Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis

Barseghyan, Hayk; Tang, W.H. Wilson; Wang, Richard T.; Almalvez, Miguel; Segura, Eva Eugenie Rose; Vilain, Éric; Lipson, Allen; Douine, Emilie D.; Lee, Hane; Délot, Emmanuèle C.; Nelson, Stanley F.

doi:10.1186/s13073-017-0479-0

Cited by 99 publications

(100 citation statements)

References 11 publications

(14 reference statements)

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“…18,19 Finally, optical mapping and electronic mapping provide an orthogonal approach capable of determining the approximate size and location of insertions, deletions, inversions, and translocations while spanning even very large SVs. [20][21][22] GIAB recently published benchmark sets for small variants for seven genomes, 9,23 and the Global Alliance for Genomics and Health Benchmarking Team established best practices for using these and other benchmark sets to benchmark germline variants. 24 These benchmark sets are widely used in developing, optimizing, and demonstrating new technologies and bioinformatics methods, as well as part of clinical laboratory validation.…”

Section: Introductionmentioning

confidence: 99%

A robust benchmark for germline structural variant detection

Zook¹,

Nf²,

Nd³

et al. 2019

Preprint

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New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, and comprehensiveness. Translating these methods to routine research and clinical practice requires robust benchmark sets. We developed the first benchmark set for identification of both false negative and false positive germline SVs, which complements recent efforts emphasizing increasingly comprehensive characterization of SVs. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle (GIAB) Consortium integrated 19 sequence-resolved variant calling methods, both alignment-and de novo assembly-based, from short-, linked-, and long-read sequencing, as well as optical and electronic mapping. The final benchmark set contains 12745 isolated, sequence-resolved insertion and deletion calls ≥50 base pairs (bp) discovered by at least 2 technologies or 5 callsets, genotyped as heterozygous or homozygous variants by long reads. The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.66 Gbp and 9641 SVs supported by at least one diploid assembly. Support for SVs was assessed using svviz with short-, linked-, and long-read sequence data. In general, there was strong support from multiple technologies for the benchmark SVs, with 90 % of the Tier 1 SVs having support in reads from more than one technology. The Mendelian genotype error rate was 0.3 %, and genotype concordance with manual curation was >98.7 %. We demonstrate the utility of the benchmark set by showing it reliably identifies both false negatives and false positives in high-quality SV callsets from short-, linked-, and long-read sequencing and optical mapping. GIAB is working towards a new version of the benchmark set that will use new technologies and methods such as PacBio Circular Consensus Sequencing and ultralong Oxford Nanopore sequencing to expand to more challenging genome regions and include more challenging SVs such as inversions. We are also developing a robust integration process to make calls on GRCh37 and GRCh38 for all seven GIAB samples.

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Section: Introductionmentioning

confidence: 99%

A robust benchmark for germline structural variant detection

Zook¹,

Nf²,

Nd³

et al. 2019

Preprint

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“…The identification of structural variants is key for the diagnostics of genetic disorders. Recent work from Barseghyan et al 10 illustrates this by showing how genome imaging correctly diagnoses Duchenne Muscular Dystrophy from clinical samples. In a another study a prostate tumor sample was profiled by comparing the cancer sample with matched blood by genome imaging.…”

Section: Discussionmentioning

confidence: 98%

“…Label pattern differences relative to a reference are detected and these differences are used to call structural variants (SVs). 10 Because of the unique value gained by optical mapping of ultra-long DNA reads, it has been used in essentially all modern reference genome assemblies (human GRCh, 11; 12 mouse, 13 goat, 14 maize, 15 as well as benchmark structural variation papers. 16-18…”

Section: Introductionmentioning

confidence: 99%

Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging

Neveling

Mantere

Vermeulen

et al. 2020

Preprint

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Somatic structural variants are important for cancer development and progression. In a diagnostic set-up, especially for hematological malignancies, the comprehensive analysis of all cytogenetic aberrations in a given sample still requires a combination of techniques, such as karyotyping, fluorescence in situ hybridization and CNV-microarrays. We hypothesize that the combination of these classical approaches could be replaced by high-resolution genome imaging.Bone marrow aspirates or blood samples derived from 48 patients with leukemia, who received a clinical diagnoses of different types of hematological malignancies, were processed for genome imaging with the Bionano Genomics Saphyr system. In all cases cytogenetic abnormalities had previously been identified using standard of care workflows. Based on these diagnostic results, the samples were divided into two categories: simple cases (<5 aberrations, n=37) and complex cases (≥5 aberrations or an unspecified marker chromosome, n=11). By imaging the labelled ultra-long gDNA molecules (average N50 >250kb), we generated on average ∼280-fold mapped genome coverage per sample. Chromosomal aberrations were called by Bionano Genomics Rare variant pipeline (RVP) specialized for the detections of somatic variants.Per sample, on average a total of 1,454 high confidence SVs were called, and on average 44 (range: 14-130) of those were rare i.e. not present in the population control database. Importantly, for the simple cases, all clinically reported aberrations with variant allele frequencies higher than 10% were detected by genome imaging. This held true for deletions, insertions, inversions, aneuploidies and translocations. The results for the complex cases were also largely concordant between the standard of care workflow and optical mapping, and in several cases, optical mapping revealed higher complexity than previously known. SV and CNV calls detected by optical mapping were more complete than any other previous single test and likely delivered the most accurate and complete underlying genomic architecture. Even complex chromothripsis structures were resolved. Finally, optical mapping also identified multiple novel events, including balanced translocations that lead to potential novel fusion-genes, opening the potential to discover new prognostic and diagnostic biomarkers.The full concordance with diagnostic standard assays for simple cases and the overall great concordance with (previously likely incompletely understood) complex cases demonstrates the potential to replace classical cytogenetic tests with genome imaging. In addition, this holds the potential to rapidly map new fusion genes and identify novel SVs and CNVs as novel potential leukemia drivers.

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“…The absence of Southern Blot analysis of fetal tissue is a limitation of the current study but some samples have demonstrated the application of Bionano optical mapping in the FSHD1 gene diagnosis. Besides, Bioano optical mapping can detect chromosome deletion, repeat, inversion . Qian Zhang et al used this method to detect a repetition of a 4q35 region successfully.…”

Section: Discussionmentioning

confidence: 99%

Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping

Zheng

Kong

et al. 2019

Prenatal Diagnosis

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Purpose To explore the feasibility of performing rapid prenatal diagnoses of FSHD1 using a combination of Bianano optical mapping and linkage‐based karyomapping. Methods DNA specimens from a family that had been previously diagnosed with FSHD1 using Southern Blot analysis were used for this study. Genetic diagnosis of the proband, fetus chorionic amniotic fluid, and aborted fetal tissue was performed using Bianano optical mapping (BOM) together with linkage‐based karyomapping. Results BOM analysis showed that the proband's 4q35.2 region contained four D4Z4 repeats and the 4qA permissible allele, consistent with the previous FSHD1 diagnosis obtained by Southern Blotting. BOM analysis of the fetus' 4q35.2 region was consistent with that of the proband. Karyomap analysis revealed that the fetus inherited the affected chromosome segment from the proband. After genetic counseling, the couple choose termination of pregnancy, and we performed gene diagnosis of the abortus tissue by BOM. Conclusions Bianano optical mapping can determine the number of D4Z4 repeats and exclude interference of the 10q26.3 homologous region, and in combination with karyomapping, can be used for rapid and accurate prenatal diagnosis of FSHD1.

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Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis

Cited by 99 publications

References 11 publications

A robust benchmark for germline structural variant detection

A robust benchmark for germline structural variant detection

Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging

Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping

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