Sökning: id:"swepub:oai:gup.ub.gu.se/294203" >
Refined detection a...
-
Nordlund, JessicaUppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
(författare)
Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing
- Artikel/kapitelEngelska2020
Förlag, utgivningsår, omfång ...
-
2020-02-13
-
Springer Science and Business Media LLC,2020
Nummerbeteckningar
-
LIBRIS-ID:oai:gup.ub.gu.se/294203
-
https://gup.ub.gu.se/publication/294203URI
-
https://doi.org/10.1038/s41598-020-59214-wDOI
-
https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-174885URI
-
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-421849URI
Kompletterande språkuppgifter
Ingår i deldatabas
Klassifikation
-
Ämneskategori:ref swepub-contenttype
-
Ämneskategori:art swepub-publicationtype
Anmärkningar
-
Structural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). Traditional methods such as karyotyping and FISH struggle to accurately identify and phase such large-scale chromosomal aberrations in ALL genomes. We therefore evaluated linked-read WGS for detecting chromosomal rearrangements in primary samples of from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations and structural variants in the ALL genomes. We found that biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified previously unknown structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. We conclude that linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping and FISH. © 2020, The Author(s).
Ämnesord och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
-
Marincevic-Zuniga, YanaraUppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab(Swepub:uu)yanma214
(författare)
-
Cavelier, LuciaUppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik(Swepub:uu)lucicava
(författare)
-
Raine, AmandaUppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab(Swepub:uu)amrai226
(författare)
-
Martin, TomUppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab(Swepub:uu)tomma920
(författare)
-
Lundmark, AndersUppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab(Swepub:uu)andlu294
(författare)
-
Abrahamsson, Jonas,1954Gothenburg University,Göteborgs universitet,Institutionen för kliniska vetenskaper, Avdelningen för pediatrik,Institute of Clinical Sciences, Department of Pediatrics,Gothenburg Univ, Sahlgrenska Acad, Inst Clin Sci, Dept Pediat, Gothenburg, Sweden.(Swepub:gu)xabrjo
(författare)
-
Norén-Nyström, UlrikaUmeå universitet,Pediatrik,Umeå Univ, Dept Clin Sci & Pediat, Umeå, Sweden.(Swepub:umu)kagr0007
(författare)
-
Lönnerholm, Gudmar,1941-Uppsala universitet,Barnneurologi/Barnonkologi(Swepub:uu)gudmarlh
(författare)
-
Syvänen, Ann-Christine,1950-Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab(Swepub:uu)anncsyva
(författare)
-
Uppsala universitetMolekylär medicin
(creator_code:org_t)
Sammanhörande titlar
-
Ingår i:Scientific Reports: Springer Science and Business Media LLC102045-2322
Internetlänk
Hitta via bibliotek
Till lärosätets databas