphism (SNP), Ukususwa Kokufaka (InDel), Ukuhluka Kwesakhiwo (SV), kanye Nokwehluka Kwenombolo Yekhophi (CNV). Ama-SV ahlanganisa ingxenye enkulu yesisekelo sokuhluka kunama-SNP futhi anomthelela omkhulu ku-genome, okuthinta kakhulu izinto eziphilayo. Nakuba ukuphinda kufundwe okufushane kuphumelela ekuhlonzeni ama-SNP nama-InDels, ukuphinda kufundwe isikhathi eside kuvumela ukuhlonza okunembe kakhudlwana kwezingcezu ezinkulu nokuhluka okuyinkimbinkimbi.
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I-Evolutionary Genetics
I-Evolutionary Genetics iyisevisi egcwele yokulandelana eklanyelwe ukunikeza incazelo enokuqonda yokuziphendukela kwemvelo eqenjini elikhulu labantu, ngokusekelwe ezinhlobonhlobo zofuzo, okuhlanganisa ama-SNP, ama-InDels, ama-SV, nama-CNV. Le sevisi ihlanganisa konke ukuhlaziya okubalulekile okudingekayo ukuze kucaciswe izinguquko zokuziphendukela kwemvelo kanye nezici zofuzo zabantu, okuhlanganisa ukuhlolwa kwesakhiwo sabantu, ukuhlukahluka kwezakhi zofuzo, nobudlelwano be-phylogenetic. Ngaphezu kwalokho, ingena ezifundweni zokugeleza kwezakhi zofuzo, okuvumela ukulinganiswa kobukhulu besibalo esisebenzayo nesikhathi sokuhlukana. Izifundo zofuzo zokuziphendukela kwemvelo zinikeza ukuqonda okubalulekile ngemvelaphi nokuvumelana kwezinhlobo zezilwane.
Kwa-BMKGENE, sinikeza izindlela ezimbili zokwenza izifundo zofuzo zokuziphendukela kwemvelo kubantu abaningi: sisebenzisa ukulandelana kwe-whole-genome (WGS) noma ukukhetha indlela encishisiwe yokulandelanisa i-genome, i-Specific-Locus Amplified Fragment (SLAF) ethuthukisiwe. Nakuba i-WGS ifanela ama-genomes amancane, i-SLAF ivela njengendlela engabizi kakhulu yokutadisha imiphakathi emikhulu enama-genome amade, inciphisa ngempumelelo izindleko zokulandelana.
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I-Genomics yokuqhathanisa
I-genomics yokuqhathanisa ihilela ukuhlolwa nokuqhathaniswa kwakho konke ukulandelana kwe-genome nezakhiwo phakathi kwezinhlobo ezahlukene. Lo mkhakha uhlose ukwembula ukuvela kwezinhlobo zezinto eziphilayo, ukunquma imisebenzi yofuzo, kanye nokucacisa izindlela zokulawula izakhi zofuzo ngokuhlonza izakhiwo zokulandelana ezilondoloziwe noma ezihlukene kanye nezakhi kuzo zonke izinto eziphilayo. Ucwaningo olunzulu lwe-genomics oluqhathanisayo luhlanganisa ukuhlaziya okufana nemindeni yezakhi zofuzo, ukukhula kokuziphendukela kwemvelo, izehlakalo zokuphindaphinda igenomu yonke, kanye nomthelela wezingcindezi ezikhethiwe.
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I-Hi-C Based Genome Assembly
I-Hi-C iyindlela edizayinelwe ukuthwebula ukucushwa kwe-chromosome ngokuhlanganisa ukusebenzelana okusekelwe ekuhloleni kanye nokulandelana komphumela ophezulu. Ukuqina kwalokhu kusebenzisana kukholakala ukuthi kuhlotshaniswa kabi nebanga elingokomzimba kuma-chromosome. Ngakho-ke, idatha ye-Hi-C isetshenziselwa ukuqondisa ukuhlanganisa, ukuhleleka, nokuqondiswa kokulandelana okuhlanganisiwe ku-genome esalungiswa kanye nokunamathisela lezo ezinombolweni ezithile zama-chromosome. Lobu buchwepheshe bunika amandla ukuhlanganiswa kwegenome yezinga le-chromosome ngaphandle kwemephu yofuzo esekelwe kubantu. Yonke i-genome eyodwa idinga i-Hi-C.
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Ukulandelanisa Kwezitshalo/Isilwane Se-De Novo Genome
De Novoukulandelana kubhekisela ekwakhiweni kwegenome yohlobo lonke kusetshenziswa ubuchwepheshe bokulandelana lapho ingekho i-genome eyireferensi. Ukwethulwa nokwamukelwa okusabalele kokulandelana kwesizukulwane sesithathu, okufaka ukufundwa okude, kuthuthukise kakhulu ukuhlangana kofuzo ngokwandisa ukugqagqana phakathi kokufundwayo. Lesi sithuthukisi sifanelekile ikakhulukazi lapho usebenza nama-genomes ayinselele, njengalawo abonisa i-heterozygosity ephezulu, isilinganiso esiphezulu sezifunda eziphindaphindayo, ama-polyploid, nezifunda ezinezici eziphindaphindayo, okuqukethwe kwe-GC okungavamile, noma ukuba yinkimbinkimbi okuphezulu ngokuvamile okungahlanganiswanga kahle kusetshenziswa ukulandelana kokufundwa okufushane. yedwa.
Isixazululo sethu sokuma okukodwa sihlinzeka ngezinsizakalo zokulandelana ezididiyelwe kanye nokuhlaziywa kwe-bioinformatic okuletha i-genome ehlanganisiwe yekhwalithi ephezulu ye-de novo. Inhlolovo yokuqala ye-genome ne-Illumina inikeza izilinganiso zobukhulu bofuzo nobunkimbinkimbi, futhi lolu lwazi lusetshenziselwa ukuqondisa isinyathelo esilandelayo sokulandelana okufundwe isikhathi eside nge-PacBio HiFi, kulandelwade novoukuhlanganiswa kwama-contigs. Ukusetshenziswa okulandelayo kokuhlanganiswa kwe-HiC kunika amandla ukunamathela kwama-contig ku-genome, kutholwe ukuhlangana kweleveli ye-chromosome. Okokugcina, i-genome ichazwa ngokubikezela kwezakhi zofuzo nangokulandelanisa izakhi zofuzo eziveziwe, iphendukela kuma-transcriptomes anokufundwa okufushane nokude.
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Ukulandelana kwe-Human Whole Exome
I-Human Whole exome sequencing (hWES) yaziwa kabanzi njengendlela engabizi kakhulu futhi enamandla yokulandelanisa ukukhomba uguquko olubanga izifo. Naphezu kokwakha cishe u-1.7% walo lonke uhlobo lofuzo, ama-exons adlala indima ebalulekile ngokubonisa ngokuqondile iphrofayili yengqikithi yokusebenza kwamaprotheni. Ngokuphawulekayo, ku-genome yomuntu, ngaphezu kwe-85% yokuguqulwa kwezifo ezihlobene nezifo kubonakala ngaphakathi kwezifunda zekhodi yamaprotheni. I-BMKGENE inikeza insizakalo yokulandelanisa ye-exome ephelele futhi eguquguqukayo enamasu amabili ahlukene okuthwebula ama-exon atholakalayo ukuze kuhlangatshezwane nezinjongo zocwaningo ezihlukahlukene.
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I-Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)
I-genotyping ephezulu kakhulu, ikakhulukazi kubantu abaningi, iyisinyathelo esibalulekile ocwaningweni lwenhlangano yofuzo futhi ihlinzeka ngesisekelo sofuzo sokutholwa kwezakhi zofuzo ezisebenzayo, ukuhlaziya kokuziphendukela kwemvelo, njll. Esikhundleni sokulandelana kabusha kwegenomu ejulile,Ukumelela Okuncishisiwe Ukulandelana Kwe-genome (RRGS)kuvame ukusetshenziswa kulezi zifundo ukuze kuncishiswe izindleko zokulandelanisa isampula ngayinye kuyilapho kugcinwa ukusebenza kahle okunengqondo ekutholweni komaka wofuzo. I-RRGS ifinyelela lokhu ngokugaya i-DNA enama-enzyme anomkhawulo futhi igxile kububanzi obuthile bosayizi wesiqephu, ngaleyo ndlela ilandelana kuphela ingxenye encane ye-genome. Phakathi kwezindlela ezihlukahlukene ze-RRGS, i-Specific-Locus Amplified Fragment Sequencing (SLAF) iyindlela yokwenza ngokwezifiso nekhwalithi ephezulu. Le ndlela, ethuthukiswe ngokuzimela yi-BMKGene, ithuthukisa i-enzyme yokuvinjelwa esethelwe yonke iphrojekthi. Lokhu kuqinisekisa ukukhiqizwa kwenani elikhulu lamathegi e-SLAF (izifunda ezingama-400-500 bps ze-genome ezilandelanayo) asatshalaliswa ngokufanayo kulo lonke uhlobo lofuzo kuyilapho kugwema ngempumelelo izifunda eziphindaphindayo, ngaleyo ndlela kuqinisekisa ukutholakala komaka kofuzo okungcono kakhulu.
