Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

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 pha...

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Published inScientific reports Vol. 10; no. 1; p. 2512
Main Authors Nordlund, Jessica, Marincevic-Zuniga, Yanara, Cavelier, Lucia, Raine, Amanda, Martin, Tom, Lundmark, Anders, Abrahamsson, Jonas, Norén-Nyström, Ulrika, Lönnerholm, Gudmar, Syvänen, Ann-Christine
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 13.02.2020
Nature Publishing Group
Subjects
45/23
45/91
692/4017
692/4028/67/1990/283/2125
692/4028/67/69
Acute lymphoblastic leukemia
Adolescent
Aneuploidy
Cancer and Oncology
Cancer och onkologi
Child
Child, Preschool
Chromosome Aberrations
Chromosome rearrangements
Copy number
Deoxyribonucleic acid
DNA
Female
Fusion protein
Gene Deletion
Gene Dosage
Genomes
Haplotypes
Heavy chains
Humanities and Social Sciences
Humans
Immunoglobulins
Karyotyping
Leukemia
Lymphatic leukemia
Male
multidisciplinary
Pediatrics
Pediatrik
Precursor Cell Lymphoblastic Leukemia-Lymphoma - genetics
Science
Science (multidisciplinary)
Translocation, Genetic
Whole Genome Sequencing
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Abstract 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.
AbstractList 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).
Abstract 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.
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.
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.
ArticleNumber 2512
Author Lundmark, Anders
Cavelier, Lucia
Abrahamsson, Jonas
Lönnerholm, Gudmar
Marincevic-Zuniga, Yanara
Nordlund, Jessica
Syvänen, Ann-Christine
Raine, Amanda
Martin, Tom
Norén-Nyström, Ulrika
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Snippet Structural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification, and...
Abstract Structural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification,...
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SubjectTerms 45/23
45/91
692/4017
692/4028/67/1990/283/2125
692/4028/67/69
Acute lymphoblastic leukemia
Adolescent
Aneuploidy
Cancer and Oncology
Cancer och onkologi
Child
Child, Preschool
Chromosome Aberrations
Chromosome rearrangements
Copy number
Deoxyribonucleic acid
DNA
Female
Fusion protein
Gene Deletion
Gene Dosage
Genomes
Haplotypes
Heavy chains
Humanities and Social Sciences
Humans
Immunoglobulins
Karyotyping
Leukemia
Lymphatic leukemia
Male
multidisciplinary
Pediatrics
Pediatrik
Precursor Cell Lymphoblastic Leukemia-Lymphoma - genetics
Science
Science (multidisciplinary)
Translocation, Genetic
Whole Genome Sequencing
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Title Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing
URI https://link.springer.com/article/10.1038/s41598-020-59214-w
https://www.ncbi.nlm.nih.gov/pubmed/32054878
https://www.proquest.com/docview/2354704999
https://pubmed.ncbi.nlm.nih.gov/PMC7018692
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Volume 10
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