At Bionano, we are committed to the relentless pursuit of the truth in genomics so we can all realize its promise to improve quality of life for all. We believe that whole genome imaging has the opportunity to empower discovery across all research areas and we want to support scientists like you in your persistent quest to uncover those genomic mysteries and share them with widely with the scientific community.
We are pleased to support researchers presenting Bionano data with a Conference Grant program to cover costs associated with attending in-person and/or virtual conferences.
Name and Title: Christopher Grochowski, Baylor College of Medicine
Conference: AGBT 2020
Abstract Title: Deciphering genomic inversion events using optical mapping
Abstract: Methods for inversions, such as fosmid clone sequencing (PMID: 18451855, 17901297) and paired-end (PE) sequencing (15895083), are limited in resolving breakpoints. Optical mapping (OM) involves tagging sequence motifs along unbroken DNA strands preserving the architecture of SVs. Given the evidence for inversion rearrangements contributing to disease, we sought to compare SV detection methods. We performed OM on a lymphoblastoid line (NA15510) using Bionano direct label stain (DSL) technology. As inversions can be mediated by repeats,...Read More
Name and Title: Jens Luebeck, University of California, San Diego
Conference: AGBT 2020
Abstract Title: Amplicon Reconstructor: Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer
Abstract: Copy number amplifications (CNAs) are a hallmark of the cancer genome. Copy number increase of oncogenes on focally amplified regions imparts positive selective pressure to cells. Focal amplifications have been associated with genome instability and increased pathogenicity. Though important, the mechanisms causing focal CNAs are incompletely understood. Proposed mechanisms include chromosomal translocation with duplication, chromothripsis and more recently, circular extrachromosomal DNA (ecDNA). Thus, methods which reconstruct focal CNAs will enable a greater understanding of the...Read More
Name and Title: Camir Ricketts, Weill Cornell Medicine of Cornell University
Conference: AGBT 2020
Abstract Title: A Comprehensive Multi-Platform Approach for Structural Variant Analysis in a Clinical Cohort of Cancer Patients
Abstract: While there have been notable advancements in structural variant analysis in tumor genomes, there is still a lack of comprehensive analysis of tumors integrating multiple technologies to fully characterize events not previously discovered using current tools. In this study, we have applied a non-sequencing-based genome mapping technology, Bionano, together with 10x Genomics linked-reads and standard whole genome sequencing to three gastric cancer, two brain cancer and one gastrointestinal stromal tumor (GIST) samples. Leveraging the Bionano...Read More
Name and Title: Brandon Labarge, Penn State University
Conference: AGBT 2020
Abstract Title: Optical Genomic Mapping Identifies the Structure of Human Papillomavirus Genomes in Head and Neck Cancers
Abstract: The architecture of Human Papillomavirus (HPV) and its interaction with the host genome in Head and Neck Cancer has not been comprehensively described, even though the nature of the viral genome is potentially associated with patient outcome. The limitation is that Next Generation Sequencing (NGS) is inadequate for resolving large structural changes in the genome. Here we integrate optical genomic mapping (OGM) with NGS to characterize the molecular state of HPV in Head and Neck...Read More
Name and Title: Marcin Imielinski, Weill Cornell Medicine
Conference: AGBT 2020
Abstract Title: Unraveling the allelic structure around recurrent complex structural variant patterns in cancer using optical mapping and linked-reads
Abstract: Complex rearrangements arise frequently in cancer, causing complex derivative alleles and copy number changes. Though subset of patterns can be readily classified into previously known categories (chromothripsis, chromoplexy, breakage fusion bridge cycles, templated insertion chains), the evolutionary origin and functional impact of many complex cancer structural variants remains obscure. The allelic phase of rearranged loci, specifically the distribution of rearranged junctions across linear or circular alleles, can yield insight into the mutational processes that gave...Read More
Name and Title: Hayk Barseghyan, Children’s National
Conference: AGBT 2020
Abstract Title: Utilization of Dual-Label Optical Genome Mapping for Genetic/Epigenetic Diagnosis
Abstract: Genomic technologies such as short-read exome/genome sequencing (SRS) and chromosomal microarrays (CMA) have helped increase diagnostic rates across many genetic disorders. However, despite this success, about half of the cases remain without a firm diagnosis. Due to the methodological limitations of both technologies (SRS, CMA) they fail to sensitively identify structural variants (SVs) or balanced rearrangements, respectively. Additionally, both technologies have limitations in assessment of epigenetic changes. For example, short-read based bisulfite sequencing or methylation...Read More
Name and Title: Christopher Grochowski, Baylor College of Medicine
Conference: AGBT 2020
Abstract Title: Deciphering genomic inversion events using optical mapping
Abstract: Methods for inversions, such as fosmid clone sequencing (PMID: 18451855, 17901297) and paired-end (PE) sequencing (15895083), are limited in resolving breakpoints. Optical mapping (OM) involves tagging sequence motifs along unbroken DNA strands preserving the architecture of SVs. Given the evidence for inversion rearrangements contributing to disease, we sought to compare SV detection methods. We performed OM on a lymphoblastoid line (NA15510) using Bionano direct label stain (DSL) technology. As inversions can be mediated by repeats,...Read More
Name and Title: Jens Luebeck, University of California, San Diego
Conference: AGBT 2020
Abstract Title: Amplicon Reconstructor: Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer
Abstract: Copy number amplifications (CNAs) are a hallmark of the cancer genome. Copy number increase of oncogenes on focally amplified regions imparts positive selective pressure to cells. Focal amplifications have been associated with genome instability and increased pathogenicity. Though important, the mechanisms causing focal CNAs are incompletely understood. Proposed mechanisms include chromosomal translocation with duplication, chromothripsis and more recently, circular extrachromosomal DNA (ecDNA). Thus, methods which reconstruct focal CNAs will enable a greater understanding of the...Read More
Name and Title: Camir Ricketts, Weill Cornell Medicine of Cornell University
Conference: AGBT 2020
Abstract Title: A Comprehensive Multi-Platform Approach for Structural Variant Analysis in a Clinical Cohort of Cancer Patients
Abstract: While there have been notable advancements in structural variant analysis in tumor genomes, there is still a lack of comprehensive analysis of tumors integrating multiple technologies to fully characterize events not previously discovered using current tools. In this study, we have applied a non-sequencing-based genome mapping technology, Bionano, together with 10x Genomics linked-reads and standard whole genome sequencing to three gastric cancer, two brain cancer and one gastrointestinal stromal tumor (GIST) samples. Leveraging the Bionano...Read More
Name and Title: Brandon Labarge, Penn State University
Conference: AGBT 2020
Abstract Title: Optical Genomic Mapping Identifies the Structure of Human Papillomavirus Genomes in Head and Neck Cancers
Abstract: The architecture of Human Papillomavirus (HPV) and its interaction with the host genome in Head and Neck Cancer has not been comprehensively described, even though the nature of the viral genome is potentially associated with patient outcome. The limitation is that Next Generation Sequencing (NGS) is inadequate for resolving large structural changes in the genome. Here we integrate optical genomic mapping (OGM) with NGS to characterize the molecular state of HPV in Head and Neck...Read More
Name and Title: Marcin Imielinski, Weill Cornell Medicine
Conference: AGBT 2020
Abstract Title: Unraveling the allelic structure around recurrent complex structural variant patterns in cancer using optical mapping and linked-reads
Abstract: Complex rearrangements arise frequently in cancer, causing complex derivative alleles and copy number changes. Though subset of patterns can be readily classified into previously known categories (chromothripsis, chromoplexy, breakage fusion bridge cycles, templated insertion chains), the evolutionary origin and functional impact of many complex cancer structural variants remains obscure. The allelic phase of rearranged loci, specifically the distribution of rearranged junctions across linear or circular alleles, can yield insight into the mutational processes that gave...Read More
Name and Title: Hayk Barseghyan, Children’s National
Conference: AGBT 2020
Abstract Title: Utilization of Dual-Label Optical Genome Mapping for Genetic/Epigenetic Diagnosis
Abstract: Genomic technologies such as short-read exome/genome sequencing (SRS) and chromosomal microarrays (CMA) have helped increase diagnostic rates across many genetic disorders. However, despite this success, about half of the cases remain without a firm diagnosis. Due to the methodological limitations of both technologies (SRS, CMA) they fail to sensitively identify structural variants (SVs) or balanced rearrangements, respectively. Additionally, both technologies have limitations in assessment of epigenetic changes. For example, short-read based bisulfite sequencing or methylation...Read More
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