ZONSE GENOME RESEQUENING
Mitundu yosiyanasiyana ya anthu aku China komanso momwe amakhudzira phenotypes, matenda komanso kusintha kwa anthu
Nanopore |PacBio |Kusanjanso kwamtundu wonse |Kuyitanira kosiyanasiyana kwamapangidwe
Mu kafukufukuyu, kutsatizana kwa Nanopore PromethION kudaperekedwa ndi Biomarker Technologies.
Mfundo zazikuluzikulu
Mu kafukufukuyu, mawonekedwe amitundu yonse yamitundu yosiyanasiyana (SVs) mu ma genome amunthu adawululidwa mothandizidwa ndi kutsata kwanthawi yayitali pa Nanopore PromethION platfrom, komwe kumakulitsa kumvetsetsa kwa ma SV mu phenotypes, matenda ndi chisinthiko.
Mapangidwe Oyesera
Zitsanzo: Ma leukocyte amagazi ozungulira a 405 anthu achi China osagwirizana (206 amuna ndi 199 akazi) okhala ndi 68 phenotypic ndi miyeso yachipatala.Pakati pa anthu onse, zigawo za makolo a anthu 124 zinali zigawo kumpoto, anthu 198 anali South, 53 anali SouthWest ndipo 30 sanali kudziwika.
Njira yotsatirira: Kutsata kwanthawi yayitali kwa genome (LRS) yokhala ndi mawerengedwe a Nanopore 1D ndikuwerenga kwa PacBio HiFi.
Sequencing nsanja: Nanopore PromethION;PacBio Sequel II
Kuyimba kwa Kusintha kwa Kapangidwe
Chithunzi 1. Kuyenda kwa ntchito kwa SV kuyimba ndi kusefa
Zochita Zazikulu
Kupezeka kwa kusintha kwa kamangidwe ndi kutsimikizira
Nanopore dateset: Pazokwana 20.7 Tb zowerengera zoyera zomwe zimapangidwa pa nsanja yotsatirira ya PromethION, ndikukwaniritsa avareji ya data ya 51 Gb pachitsanzo chilichonse, pafupifupi.17-kuzama mozama.
Reference genome alignment(GRCh38): Avereji yamapu a 94.1% adakwaniritsidwa.Chiwerengero cha zolakwika (12.6%) chinali chofanana ndi kafukufuku wam'mbuyomu (12.6%) (Chithunzi 2b ndi 2c)
Kuyimba kwa Structure (SV): Oyimba a SV omwe adagwiritsidwa ntchito mu kafukufukuyu adaphatikizapo Sniffles, NanoVar ndi NanoSV.Ma SV odalirika kwambiri amatanthauzidwa kuti ndi ma SV omwe amadziwika ndi osachepera awiri oimba ndipo adadutsa zosefera pakuya, kutalika ndi dera.
Pafupifupi 18,489 (kuyambira 15,439 mpaka 22,505) ma SV odzidalira kwambiri adadziwika pachitsanzo chilichonse.(Chithunzi 2d, 2e ndi 2f)
Chithunzi 2. Mawonekedwe onse a ma SV odziwika ndi Nanopore dataset
Kutsimikiziridwa ndi PacBio: Ma SV odziwika mu chitsanzo chimodzi (HG002, mwana) adatsimikiziridwa ndi deta ya PacBio HiFi.Chiwopsezo chodziwika bwino chabodza (FDR) chinali 3.2%, kuwonetsa chizindikiritso chodalirika cha SV chowerengedwa ndi Nanopore.
Ma SV osafunikira komanso mawonekedwe a genomic
Ma SV osagwiritsidwa ntchito: Gulu la 132,312 losagwiritsidwa ntchito linapezedwa mwa kuphatikiza ma SV mu zitsanzo zonse, zomwe zimaphatikizapo 67,405 DELs, 60,182 INSs, 3,956 DUPs ndi 769 INVs.(Chithunzi 3a)
Poyerekeza ndi ma data a SV omwe analipo: Seti iyi idayerekezedwa ndi dataset ya TGS kapena NGS yosindikizidwa.M'kati mwazinthu zinayi zofananira, LRS15, yomwenso ndi data yokhayo yochokera papulatifomu yowerengera nthawi yayitali (PacBio) idagawana kuphatikizika kwakukulu ndi deta iyi.Komanso, 53.3% (70,471) ya SVs mu dataset iyi idanenedwa koyamba.Poyang'ana mumtundu uliwonse wa SV, kuchuluka kwa ma INS omwe adachira omwe ali ndi data yowerengera nthawi yayitali kunali kokulirapo kuposa ena onse owerengeka mwachidule, zomwe zikuwonetsa kuti kutsata kowerengera nthawi yayitali kumakhala kothandiza kwambiri pakuzindikira ma INS.(Chithunzi 3b ndi 3c)
Chithunzi 3. Katundu wa ma SV osagwiritsidwa ntchito pamtundu uliwonse wa SV
Mawonekedwe a Genomic: Chiwerengero cha ma SV chinapezeka chogwirizana kwambiri ndi kutalika kwa chromosome.Kugawidwa kwa majini, kubwereza, DELs (wobiriwira), INS (buluu), DUP (yellow) ndi INV (lalanje) adawonetsedwa pazithunzi za Circos, pomwe kuwonjezeka kwakukulu kwa SV kunawonedwa kumapeto kwa mikono ya chromosome.(Chithunzi 3d ndi 3e)
Kutalika kwa SVs: Kutalika kwa INSs ndi DELs kunapezeka kuti ndi kochepa kwambiri kuposa ma DUPs ndi INVs, omwe adagwirizana ndi omwe amadziwika ndi PacBio HiFi dataset.Utali wa ma SV onse odziwika adawonjezedwa mpaka 395.6 Mb, yomwe idatenga 13.2% yamtundu wonse wamunthu.Ma SV adakhudza 23.0 Mb (pafupifupi 0.8%) ya genome pa munthu aliyense pafupifupi.(Chithunzi 3f ndi 3g)
Kugwira ntchito, phenotypical ndi zotsatira zachipatala za SVs
Kutayika kwadziwikiratu kwa ntchito (pLoF) SVs: pLoF SVs amatanthauzidwa ngati ma SV omwe amalumikizana ndi ma CDS, pomwe ma nucleotide olembera adachotsedwa kapena ORF adasinthidwa.Pazonse za 1,929 pLoF SVs zomwe zimakhudza CDS za majini 1,681 zidafotokozedwa.Mkati mwawo, majini 38 adawunikira "kumanga kwa immunoglobulin receptor" pakuwunika kopindulitsa kwa GO.PLoF SVs izi zidafotokozedwanso ndi GWAS, OMIM ndi COSMIC, motsatana.(Chithunzi 4a ndi 4b)
Ma SV a Phenotypically and Clinical SVs: Ma SV angapo mu dataset ya nanopore adawonetsedwa kuti ndi a phenotypically komanso achipatala.Heterozygous DEL yosowa kwambiri ya 19.3 kb, yomwe imadziwika kuti imayambitsa alpha-thalassemia, idadziwika mwa anthu atatu, omwe amasokonekera mwa majini a Hemoglobin Subunit Alpha 1 ndi 2(HBA1 ndi HBA2).DEL ina ya 27.4 kb pa gene coding Hemoglobin Subunit Beta(HBB) idadziwika mwa munthu wina.SV iyi idadziwika kuti imayambitsa hemoglobinopathies.(Chithunzi 4c)
Chithunzi 4. pLoF SVs yokhudzana ndi phenotypes ndi matenda
DEL wamba wa 2.4 kb adawonedwa mu 35 homozygous ndi 67 heterozygous zonyamulira, zomwe zimaphimba chigawo chonse cha 3rd exon ya Growth Homone Receptor(GHR).Zonyamula homozygous zinapezeka zazifupi kwambiri kuposa za heterzygous (p=0.033).(Chithunzi 4d)
Kuphatikiza apo, ma SV awa adasinthidwa kuti aphunzire za chisinthiko cha anthu pakati pa magulu awiri amchigawo: Kumpoto ndi Kumwera kwa China.Ma SV osiyanitsa kwambiri adapezeka akugawidwa pa Chr 1, 2, 3, 6,10,12,14 ndi 19, momwemo, apamwamba adalumikizidwa ndi zigawo zachitetezo, monga IGH, MHC, ndi zina. Ndizomveka kuganiza kuti kusiyana kwa ma SV awa kutha chifukwa cha kusuntha kwa majini komanso kuwonekera kwanthawi yayitali kumadera osiyanasiyana a anthu okhala ku China.
Buku
Wu, Zhikun, et al."Kusiyanasiyana kwamapangidwe a anthu aku China komanso momwe amakhudzira phenotypes, matenda komanso kusintha kwa anthu."bioRxiv(2021).
Nkhani ndi Mfundo Zazikulu ikufuna kugawana milandu yaposachedwa kwambiri ndi Biomarker Technologies, kujambula zomwe zakwaniritsa zasayansi komanso njira zodziwika bwino zomwe zimagwiritsidwa ntchito pophunzira.
Nthawi yotumiza: Jan-06-2022