Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope.
Identifieur interne : 000184 ( Main/Exploration ); précédent : 000183; suivant : 000185Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope.
Auteurs : Neetha Nanoth Vellichirammal [États-Unis] ; Abrar Albahrani [États-Unis] ; You Li [République populaire de Chine] ; Chittibabu Guda [États-Unis]Source :
- Methods in molecular biology (Clifton, N.J.) [ 1940-6029 ] ; 2020.
Abstract
Fusion transcripts that are frequent in cancer can be exploited to understand the mechanisms of malignancy and can serve as diagnostic or prognostic markers. Several algorithms have been developed to predict fusion transcripts from DNA or RNA data. The majority of these algorithms align sequencing reads to the reference transcriptome for predicting fusions; however, this results in several undetected fusions due to the highly perturbed nature of cancer genomes. Here, we describe a novel method that uses a k-mer based algorithm to predict fusion transcripts accurately using the unaligned reads from the regular RNA-seq data analysis pipelines.
DOI: 10.1007/978-1-4939-9904-0_2
PubMed: 31728959
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000361
- to stream PubMed, to step Curation: 000361
- to stream PubMed, to step Checkpoint: 000183
- to stream Ncbi, to step Merge: 002403
- to stream Ncbi, to step Curation: 002403
- to stream Ncbi, to step Checkpoint: 002403
- to stream Main, to step Merge: 000187
- to stream Main, to step Curation: 000184
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope.</title><author><name sortKey="Vellichirammal, Neetha Nanoth" sort="Vellichirammal, Neetha Nanoth" uniqKey="Vellichirammal N" first="Neetha Nanoth" last="Vellichirammal">Neetha Nanoth Vellichirammal</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author><author><name sortKey="Albahrani, Abrar" sort="Albahrani, Abrar" uniqKey="Albahrani A" first="Abrar" last="Albahrani">Abrar Albahrani</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author><author><name sortKey="Li, You" sort="Li, You" uniqKey="Li Y" first="You" last="Li">You Li</name><affiliation wicri:level="1"><nlm:affiliation>HitGen Ltd., Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>HitGen Ltd., Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Guda, Chittibabu" sort="Guda, Chittibabu" uniqKey="Guda C" first="Chittibabu" last="Guda">Chittibabu Guda</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA. babu.guda@unmc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:31728959</idno><idno type="pmid">31728959</idno><idno type="doi">10.1007/978-1-4939-9904-0_2</idno><idno type="wicri:Area/PubMed/Corpus">000361</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000361</idno><idno type="wicri:Area/PubMed/Curation">000361</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000361</idno><idno type="wicri:Area/PubMed/Checkpoint">000183</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000183</idno><idno type="wicri:Area/Ncbi/Merge">002403</idno><idno type="wicri:Area/Ncbi/Curation">002403</idno><idno type="wicri:Area/Ncbi/Checkpoint">002403</idno><idno type="wicri:Area/Main/Merge">000187</idno><idno type="wicri:Area/Main/Curation">000184</idno><idno type="wicri:Area/Main/Exploration">000184</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope.</title><author><name sortKey="Vellichirammal, Neetha Nanoth" sort="Vellichirammal, Neetha Nanoth" uniqKey="Vellichirammal N" first="Neetha Nanoth" last="Vellichirammal">Neetha Nanoth Vellichirammal</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author><author><name sortKey="Albahrani, Abrar" sort="Albahrani, Abrar" uniqKey="Albahrani A" first="Abrar" last="Albahrani">Abrar Albahrani</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author><author><name sortKey="Li, You" sort="Li, You" uniqKey="Li Y" first="You" last="Li">You Li</name><affiliation wicri:level="1"><nlm:affiliation>HitGen Ltd., Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>HitGen Ltd., Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Guda, Chittibabu" sort="Guda, Chittibabu" uniqKey="Guda C" first="Chittibabu" last="Guda">Chittibabu Guda</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA. babu.guda@unmc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author></analytic><series><title level="j">Methods in molecular biology (Clifton, N.J.)</title><idno type="eISSN">1940-6029</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Fusion transcripts that are frequent in cancer can be exploited to understand the mechanisms of malignancy and can serve as diagnostic or prognostic markers. Several algorithms have been developed to predict fusion transcripts from DNA or RNA data. The majority of these algorithms align sequencing reads to the reference transcriptome for predicting fusions; however, this results in several undetected fusions due to the highly perturbed nature of cancer genomes. Here, we describe a novel method that uses a k-mer based algorithm to predict fusion transcripts accurately using the unaligned reads from the regular RNA-seq data analysis pipelines.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Nebraska</li></region></list><tree><country name="États-Unis"><region name="Nebraska"><name sortKey="Vellichirammal, Neetha Nanoth" sort="Vellichirammal, Neetha Nanoth" uniqKey="Vellichirammal N" first="Neetha Nanoth" last="Vellichirammal">Neetha Nanoth Vellichirammal</name></region><name sortKey="Albahrani, Abrar" sort="Albahrani, Abrar" uniqKey="Albahrani A" first="Abrar" last="Albahrani">Abrar Albahrani</name><name sortKey="Guda, Chittibabu" sort="Guda, Chittibabu" uniqKey="Guda C" first="Chittibabu" last="Guda">Chittibabu Guda</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Li, You" sort="Li, You" uniqKey="Li Y" first="You" last="Li">You Li</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000184 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000184 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:31728959
|texte= Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:31728959" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |