Tsiv muab sib dhos cim ntxiv mus rau hauv lub tsev kho mob, ib feem 2

thawj zaug los kom nyob tweets los #ngs2013 http://t.co/SbWrGx8weI

— Paul Denny (@pauldennyuk) Lub peb hlis ntuj 12, 2013

Nyob hauv kuv Tus ncej tas los, Kuv summarised hais lus plaub thawj zaug ntawm no symposium:

1St Oxford Rhiav thiab Symposium, 4th Techgene paub Network rooj,
“Tiam NGS2013 tom qab muab sib dhos: Bioinformatics thiab Data Analysis”

Koj yuav nyeem cov Tweets los ntawm lub rooj sab laj ntawm no. Tab sis kuv digress. Qhov su qhib impressively pib nrog Marcel Nelen, ntawm Radboud University Centre kho mob, Nijmegen, Netherlands hais txog:

“Tej dej uas exome sequencing nyob hauv heterogeneous cov kab mob.”

Dr Nelen piav li cas lub tswv yim muaj zog ntawm kev tshawb fawb thiab diagnostics no–piv coj los exome sequencing rau ntawm heterogeneous uantej tus mob daim ntawv thov. nws emphasised qhov tseem ceeb ntawm ib multidisciplinary pab dag zog rau txhais kom meej “tej pob khoom” cov noob uas muaj ib qhov tseeb ntawm kev koom tes rau neb cov txuj uas xiam hoob qhab (ID), noob dig muag, noob lag ntseg, zog tsis meej los yog oxidative phosphorylation ntshawv siab. ntau haiv neeg lus dav ntawm kev tshuaj ntsuam genetic variants uas yuav ua rau yus tus txhais tau tias cov kab mob ntawd Sanger sequencing, ib zaug rau tus kub txheej txheem, kuj yog dhau sij hawm haus mas thiab kim thiab muab ib tug tsawg dua “Diagnostic yield” tshaj li exome sequencing.

Ib qho tseemceeb nam tim-throughput sequencing ntawm exomes nyob rau hauv ib cov chaw diagnostic yog nkag mus rau hauv kom tsim nyog qhov kev tso cai los ntawm tus neeg mob thiab lawv tsev neeg. cov neeg mob thiab/los yog lawv niam thiab txiv tau muab qhov kev tso cai rau lub exome tag nrho tsom. Cov ntaub ntawv sib lawv liag ntawm tus exomes ~ 550 neeg nkag ib generic annotation pipeline thiab exome tsom tau raws tog twg los ib tug 'tsib novo' zoo rau daim ID los yog ib tug 'nyob rau hauv silico' targeted uas zoo rau cov kab mob.

Tsom raws li ib cov theem ob mus kom ze:

1. tsom xam muaj ib “pob” cov noob yuav nqa pathogenic variants heev li:
   • Nrhiav kev variants nyob xwb no hais txog kab mob noob.
   • Yog tias luag nrhiav pathogenic variant, kawg tsom xam thiab qhia.
   • Yog hais tias tsis muaj cov pathogenic variant nyob, tsiv mus rau cov theem ob:
2. Exome tseem soj:
   • Yog hais tias tsis muaj cov pathogenic variant nyob, nrhiav tus noob rau hauv tej txheej tus neeg sib tw noob.
   • Yog hais tias pom muaj ib cov pathogenic variant thiab muaj ntawv pov thawj rau kev soj ntsuam los txhais tau, qhia txog.
   • Thaum kawg, Yog hais tias tus analyses ua ntej lawm tsis, qhov seem ntawm tus exome yog nrhiav tau nyob rau hauv lub tswv yim rau kev soj ntsuam ntawm thiab tej zaum yuav muab qhia rau hauv yog hais tias "tshiab" tej ntawv no tuas.

Ib tug zoo dab neeg recounted yog Dr Nelen concerned ib rooj lus kev txuj kev, thaum uas tsis muaj cov causative variant twb tau qhia ntau xyoo ntawm kev tshawb nrhiav los ntawm Sanger muab los sib dhos ntawm tus neeg sib tw rau successive noob, whereas exome tseem tsom xam pom tias variant pathogenic hauv lubPACS1 noob.

Nyob rau hauv tus neeg mob qhov twg “tsuav yog tau vim” variants yog muab, uas yuav tshwm sim li yuav tsis muaj kev txheeb ze rau tus kab mob nyob rau hauv kev tshawb nrhiav, Cov no yog kis rau thiab txheeb xyuas los ntawm pab neeg ywj siab hais txog kev ua hauj lwm pab tswv yim, ua ntej mus txog.

Qhov kev tsom tiered muaj gained muab ntawv pov thawj los ntawm Dutch mob tub ceev xwm raws li kev tshuaj ntsuam genetic ntsuam thiab thiaj yuav ua ib tug qauv rau lwm lub teb chaws EU.

Peb hnov ntxiv ntawm Michael Mueller, ntawm qhov NIHR Biomedical Research Centre, Imperial College London, UK, hais txog:

“Ceev ceev kheej-genome sequencing: optimising tus bioinformatics pipeline turnaround zaug sai.”

Siv tus kheej-genome sequencing (WGS) kev hloov kom paub tias yuav ua tau haib tshaj li soj tau txwv kom cov exome xwb. Txawm li cas los, cov ntaub ntawv ua thiab tuav nyaav heev posed los mus WGS rau hauv lub (lab) diagnostic yog nco. Dr Mueller piav ntau npaum li cas yeej hardware thiab le caag rau thaum uas tig mus ua ntawm NGS ntaub ntawv yuav tau optimised, cuag ib co ua txoj kev txhim kho. paub ntawm systematically bottlenecks rau txhua theem, nws yuav txo tau lub sij hawm coj mus ua annotated variants, pib nrog nyoos Illumina luv-nyeem cov ntaub ntawv los ntawm ib tug ~ 30 x mam tib genome, ntawm ~ 24 mus txog 7 teev. qhov no yuav nyob tiav tsis compromising kuas nyeem los variant hu rau zoo.

Nyob rau hauv tus taug qab rau cov hais lus ntawm Marcel Nelen, Kornelia Neveling, ntawm qhov Radboud University Medical Centre kuj, Nijmegen, rau:

“Tsom xam cov ntaub ntawv rau diagnostic exome sequencing”

Dr Neveling pib los txog cov rooj teeb ntawm lub Radboud University Medical Centre, ces coj yoog thiab kev tswjhwm thiab thaum kawg software cuab yeej los pab rau cov exome lawv liag variant filtering thiab tsom xam. Diagnostics ib tug mus rau peb lub neej yees 5500 sequencers siv lub platform khoom thiab kuj ob Ion Torrent PGM sequencers.

Ib kauj ruam tseem ceeb heev nyob rau hauv cov qauv thiab cov ntaub ntawv tuav yog Tswjhwm (QC) los xyuas kom meej tias soj ntsuam txiav txim zaum kawg no robust; muaj ib txhia cov ruam teev yog Dr Neveling QC:

1. Kev qhia kom paub txhim khu kev qha ntawm cov tib neeg thiab kev sib raug zoo (nus muag / niam txiv / ncaj)
2. Yog cov ntaubntawv povthawj siv cov metadata rau txhua tus qauv e.g. twg cov version software yog siv rau kev tsom xam? Dab tsi yog tus tsom xam hnub?, yam.
3. Cov ntaub ntawv sib lawv liag yog mas hais thiab rhiab e.g. muab tsis txaus, tej qhov kev pab los ntawm cov exons.
4. Sib lawv liag variant hu tau rua lom e.g. tus piv ntawm zaus rau transversions no qhia ntuj variation.

Radboud sequencing diagnostics pab tam sim no muaj ib tug database ntawm txog 1500 ib tug neeg exomes thiab tau pom tias muaj cov neeg exome raug yields txog 40,000 variants, nrog ~ 150-200 ntawm cov variants rau “lwm yam” rau ib tus qauv. Dr Neveling hais no ib variant filtering tuam, muaj ib tug neeg graphical interface uas ntsia reminiscent cov softwarepiav lawm ntawm Elliot Margulies thiab piav tau luv luv siv lub cuab tam nyob rau ib rooj plaub ntawm yam mob muaj keeb spastic paraplegia kom pab nrhiav etiologic variant ntxim.

Prof. Anthony J Brookes lawm cov Symposium, tham tsis tau txog:

“Muab cov pathogenicity los NGS derived variants”

Prof. Brookes yog fizzing uas muaj tswv yim, Peb xav txog dab tsi peb yeej txhais hais tias yog provoking “pathogenic”. ntawm cov kab mob tsis tshua muaj, peb tau qhia sawv daws tias lub tswvyim ntawm kev pathogenicity yog ib nplua, ncau ntau ib. inferring pathogenicity tau txhais tej thaum lawv tseem:

• allele frequencies nyob rau hauv rooj plaub thiab kev tswj kev ceev kev paub txog
• seb tus variant twb nyob lawm los ntawm lwm leej lwm tus li pathogenic
• seb tus variant yog heev tsis tuaj kawm ntawv ntawm cov databases uas muaj (tej zaum wrongly) mus txhaj mas “dab tsi” variants e.g. dbSNP
• seb tus variant puag segregates uas muaj tus kab mob nyob hauv lub pedigree
• cas lub predicted (los yog paub tias) ntawm ib variant yog ib cov qauv protein ntau
• txoj hau kev yuav nyob rau hauv silico los ntawm cov cuab yeej xws li PolyPhen los yog Sift
• tej yam ua nyob tib neeg hlwb assays
• tej qhov chaw los yog phenotypic assays ua qauv kab e.g. nas mutants

Lwm qib subtlety txoj kev uas peb txhais pathogenicity yog tias peb yuav xav hais tias muaj ob contexts:

1. muaj ib tug variant ' los’ lub phenotype nyob hauv ib tug neeg mob los sis tsev neeg (uas koom expressivity)?
2. tau ib tug variant 'cause’ lub phenotype nyob hauv ib tug pejxeem (penetrance)?

Prof. Brookes argued tias cov kev soj ntsuam actionability ntawm ib variant yuav tsum muab xav li cas txog li thaum lawv tseem pathogenicity, penetrance thiab expressivity. Nws mus rau txoj kev tawm uas dhau tsawg yog paub txog cov kev sib raug zoo ntawm cov genotype thiab cov phenotype thiab cov uas peb xav tau ib tug xov tooj ntawm cov uas mus choj uas ntxi thiab ua kom peb muaj peev xwm recognise pathogenic variants. Nyob rau tej, nws argued tias ib qhov system intermediary database ntawd yuav tsum txuas ua ke cov hom kev pab xws li dbSNP los yog Ensembl nrog soj ntsuam databases, tsom cov ntaub ntawv sib qiv tsis tau compromising xwb. combining no database ' ecosystem’ uas siab zoo cov ntaub ntawv hauv kev cov ntaub ntawv yuav tsum tau ua kom peb nkag siab txog cov kev sib raug zoo genotype-phenotype.

Lub symposium muab ib lub luag zoo li nyob rau hauv cov NGS uas yog muab coj caj no–piv diagnostic thiab siv los ua kom tau zoo npaum li cas hauv paub causative variants. nyeg, no hauj txoj kev loj hlob yuav ua kom zoo dua paub xaiv txog yam kev kho mob los yog kev kho mob. nws yuav saib deb li cas peb muaj progressed hauv ib xyoo lub caij intriguing, Thaum twg ib tug followup lub rooj sib tham los.

Yog leej twg xav tau kov los tham txog, kho los yog hloov kuv thaug, thov logged, hauv qab, los yog xa kuv ib tweet:

Tweet los @pauldennyuk