Gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection
Pooled CRISPR screens are a powerful tool to probe genotype-phenotype relationships at genome-wide scale. However, criteria for optimal design are missing, and it remains unclear how experimental parameters affect results. Here, we report that random decreases in gRNA abundance are more likely than...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article (Journal) |
| Language: | English |
| Published: |
02 March 2020
|
| In: |
Genome biology
Year: 2020, Volume: 21 |
| ISSN: | 1474-760X |
| DOI: | 10.1186/s13059-020-1939-1 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1186/s13059-020-1939-1
|
| Author Notes: | Katharina Imkeller, Giulia Ambrosi, Michael Boutros and Wolfgang Huber |
MARC
| LEADER | 00000caa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 1696146275 | ||
| 003 | DE-627 | ||
| 005 | 20220818053955.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 200427s2020 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1186/s13059-020-1939-1 |2 doi | |
| 035 | |a (DE-627)1696146275 | ||
| 035 | |a (DE-599)KXP1696146275 | ||
| 035 | |a (OCoLC)1341316841 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 32 |2 sdnb | ||
| 100 | 1 | |a Imkeller, Katharina |e VerfasserIn |0 (DE-588)116155808X |0 (DE-627)1024839001 |0 (DE-576)506724816 |4 aut | |
| 245 | 1 | 0 | |a Gscreend |b modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection |c Katharina Imkeller, Giulia Ambrosi, Michael Boutros and Wolfgang Huber |
| 264 | 1 | |c 02 March 2020 | |
| 300 | |a 13 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Gesehen am 27.04.2020 | ||
| 520 | |a Pooled CRISPR screens are a powerful tool to probe genotype-phenotype relationships at genome-wide scale. However, criteria for optimal design are missing, and it remains unclear how experimental parameters affect results. Here, we report that random decreases in gRNA abundance are more likely than increases due to bottle-neck effects during the cell proliferation phase. Failure to consider this asymmetry leads to loss of detection power. We provide a new statistical test that addresses this problem and improves hit detection at reduced experiment size. The method is implemented in the R package gscreend, which is available at http://bioconductor.org/packages/gscreend. | ||
| 700 | 1 | |a Ambrosi, Giulia |d 1988- |e VerfasserIn |0 (DE-588)1189461374 |0 (DE-627)1668119870 |4 aut | |
| 700 | 1 | |a Boutros, Michael |e VerfasserIn |0 (DE-588)1023031132 |0 (DE-627)717350045 |0 (DE-576)366291831 |4 aut | |
| 700 | 1 | |a Huber, Wolfgang |e VerfasserIn |0 (DE-588)1115277685 |0 (DE-627)870097997 |0 (DE-576)477724442 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Genome biology |d London : BioMed Central, 2000 |g 21(2020) Artikel-Nummer 53, 13 Seiten |h Online-Ressource |w (DE-627)326173617 |w (DE-600)2040529-7 |w (DE-576)110736192 |x 1474-760X |7 nnas |a Gscreend modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection |
| 773 | 1 | 8 | |g volume:21 |g year:2020 |g extent:13 |a Gscreend modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection |
| 856 | 4 | 0 | |u https://doi.org/10.1186/s13059-020-1939-1 |x Verlag |x Resolving-System |z lizenzpflichtig |3 Volltext |
| 951 | |a AR | ||
| 992 | |a 20200427 | ||
| 993 | |a Article | ||
| 994 | |a 2020 | ||
| 998 | |g 1115277685 |a Huber, Wolfgang |m 1115277685:Huber, Wolfgang |d 140000 |e 140000PH1115277685 |k 0/140000/ |p 4 |y j | ||
| 998 | |g 1023031132 |a Boutros, Michael |m 1023031132:Boutros, Michael |d 60000 |e 60000PB1023031132 |k 0/60000/ |p 3 | ||
| 998 | |g 116155808X |a Imkeller, Katharina |m 116155808X:Imkeller, Katharina |d 140000 |e 140000PI116155808X |k 0/140000/ |p 1 |x j | ||
| 999 | |a KXP-PPN1696146275 |e 363693628X | ||
| BIB | |a Y | ||
| SER | |a journal | ||
| JSO | |a {"note":["Gesehen am 27.04.2020"],"relHost":[{"language":["eng"],"disp":"Gscreend modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detectionGenome biology","recId":"326173617","type":{"media":"Online-Ressource","bibl":"periodical"},"pubHistory":["1.2000 -"],"title":[{"title":"Genome biology","title_sort":"Genome biology","subtitle":"biology for the post-genomic era"}],"origin":[{"publisherPlace":"London","dateIssuedKey":"2000","dateIssuedDisp":"2000-","publisher":"BioMed Central"}],"note":["ISSN-Portal 1465-6914: GenomeBiology.com","Gesehen am 11.02.15"],"part":{"extent":"13","year":"2020","volume":"21","text":"21(2020) Artikel-Nummer 53, 13 Seiten"},"id":{"eki":["326173617"],"zdb":["2040529-7"],"issn":["1474-760X"]},"physDesc":[{"extent":"Online-Ressource"}]}],"id":{"doi":["10.1186/s13059-020-1939-1"],"eki":["1696146275"]},"type":{"bibl":"article-journal","media":"Online-Ressource"},"physDesc":[{"extent":"13 S."}],"title":[{"title_sort":"Gscreend","subtitle":"modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection","title":"Gscreend"}],"language":["eng"],"origin":[{"dateIssuedKey":"2020","dateIssuedDisp":"02 March 2020"}],"name":{"displayForm":["Katharina Imkeller, Giulia Ambrosi, Michael Boutros and Wolfgang Huber"]},"recId":"1696146275","person":[{"family":"Imkeller","display":"Imkeller, Katharina","given":"Katharina","role":"aut"},{"family":"Ambrosi","given":"Giulia","display":"Ambrosi, Giulia","role":"aut"},{"role":"aut","family":"Boutros","display":"Boutros, Michael","given":"Michael"},{"role":"aut","display":"Huber, Wolfgang","given":"Wolfgang","family":"Huber"}]} | ||
| SRT | |a IMKELLERKAGSCREEND0220 | ||