scholarly journals Application of Optical Genome Mapping For Comprehensive Assessment of Chromosomal Structural Variants for Clinical Evaluation of Myelodysplastic Syndromes

2021 ◽  
Author(s):  
Hui Yang ◽  
Guillermo Garcia-Manero ◽  
Diana Rush ◽  
Guillermo Montalban-Bravo ◽  
Saradhi Mallampati ◽  
...  
Keyword(s):  
High Throughput ◽  
Myelodysplastic Syndromes ◽  
Copy Number ◽  
Genome Mapping ◽  
Limit Of Detection ◽  
Standard Of Care ◽  
Chromosomal Microarray ◽  
Structural Variants ◽  
Accurate Identification ◽  
Chromosomal Variants

ABSTRACTStructural chromosomal variants [copy number variants (CNVs): losses/ gains and structural variants (SVs): inversions, balanced and unbalanced fusions/translocations] are important for diagnosis and risk-stratification of myelodysplastic syndromes (MDS). Optical genome mapping (OGM) is a novel single-platform cytogenomic technique that enables high-throughput, accurate and genome-wide detection of all types of clinically important chromosomal variants (CNVs and SVs) at a high resolution, hence superior to current standard-of-care cytogenetic techniques that include conventional karyotyping, FISH and chromosomal microarrays. In this proof-of-principle study, we evaluated the performance of OGM in a series of 12 previously well-characterized MDS cases using clinical BM samples. OGM successfully facilitated detection and detailed characterization of twenty-six of the 28 clonal chromosomal variants (concordance rate: 93% with conventional karyotyping; 100% with chromosomal microarray). These included copy number gains/losses, inversions, inter and intra-chromosomal translocations, dicentric and complex derivative chromosomes; the degree of complexity in latter aberrations was not apparent using standard technologies. The 2 missed aberrations were from a single patient within a composite karyotype, below the limit of detection. Further, OGM uncovered 6 additional clinically relevant sub-microscopic aberrations in 4 (33%) patients that were cryptic by standard-of-care technologies, all of which were subsequently confirmed by alternate platforms. OGM permitted precise gene-level mapping of clinically informative genes such as TP53, TET2 and KMT2A, voiding the need for multiple confirmatory assays. OGM is a potent single-platform assay for high-throughput and accurate identification of clinically important chromosomal variants.

scholarly journals Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 398
Author(s):  
Nikhil Shri Sahajpal ◽  
Hayk Barseghyan ◽  
Ravindra Kolhe ◽  
Alex Hastie ◽  
Alka Chaubey
Keyword(s):  
Copy Number ◽  
Southern Blotting ◽  
Genome Mapping ◽  
Genetic Disorders ◽  
Prenatal Testing ◽  
Standard Of Care ◽  
Copy Number Variations ◽  
Repeat Expansion ◽  
Chromosomal Microarray ◽  
Next Generation

Global medical associations (ACOG, ISUOG, ACMG) recommend diagnostic prenatal testing for the detection and prevention of genetic disorders. Historically, cytogenetic methods such as karyotype analysis, fluorescent in situ hybridization (FISH) and chromosomal microarray (CMA) are utilized worldwide to diagnose common syndromes. However, the limitations of each of these methods, either performed in tandem or simultaneously, demonstrates the need of a revolutionary technology that can alleviate the need for multiple technologies. Optical genome mapping (OGM) is a novel method that fills this void by being able to detect all classes of structural variations (SVs), including copy number variations (CNVs). OGM is being adopted by laboratories as a tool for both postnatal constitutional genetic disorders and hematological malignancies. This commentary highlights the potential for OGM to become a standard of care in prenatal genetic testing based on its capability to comprehensively identify large balanced and unbalanced SVs (currently the strength of karyotyping and metaphase FISH), CNVs (by CMA), repeat contraction disorders (by Southern blotting) and multiple repeat expansion disorders (by PCR-based methods or Southern blotting). Next-generation sequencing (NGS) methods are excellent at detecting sequence variants, but they are unable to accurately resolve repeat regions of the genome, which limits their ability to detect all classes of SVs. Notably, multiple molecular methods are used to identify repeat expansion and contraction disorders in routine clinical laboratories around the world. With non-invasive prenatal testing (NIPT) becoming the standard of care screening assay for all global pregnancies, we anticipate that OGM can provide a high-resolution, cytogenomic assay to be employed following a positive NIPT screen or for high-risk pregnancies with an abnormal ultrasound. Accurate detection of all types of genetic disorders by OGM, such as liveborn aneuploidies, sex chromosome anomalies, microdeletion/microduplication syndromes, repeat expansion/contraction disorders is key to reducing the global burden of genetic disorders.

scholarly journals Optical genome mapping as a next-generation cytogenomic tool for detection of structural and copy number variations for prenatal genomic analyses

2021 ◽  
Author(s):  
Nikhil Shri Sahajpal ◽  
Hayk Barseghyan ◽  
Ravindra Kolhe ◽  
Alex Hastie ◽  
Alka Chaubey
Keyword(s):  
Copy Number ◽  
Southern Blotting ◽  
Sex Chromosome ◽  
Genome Mapping ◽  
Genetic Disorders ◽  
Standard Of Care ◽  
Copy Number Variations ◽  
Repeat Expansion ◽  
Chromosomal Microarray ◽  
Next Generation

Global medical associations (ACOG, ISUOG, ACMG) recommend diagnostic prenatal testing for the detection and prevention of genetic disorders. Historically, cytogenetic methods such as karyotype analysis, fluorescent in situ hybridization (FISH), and chromosomal microarray (CMA) are utilized worldwide to diagnose common syndromes. However, the limitations of each of these methods, either performed in tandem or simultaneously, demonstrates the need of a revolutionary technology that can alleviate the need of multiple technologies. Optical genome mapping (OGM) is a novel technology that fills this void by being able to detect all classes of structural variations (SVs), including copy number variations (CNVs). OGM is being adopted by laboratories as a next-generation cytogenomic tool for both postnatal constitutional genetic disorders and hematological malignancies. This commentary highlights the potential of OGM to become a standard of care in prenatal genetic testing by its ability to identify large balanced and unbalanced SVs (currently the strength of karyotyping and metaphase FISH), CNVs (by CMA), repeat contraction disorders (by Southern blotting) and multiple repeat expansion disorders (by PCR based methods or Southern blotting). Also, next-generation sequencing (NGS) methods are excellent at detecting sequencing variants but are unable to accurately detect the repeat regions of the genome which limits the ability to detect all classes of SVs. Notably, multiple molecular methods are used to identify repeat expansion and contraction disorders in routine clinical laboratories around the world. With non-invasive prenatal screening test (NIPT) as the standard of care screening assay for all global pregnancies, we anticipate OGM as a high-resolution cytogenomic diagnostic tool employed following a positive NIPT screen or for high-risk pregnancies with an abnormal ultrasound. Accurate detection of all types of genetic disorders by OGM, such as liveborn aneuploidies, sex chromosome anomalies, microdeletion/microduplication syndromes, repeat expansion/contra5ction disorders is key to reducing the global burden of genetic disorders.

scholarly journals Optical Mapping Uncovers Multiple Novel Genomic Structural Variants in Patient Leukemias

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 33-34
Author(s):  
Darren Finlay ◽  
Rabi Murad ◽  
Karl Hong ◽  
Joyce Lee ◽  
Andy Pang ◽  
...  
Keyword(s):  
Optical Mapping ◽  
Imaging System ◽  
Genome Mapping ◽  
Treatment Options ◽  
Standard Of Care ◽  
Driver Mutations ◽  
Structural Variants ◽  
Advisory Committees ◽  
Dismal Prognosis ◽  
Genomic Structural Variants

Leukemias are a diverse collection of hematopoietic cancers with limited chemotherapeutic treatment options. Patients unsuitable or unable for bone marrow transplantation have a dismal prognosis. Although previous studies have shown that there are only a limited number of potential driver mutations (3-8) per leukemia, there is an extensive heterogeneity of subtypes of disease. Using optical mapping with the Saphyr genome imaging system we confirm what other laboratories have found; that leukemias have additionally approximately 30-70 genomic structural variants per patient. This suggests that these SVs could ascribe the observed heterogeneity and could be responsible for individual pathogenesis of disease. Furthermore, we show that of many these SVs involve genes with functions associated with cellular processes relevant to cancer. Whilst known SVs, such asBCR-ABLtranslocations, are readily detected, multiple novel variants are also uncovered by Saphyr. Here we demonstrate the utility of this technique to uncover potential driver SV events and provide examples of such, some of which are associated with sensitivity and resistance to chemotherapeutics, including the standard of care drug Idarubicin (Idamycin). Finally, optical genome mapping shows 100% concordance with extant cytogenetic analyses, yet with a more streamlined methodology, a greater resolution, and higher sensitivity of detection. Figure Disclosures Hong: Bionano Genomics:Current Employment.Lee:Bionano Genomics, San Diego:Current Employment.Pang:Bionano Genomics:Current Employment.Lai:Bionano Genomics:Current Employment.Hastie:Bionano Genomics:Current Employment.Vuori:Bionano Genomics:Membership on an entity's Board of Directors or advisory committees.

scholarly journals A National Multicenter Evaluation of the Clinical Utility of Optical Genome Mapping for Assessment of Genomic Aberrations in Acute Myeloid Leukemia

2020 ◽  
Author(s):  
Brynn Levy ◽  
Linda B. Baughn ◽  
Scott Chartrand ◽  
Brandon LaBarge ◽  
David Claxton ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Genome Mapping ◽  
Genomic Structure ◽  
World Health ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Accurate Identification ◽  
Genomic Aberrations ◽  
Acute Myeloid

AbstractDetection of hallmark genomic aberrations in acute myeloid leukemia (AML) is essential for prognosis and patient management. Clinical practice guidelines for identifying such structural variants (SVs), established by the World Health Organization (WHO), European Leukemia Net (ELN) and National Comprehensive Cancer Network (NCCN), rely substantially on cytogenetic/cytogenomic techniques such as karyotyping, fluorescence in situ hybridization (FISH) or chromosomal microarray analysis (CMA). However, these techniques are limited by the need for skilled personnel as well as significant time and labor, making them cost-prohibitive for some patients. Optical genome mapping (OGM) addresses these limitations and allows for the accurate identification of clinically significant SVs using a novel, high throughput, inexpensive methodology. In a single assay, OGM offers a significantly higher resolution than karyotyping with comprehensive genome-wide analysis comparable to CMA and the added unique ability to detect balanced SVs that are missed by microarray. Here, we report the performance of OGM in a cohort of 100 AML cases, which were previously characterized by karyotype alone or karyotype and FISH. CMA was performed as an additional test in some cases. OGM identified all the clinically relevant SVs and CNVs reported by these standard cytogenetic methods. Moreover, OGM identified clinically relevant SVs in 11% of cases that had been missed by the routine methods. In 24% of cases, OGM refined the underlying genomic structure reported by traditional cytogenomic testing (13%), identified additional clinically relevant variants (7%) or both (4%). Three of 48 (6.25%) cases reported with normal karyotypes were shown to have cryptic translocations involving gene fusions. Two of these cases included fusion between NSD1-NUP98. Based on the comprehensive genomic profiling of the AML patients in this multi-institutional study, we recommend that OGM be considered as a first-line test for detection and identification of clinically relevant SVs.

scholarly journals nanotatoR: a tool for enhanced annotation of genomic structural variants

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Surajit Bhattacharya ◽  
Hayk Barseghyan ◽  
Emmanuèle C. Délot ◽  
Eric Vilain
Keyword(s):  
De Novo ◽  
Genome Mapping ◽  
Gene List ◽  
Sufficient Information ◽  
Rna Seq ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Pathogenic Variants ◽  
Increased Sensitivity

Abstract Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. Results We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. Conclusions The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.

Application of Copy Number Variation Sequencing in Genetic Analysis of Miscarriages in Early and Middle Pregnancy

2020 ◽  
Vol 160 (11-12) ◽  
pp. 634-642
Author(s):  
Shiqiang Luo ◽  
Xingyuan Chen ◽  
Tizhen Yan ◽  
Jiaolian Ya ◽  
Zehui Xu ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
High Throughput ◽  
Copy Number ◽  
High Throughput Sequencing ◽  
Chromosomal Abnormalities ◽  
Pregnancy Termination ◽  
Mendelian Inheritance ◽  
Copy Number Variations ◽  
Abnormal Chromosome ◽  
Number Variation

High-throughput sequencing based on copy number variation (CNV-seq) is commonly used to detect chromosomal abnormalities. This study identifies chromosomal abnormalities in aborted embryos/fetuses in early and middle pregnancy and explores the application value of CNV-seq in determining the causes of pregnancy termination. High-throughput sequencing was used to detect chromosome copy number variations (CNVs) in 116 aborted embryos in early and middle pregnancy. The detection data were compared with the Database of Genomic Variants (DGV), the Database of Chromosomal Imbalance and Phenotype in Humans using Ensemble Resources (DECIPHER), and the Online Mendelian Inheritance in Man (OMIM) database to determine the CNV type and the clinical significance. High-throughput sequencing results were successfully obtained in 109 out of 116 specimens, with a detection success rate of 93.97%. In brief, there were 64 cases with abnormal chromosome numbers and 23 cases with CNVs, in which 10 were pathogenic mutations and 13 were variants of uncertain significance. An abnormal chromosome number is the most important reason for embryo termination in early and middle pregnancy, followed by pathogenic chromosome CNVs. CNV-seq can quickly and accurately detect chromosome abnormalities and identify microdeletion and microduplication CNVs that cannot be detected by conventional chromosome analysis, which is convenient and efficient for genetic etiology diagnosis in miscarriage.

scholarly journals INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. eabe5054
Author(s):  
Qianxin Wu ◽  
Chenqu Suo ◽  
Tom Brown ◽  
Tengyao Wang ◽  
Sarah A. Teichmann ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Limit Of Detection ◽  
Point Of Care ◽  
Population Level ◽  
Reaction Products ◽  
Testing Strategy ◽  
Asymptomatic Patients ◽  
Testing Stage ◽  
Population Scale

We present INSIGHT [isothermal NASBA (nucleic acid sequence–based amplification) sequencing–based high-throughput test], a two-stage coronavirus disease 2019 testing strategy, using a barcoded isothermal NASBA reaction. It combines point-of-care diagnosis with next-generation sequencing, aiming to achieve population-scale testing. Stage 1 allows a quick decentralized readout for early isolation of presymptomatic or asymptomatic patients. It gives results within 1 to 2 hours, using either fluorescence detection or a lateral flow readout, while simultaneously incorporating sample-specific barcodes. The same reaction products from potentially hundreds of thousands of samples can then be pooled and used in a highly multiplexed sequencing–based assay in stage 2. This second stage confirms the near-patient testing results and facilitates centralized data collection. The 95% limit of detection is <50 copies of viral RNA per reaction. INSIGHT is suitable for further development into a rapid home-based, point-of-care assay and is potentially scalable to the population level.

Advantages and Challenges of Using Breast Biopsy Markers

2021 ◽  
Author(s):  
Taghreed I Alshafeiy ◽  
Alison Matich ◽  
Carrie M Rochman ◽  
Jennifer A Harvey
Keyword(s):  
Breast Biopsy ◽  
Percutaneous Biopsy ◽  
Standard Of Care ◽  
Benign Lesions ◽  
Accurate Identification ◽  
Biopsy Tissue ◽  
Local Practices ◽  
Frequency Of Use ◽  
Lesion Localization

Abstract Percutaneous image-guided biopsy procedures are the standard of care for histologic assessment of suspicious breast lesions. Post-biopsy tissue markers (clips) optimize patient management by allowing for assessment on follow-up imaging and precise lesion localization. Markers are used to ensure accurate correlation between imaging modalities, guide preoperative localization for malignant and high-risk lesions, and facilitate accurate identification of benign lesions at follow-up. Local practices differ widely, and there are no data detailing the exact frequency of use of clips for different breast biopsies. There are many indications for biopsy marker deployment, and some difficulties may be encountered after placement. The placement of biopsy markers has many advantages and few disadvantages, such that deployment should be routinely used after percutaneous biopsy procedures with rare exception.

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