BUKATAR GENOME DUK
Bambance-bambancen tsari a cikin yawan jama'ar Sinawa da tasirinsu kan nau'ikan halittu, cututtuka da daidaita yawan jama'a
Nanopore |PacBio |Cikakken tsarin sake fasalin kwayoyin halitta |Kiran bambancin tsari
A cikin wannan binciken, Biomarker Technologies ne ya samar da jerin Nanopore PromethION.
Karin bayanai
A cikin wannan binciken, an bayyana cikakken yanayin bambance-bambancen tsarin (SVs) a cikin kwayoyin halittar ɗan adam tare da taimakon dogon karantawa akan dandamalin Nanopore PromethION, wanda ke zurfafa fahimtar SVs a cikin phenotypes, cututtuka da juyin halitta.
Tsarin Gwaji
Misalai: Leukocytes na jini na 405 mutanen Sinawa marasa alaƙa (maza 206 da mata 199) tare da ma'auni 68 na phenotypic da na asibiti.Daga cikin dukkanin mutane, yankunan kakanni na mutane 124 sun kasance larduna a Arewa, na mutane 198 sun kasance Kudu, 53 sun kasance Kudu maso Yamma kuma 30 ba a san su ba.
Dabarun jeri: Gabaɗayan jerin abubuwan dogon-tsara (LRS) tare da karanta Nanopore 1D da karanta PacBio HiFi.
Tsarin tsari: Nanopore PromethION;PacBio Sequel II
Kiran Bambancin Tsari
Hoto 1. Gudun aiki na kiran SV da tacewa
Babban Nasarorin
Gano bambancin tsari da tabbatarwa
Nanopore dateset: A cikin jimlar 20.7 Tb tsaftataccen karantawa da aka samar akan dandamalin jerin abubuwan PromethION, cimma matsakaita na 51 Gb bayanai akan kowane samfurin, kusan.17- ninka a cikin zurfin.
Matsakaicin daidaitawar kwayoyin halitta (GRCh38): Matsakaicin adadin taswira na 94.1% an cimma.Matsakaicin kuskuren kuskure (12.6%) yayi kama da binciken bincike na farko (12.6%) (Hoto 2b da 2c)
Bambancin tsarin (SV) kira: Masu kiran SV da aka yi amfani da su a cikin wannan binciken sun haɗa da Sniffles, NanoVar da NanoSV.An bayyana SV masu ƙarfi a matsayin SVs da aka gano ta aƙalla masu kira biyu kuma sun wuce tacewa akan zurfin, tsayi da yanki.
Matsakaicin 18,489 (daga 15,439 zuwa 22,505) an gano SVs masu ƙarfi a cikin kowane samfurin.(Hoto na 2d, 2e da 2f)
Hoto 2. Gabaɗaya shimfidar wuri na SVs da saitin Nanopore ya gano
Tabbatarwa ta PacBio: SVs da aka gano a cikin samfuri ɗaya (HG002, yaro) an inganta su ta hanyar saitin bayanan PacBio HiFi.Adadin binciken karya (FDR) ya kasance 3.2%, yana nuna ingantaccen ingantaccen ganewar SV ta Nanopore ya karanta.
SVs marasa ƙari da fasalin genomic
SVs marasa ƙarfi: An samo saitin 132,312 ba SVs mara amfani ba ta hanyar haɗa SVs a cikin duk samfuran, wanda ya haɗa da 67,405 DELs, 60,182 INSs, 3,956 DUPs da 769 INVs.(Hoto na 3 a)
Kwatanta da data kasance na SV: An kwatanta wannan saitin bayanan da aka buga TGS ko na NGS.A cikin rukunoni huɗun da aka kwatanta, LRS15, wanda kuma shine kawai saitin bayanai daga dandali mai tsayin karatu (PacBio) ya raba mafi girma tare da wannan bayanan.Bugu da ƙari, 53.3% (70,471) na SVs a cikin wannan saitin bayanan an ba da rahoton a karon farko.Ta hanyar duba cikin kowane nau'in SV, adadin INS ɗin da aka dawo dasu tare da bayanan jeri na dogon lokaci ya fi girma fiye da sauran gajerun karantawa, yana nuna cewa jerin dogon karantawa yana da inganci musamman a gano INSs.(Hoto na 3 da 3c)
Hoto 3. Abubuwan da ba su da yawa SVs ga kowane nau'in SV
Siffofin genomic: An sami adadin SVs masu alaƙa da alaƙa da tsayin chromosome.Rarraba kwayoyin halitta, maimaitawa, DELs (kore), INS (blue), DUP (rawaya) da INV (orange) an nuna su akan zane-zane na Circos, inda aka sami karuwar SV gaba ɗaya a ƙarshen makamai na chromosome.(Hoto na 3d da 3e)
Tsawon SVs: Tsawon INSs da DELs an gano sun fi guntu fiye da na DUPs da INVs, waɗanda suka yarda da waɗanda bayanan PacBio HiFi suka gano.Tsawon duk SVs da aka gano an ƙara har zuwa 395.6 Mb, wanda ya mamaye 13.2% na dukkan kwayoyin halittar ɗan adam.SVs sun shafi 23.0 Mb(kimanin. 0.8%) na kwayoyin halitta ga kowane mutum a matsakaici.(Hoto na 3f da 3g)
Tasirin aiki, phenotypical da na asibiti na SVs
Hasashen hasarar aiki(pLoF) SVs: pLoF SVs an ayyana su azaman SVs suna mu'amala da CDS, inda aka share nucleotides codeing ko aka canza ORFs.A cikin jimlar 1,929 pLoF SVs da ke shafar CDS na kwayoyin halitta 1,681 an bayyana su.A cikin waɗancan, kwayoyin halitta 38 sun ba da haske game da "ɗaurin mai karɓar immunoglobulin" a cikin binciken haɓakar GO.GWAS, OMIM da COSMIC sun kara bayanin waɗannan pLoF SVs, bi da bi.(Hoto na 4a da 4b)
Phenotypically da SVs masu dacewa na asibiti: Yawan SV a cikin bayanan nanopore an nuna su zama phenotypically da dacewa da asibiti.Wani ɗan ƙaramin heterozygous DEL na 19.3 kb, wanda aka sani yana haifar da alpha-thalassaemia, an gano shi a cikin mutane uku, waɗanda ba su da aiki ga ƙwayoyin haemoglobin Subunit Alpha 1 da 2 (HBA1 da HBA2).Wani DEL na 27.4kb akan gene codeing Haemoglobin Subunit Beta(HBB) an gano shi a cikin wani mutum.An san wannan SV yana haifar da mummunan haemoglobinopathies.(Hoto na 4c)
Hoto 4. pLoF SVs hade da phenotypes da cututtuka
An lura da DEL na kowa na 2.4 kb a cikin masu ɗaukar homozygous 35 da 67 heterozygous, wanda ya ƙunshi cikakken yanki na 3rd exon na Girman Homone Receptor (GHR).An sami masu ɗaukar homozygous sun fi guntu fiye da na heterzygous (p=0.033).(Hoto na 4d)
Bugu da ƙari, an sarrafa waɗannan SVs don nazarin juyin halittar jama'a tsakanin ƙungiyoyin yanki guda biyu: Arewa da Kudancin China.An sami SVs masu mahimmanci waɗanda aka rarraba akan Chr 1, 2, 3, 6,10,12,14 da 19, wanda a ciki, manyan waɗanda ke da alaƙa da yankuna na rigakafi, kamar IGH, MHC, da sauransu. Yana da kyau a yi la'akari da cewa Bambance-bambance a cikin waɗannan SVs na iya zama saboda rarrabuwar kawuna na kwayoyin halitta da kuma fallasa na dogon lokaci ga yanayi daban-daban na ƙananan jama'a a China.
Magana
Wu, Zhikun, et al."Bambance-bambancen tsarin jama'ar Sinawa da tasirinsu kan nau'ikan halittu, cututtuka da daidaitawar yawan jama'a."bioRxiv(2021).
Labarai da Labarai yana da niyyar raba sabbin maganganu masu nasara tare da Biomarker Technologies, ɗaukar sabbin nasarorin kimiyya gami da fitattun dabarun da aka yi amfani da su yayin binciken.
Lokacin aikawa: Janairu-06-2022