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Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia
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- Rezayee, F. (author)
- Karolinska Institute,Karolinska Institutet,Karolinska University Hospital
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- Eisfeldt, J. (author)
- Karolinska Institute,Karolinska Institutet,Karolinska University Hospital
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- Skaftason, A. (author)
- Karolinska Institute,Karolinska Institutet
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- Ofverholm, I. (author)
- Karolinska Institute,Karolinska Institutet,Karolinska University Hospital
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- Sayyab, Shumaila (author)
- Uppsala University,Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinska vetenskaper
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- Syvänen, Ann-Christine, 1950- (author)
- Uppsala University,Uppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab
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- Maqbool, K. (author)
- Karolinska Institute
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- Lilljebjörn, Henrik (author)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Translationella genomiska och funktionella studier av leukemi,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,Translational Genomic and Functional Studies of Leukemia,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Johansson, Bertil (author)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Genetiska och epigenetiska studier av barnleukemi,Forskargrupper vid Lunds universitet,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,Genetic and epigenetic studies of pediatric leukemia,Lund University Research Groups,Region Skåne
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- Olsson-Arvidsson, Linda (author)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Genetiska och epigenetiska studier av barnleukemi,Forskargrupper vid Lunds universitet,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,Genetic and epigenetic studies of pediatric leukemia,Lund University Research Groups,Region Skåne
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- Pietras, Christina Orsmark (author)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Translationella genomiska och funktionella studier av leukemi,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,Translational Genomic and Functional Studies of Leukemia,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Staffas, Anna, 1982 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för mikrobiologi och immunologi,Institute of Biomedicine, Department of Microbiology and Immunology,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Sahlgrens Univ Hosp, Dept Clin Genet & Genom, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Microbiol & Immunol, Gothenburg, Sweden.
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- Palmqvist, Lars, 1965 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Laboratory Medicine,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Sahlgrens Univ Hosp, Dept Clin Chem, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Dept Lab Med, Gothenburg, Sweden.
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- Fioretos, Thoas (author)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Translationella genomiska och funktionella studier av leukemi,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,LTH profilområde: Teknik för hälsa,LTH profilområden,Lunds Tekniska Högskola,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,Translational Genomic and Functional Studies of Leukemia,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,LTH Profile Area: Engineering Health,LTH Profile areas,Faculty of Engineering, LTH,Region Skåne
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- Cavelier, L. (author)
- Karolinska Institute,Karolinska University Hospital
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- Fogelstrand, L. (author)
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Sahlgrens Univ Hosp, Dept Clin Chem, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Dept Lab Med, Gothenburg, Sweden.
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- Nordlund, Jessica (author)
- Uppsala University,Uppsala universitet,Science for Life Laboratory, SciLifeLab,Molekylär precisionsmedicin
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- Wirta, Valtteri (author)
- KTH Royal Institute of Technology,Karolinska Institutet,KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden,KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, Stockholm, Sweden.;Karolinska Univ Hosp, Genom Med Ctr Karolinska, Stockholm, Sweden.
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- Rosenquist, R. (author)
- Karolinska Institute,Karolinska Institutet,Karolinska University Hospital
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- Barbany, G. (author)
- Karolinska Institute,Karolinska Institutet,Karolinska University Hospital
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(creator_code:org_t)
- Frontiers Media SA, 2023
- 2023
- English.
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In: FRONTIERS IN ONCOLOGY. - : Frontiers Media SA. - 2234-943X. ; 13
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Abstract
Subject headings
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- Introduction The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods.Methods For this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL.Results Both the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions.Discussion The filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- B-cell acute lymphoblastic leukemia
- whole-genome sequencing
- genomic
- aberrations
- diagnostic validation
- class-defining genetic lesions
- ikzf1 deletions
- erg
- stratification
- classification
- translocation
- genotype
- crlf2
- gene
- Oncology
- B-cell acute lymphoblastic leukemia
- genomic aberrations
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
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Rezayee, F.
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Eisfeldt, J.
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Skaftason, A.
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Ofverholm, I.
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Sayyab, Shumaila
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Syvänen, Ann-Chr ...
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show more...
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Maqbool, K.
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Lilljebjörn, Hen ...
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Johansson, Berti ...
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Olsson-Arvidsson ...
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Pietras, Christi ...
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Staffas, Anna, 1 ...
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Palmqvist, Lars, ...
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Fioretos, Thoas
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Cavelier, L.
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Fogelstrand, L.
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Nordlund, Jessic ...
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Wirta, Valtteri
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Rosenquist, R.
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Barbany, G.
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show less...
- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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FRONTIERS IN ONC ...
- By the university
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University of Gothenburg
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Royal Institute of Technology
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Uppsala University
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Karolinska Institutet
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Lund University