Riba:
- Ƙarfin fahimtar tsarin VCF, bayanin HGVS (c./p./g.) da ma'auni na ACMG pathogenicity kuma suna da basirar wucin gadi suna samar da daftarin shaida.
- Ikon tabbatar da kowace shaida ta ACMG (yawan yawan jama'a, a cikin siliki, rarrabuwa, wallafe-wallafe) a cikin kafofin kamar ClinVar da gnomAD
- Ability don amfani da ka'idodin kama nau'in genome da daidaita kurakuran tsarin kuma ba barin rarrabuwa ta ƙarshe zuwa hankali na wucin gadi.
Halin halittar mutum ya bambanta da abin da aka ambata a miliyoyin maki; Yawancin waɗannan bambance-bambance ba su da lahani ("m"), kaɗan ne ke haifar da cuta ("pathogenic"). Bambance-bambancen fassarar shine aikin yanke shawarar wane nau'in bambanci ya shiga kuma shine zuciyar kwayoyin halitta na asibiti. A cikin wannan rukunin, zaku koyi yadda ake amfani da hankali na wucin gadi (AI) azaman tattara shaida, taƙaitawa da tsara mataimaki a cikin fassarar bambance-bambancen; amma za ku koyi dalilin da yasa yanke shawara na ƙarshe ya kamata ya kasance ƙarƙashin amincewar masana.
Gargadi mai mahimmanci da farko: Tambayi AI "wannan bambance-bambancen pathogenic?" Kar a taba amincewa da amsar kalma daya da kuka tambaya. AI na iya amincewa da cewa aji ba tare da shaida ba; zai iya dacewa da mitar yawan jama'a na bambance-bambancen, bayanan asibiti na baya, ko nazarin aiki. Hanyar da ta dace ita ce yin amfani da AI don gina tsarin shaida kuma da kaina tabbatar da kowane yanki na shaida a tushen farko.
Ka'idoji na asali
- VCF (Tsarin Kira na Bambanci): Daidaitaccen tsarin fayil wanda ke jera bambance-bambance a cikin samfurin; Kowane layi yana ɗauke da chromosome, matsayi, tushen tunani, madadin tushe da ingantaccen bayani.
- Bayanan HGVS: Daidaitaccen tsarin rubutu tare da bambance-bambancen karatu. c. matsayinsa a cikin jerin coding, p. canjin furotin, g. Yana nuna wurin genomic. Misali NM_000546.6:c.743G>A da p.Arg248Gln.
- gnomAD: Database tattara bambance-bambancen mitoci na dubban daruruwan mutane; Yana nuna yadda bambancin ya zama gama gari a cikin al'umma. Bambance-bambancen gama-gari ba gabaɗaya ba cuta bane.
- ClinVar: bayanan jama'a suna tattara fassarori na asibiti na bambance-bambancen.
- Sharuɗɗan ACMG/AMP: Tsarin shaida na Kwalejin Ilimin Jiniyoyin Kiwon Lafiyar Jama'a na Amurka wanda ya raba bambance-bambancen zuwa nau'i biyar: Pathogenic, Mai yiwuwa Pathogenic, Bambancin Muhimmancin Rashin tabbas (VUS), Yiwuwa Mai Kyau, Mai Kyau.
Lambobin shaida na ACMG: taƙaitaccen taswira
Tsarin ACMG yana bayyana lambobin shaida a cikin jagorancin pathogenic (PVS, PS, PM, PP) da kuma a cikin m shugabanci (BA, BS, BP); Waɗannan suna taruwa don tantance aji. AI yana da kyau wajen bayyana abin da waɗannan lambobin ke nufi, amma dole ne ku tabbatar da bayanan da aka aiwatar da lambar a zahiri.
Lambar
Ma'ana (taƙaice)
Inda za a tabbatar da tushen
Farashin PVS1
Shaida mai ƙarfi da ke haifar da asarar aiki (misali dakatarwa da wuri)
Rubuce-rubucen, yanki, dangantakar cututtuka-jini
PS1/PS3
Amino acid iri ɗaya / nazarin aiki kamar yadda aka sani pathogenic
ClinVar, labarin aikin da aka yi bita na tsara
PM2
Yana da wuya/ba a samuwa a cikin yawan jama'a
mitar gnomAD
PP3/BP4
Hasashen ƙididdigewa a cikin jagorar cututtukan cututtuka / mara kyau
Kayan aikin kimantawa (ijma'i)
BA1/BS1
Yawan yawa ya yi yawa don zama pathogenic
mitar gnomAD
BP6/PP5
(Ba a ƙara ba da shawarar) dogaro da fassarar wani
-
Tukwici: PM2 (rarity) da BA1/BS1 (na kowa) yanke shawara sun dogara kai tsaye akan mitar gnomAD kuma sune mafi sauƙin tabbatarwa shaida. Duba bambance-bambancen farko akan gnomAD; Bambance-bambancen da ke cikin fiye da kashi 1% na yawan jama'a ba shi da haɗari.
Mataki-mataki: bambance-bambancen taimakon AI
1. Gyara bambance-bambance zuwa daidaitaccen bayanin kula. Bayyana sigar genome, kwafi, da wakilcin HGVS. Bambanci daga AI duka c. biyu p. biyu g. , sannan tabbatar da shi tare da mai inganci (kamar VariantValidator).
2. Shin AI ta gina tsarin shaida. Ga kowane lambar ACMG, "wane bayanai zan duba?" Shin AI ta amsa tambayar - amma kar a saka ajin tukuna.
3. Tabbatar da kowace shaida a tushen farko. mitar gnomAD, rikodin ClinVar, nazarin aiki - buɗe kuma karanta su duka da kanku. Bincika da'awar "babu a cikin gnomAD" AI ta nemansa a gnomAD.
4. Haɗa lambobin kuma cire ajin. Dokokin haɗin ACMG tare da AI; Amma bari gwani ya amince da aji na ƙarshe.
5. Rahoton VUS gaskiya. Idan shaida bai isa ba, ajin shine "Ma'anar da ba ta da tabbas"; Kuskure ne don tura shi azaman pathogenic ko benign.
uku mini lokuta
Case 1 - Mitar da aka yi. Wani masani ya tambayi AI game da mitar bambance-bambancen gnomAD; "0.002%," in ji AI. Lokacin da gwani ya duba shi a kan gnomAD da kansa, ya gano cewa mitar bambance-bambancen shine 1.3% - ma'ana shaidar BS1 (mai ƙarfi a cikin ingantacciyar hanya) tana da inganci kuma bambance-bambancen ba shi da lahani. Ƙirƙirar ƙarancin mitar AI ya sa bambance-bambancen ya zama ba kasafai ba.
Case 2-Sham aikin binciken. Wani mai bincike ya so aiwatar da PS3 (tabbacin aiki) don bambance-bambancen; AI ya ba da labari mai gamsarwa ta layi. Lokacin da mai binciken ya bincika a kan PubMed, ya gano cewa babu irin wannan labarin. Halin ƙarya zai ruguza sarkar shaida.
Case 3 - Tabbatar da samu. Wani mashawarcin kwayoyin halitta ya sake kimanta bambance-bambancen "yiwuwar cututtuka" tare da AI. YZ ya nuna sabbin maganganu masu karo da juna akan ClinVar; Mashawarcin ya buɗe ClinVar, ya ga cewa labs biyu sun gano bambance-bambancen akan VUS, kuma sun sabunta rahoton. Anan, AI ya taimaka ta tunatar da mu sabuntawa wanda wataƙila ba a lura da shi ba - amma kuma, ɗan adam ya yanke shawarar.
Samfura huɗu masu kwafi
1) Ƙaddamar da tsarin shaida (ba tare da sanya aji ba):
Matsayinku: Mataimakin fassarar bambance-bambancen asibiti. Ƙirƙiri tsarin shaida na ACMG/AMP don bambance-bambancen masu zuwa: [ sigar genome, kwafin, HGVS]. Ga kowane lambar shaida mai yiwuwa (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) "wane bayanai zan duba, a wane tushe, don amfani da wannan?" Rubuta. Kar a ce ajin tukuna; kawai jera bayanan da ake buƙata.
2) GnomAD/ClinVar shirin tabbatarwa:
Rubuta mataki-mataki ainihin abin da zan nema a gnomAD da ClinVar don bambance-bambancen mai zuwa: [bambance-bambancen]. Bayyana wanne iyakar mitar yawan jama'a yayi daidai da wace lambar ACMG. Ba ku sanya dabi'u ba; gaya mani inda zan samo shi.
3) Fassarar aji (ta yarda da ni):
Na ba da waɗannan tabbataccen shaida: [PM2 yana nan, PP3 yana nan, BS1 ba ya nan ...] . Zayyana yiwuwar aji da gaskatawa bisa ga ka'idodin haɗin ACMG. Jin kyauta don faɗi "VUS" idan shaidar ba ta isa ba. Zan amince da hukuncin ƙarshe.
4) Rahoton daftarin:
Fassara rabe-rabe mai zuwa cikin sakin layi na rahoto a cikin bayyanannen harshe da ya dace da majiyyaci da likita: [bambancin, aji, mahimmin shaida]. Kada ku wuce gona da iri na hakika; idan akwai rashin tabbas, bayyana shi a fili. Koma zuwa ga ƙwararren don yanke shawara na asibiti.
Rauni mai ƙarfi / Ƙarfi mai ƙarfi
Rauni: "Shin TP53 c.743G> Mai cutarwa ne?"
Matsala: Babu sigar genome/kwafi, babu wata shaida da ake buƙata, AI na iya faɗawa aji kawai kuma ta daidaita mitar.
Ƙarfafa: "Shigar da tsarin tabbatar da ACMG don GRCh38, TP53 NM_000546.6:c.743G>A (p.Arg248Gln); gaya mani abin da zan nema a cikin wane tushe don kowane lambar, ƙimar da ta dace, tsara ajin bayan na inganta shi."
Dalilin da ya sa yake da ƙarfi: mahallin a bayyane yake, hanyar shaida a buɗe take, fagen ƙirƙira ya kuntace, yanke shawara yana hannun mutum.
Kuskuren gama gari
- Dogaro da amsar cututtukan cututtuka na kalma ɗaya. Ajin da aka ba da ba tare da jerin shaidu ba ba shi da amfani.
- Rashin tabbatar da mita da sifa. GnomAD mita da labaran labaran za a iya daidaita su; Bude shi da kanka.
- Gujewa VUS. Fadin "pathogenic/benign" lokacin da shaidar bata isa ba kuskuren asibiti ne.
- Juyin Halittar Halittar Halittar Halitta / Rubutu. Rubutun da ba daidai ba, kuskure c. Yana nufin wuri.
- Tsallake sabuntawar ClinVar. Fassarorin suna canzawa akan lokaci; Duba mafi yawan rikodi na yanzu.
Tsanaki: Haɗa lambobin ACMG bisa ƙa'ida ne amma yana buƙatar yanke hukunci na ƙwararru; Shaida iri ɗaya na iya ɗaukar nauyi daban-daban a cikin mahallin cutar-cututtuka daban-daban. Haɗin AI wani tsari ne, ba kalmar ƙarshe ba.
Zurfi: daidai karanta layin VCF da madaidaitan mitoci
Ko da layi daya a cikin fayil na VCF ya ƙunshi ramummuka da yawa. Misalin layi: 17 43091983. G A 60 PASS AF=0.0003;DP=45 GT:AD 0/1:22,23. Kuna iya samun AI ta bayyana filayen nan, amma tabbatar da maki uku da kanku. Na farko, wane nau'in kwayoyin halitta ne na biyu-matsayin chromosome ke cikin? Bambancin iri ɗaya yana bayyana a wani wuri daban a GRCh37 da GRCh38; Ba tare da fayyace sigar ba, wurin ba shi da ma'ana. Na biyu shine yankin GT (genotype): 0/1 heterozygous, 1/1 homozygous; A cikin cututtukan da ba su da ƙarfi, bambance-bambancen heterozygous ɗaya kaɗai ba ya bayyana. Na uku, DP (zurfin karantawa) da AD (zurfin allele): ƙananan zurfin (misali DP = 8) yana yin kira mai ban sha'awa; Dabarar na iya zama tabbataccen ƙarya. AI yayi bayanin waɗannan fagagen bisa ƙa'ida, amma "wannan kiran abin dogara ne?" Hukuncin naku ne.
Misalin ƙayyadaddun ƙayyadaddun ƙayyadaddun ƙofofin mitoci: ƙwararren ƙwararren ya so ya yi amfani da PM2 (rarity) zuwa bambance-bambancen cutar da ba kasafai ba tare da rabon gado. Leken asiri na wucin gadi ya ce, "gnomAD ba shi da shi, PM2 tabbas." Lokacin da masanin ya buɗe gnomAD, ya gano cewa bambance-bambancen yana da mitar 0.8% a cikin yawan jama'a - wanda ya isa ya kawar da PM2, saboda yawan cutar. Kuskure na gama gari shine duba yawan mitar yawan jama'a da tsallake yawan jama'a.
Mitar Allele (yawan jama'a)
Sharhin ACMG na al'ada
bayanin kula
Babu / sosai rare
Zai iya tallafawa PM2
Hakanan duba yawan jama'a
Fiye da yaduwar cututtuka
BS1 (mai ƙarfi)
Bambance-bambancen ragi / rinjaye yana da mahimmanci
sama da 5%
BA1 (mai zaman kansa benign)
Kusan tabbas mara lahani
5) Samfurin sarrafa layin VCF:
Yi bayanin filin layi na VCF mai zuwa ta filin, amma kar a yanke hukunci mai dogaro: fassara sigar genome, GT (zygosity), filayen DP da AD daban. Yi lissafin lokuta inda wannan kiran na iya zama abin tambaya a fasaha. Layi: [manna].
A takaice
- Bambance-bambancen fassarar ya dogara ne akan shaida; AI yana da ƙarfi a ƙirƙira da taƙaita shaida, amma shawarar aji ya rage ga gwani.
- Duk wani shaida (mitar gnomAD, rajista na ClinVar, nazarin aikin) dole ne a tabbatar da kansa da kansa a tushen farko.
- Gyara bambance-bambancen ta nau'in genome, kwafi da HGVS; Tabbatar da mai tabbatarwa.
- Idan shaidar ba ta isa ba, amsar gaskiya ita ce "Mahimmanci mara tabbas (VUS)."
Aikin aikace-aikace
Zaɓi bambance-bambancen misali (misali sanannen rikodi daga ClinVar). Shin AI ta gina tsarin shaida tare da samfuri 1 da 2 a sama. Sannan bude mitar gnomAD kuma ClinVar yayi sharhi da kanka kuma kwatanta su da da'awar AI. Lura ko akwai bambanci tsakanin AI da tushen a cikin aƙalla yanki ɗaya na shaida kuma ku ba da hujjar yiwuwar aji da kanku.
jerin abubuwan dubawa
- [ ] Na gyara bambance-bambancen tare da nau'in genome, kwafi da HGVS.
- [ ] Na kafa tsarin hujja, ban sa AI ta ce aji daga farkon ba.
- [ ] Ni da kaina na duba mitar gnomAD.
- [ ] Na tabbatar da rajistar ClinVar da sabuntawa.
- [ ] Na tabbatar da ambaton binciken aiki a cikin PubMed.
- [ ] Idan shaidar ba ta isa ba, ban yi jinkiri ba in faɗi VUS kuma na amince da shawarar da kaina.