Watch the exceptional presentations, plus the Q&A panel discussions, on demand from Symposium 2023!

Key Publications

key publication

Optical genome mapping refines cytogenetic diagnostics, prognostic stratification and ...

Estelle Balducci, Sophie Kaltenbach, Patrick Villarese, Eugénie Duroyon, Loria Zalmai, Chloé Friedrich, Felipe Suarez, Ambroise Marcais, Didier Bouscary, Justine Decroocq, Rudy Birsen, Michaëla Fontenay, Marie Templé, Chantal Brouzes, Aurore Touzart, Thomas Steimlé, Agata Cieslak, Ludovic Lhermitte, Carole Almire, Nicolas Chapuis, Olivier Hermine, Vahid Asnafi, Olivier Kosmider, Lucile Couronné

Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are clinically and genetically heterogeneous myeloid malignancies associated with a broad range of recurring mutations and cytogenetic abnormalities. To date, their diagnostic workup includes a conventional karyotype to establish the IPSS-R (Revised International Prognostic Scoring System) and ELN (European Leukemia Net) prognostic ...
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key publication

High-resolution structural variant profiling of myelodysplastic syndromes by optical ...

Hui Yang, Guillermo Garcia-Manero, Koji Sasaki, Guillermo Montalban-Bravo, Zhenya Tang, Yue Wei, Tapan Kadia, Kelly Chien, Diana Rush, Ha Nguyen, Awdesh Kalia, Manjunath Nimmakayalu, Carlos Bueso-Ramos, Hagop Kantarjian, L. Jeffrey Medeiros, Rajyalakshmi Luthra, Rashmi Kanagal-Shamanna

Kanagal-Shamanna Lab MD Anderson Cancer Center Leukemia. August 1, 2022 doi: ...
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Key Points:

  • 101 consecutive MDS samples were evaluated with traditional cytogenetic methods (karyotyping, FISH, CMA), an 81-gene NGS panel, and OGM
  • OGM found nearly double the number of clinically relevant pathogenic variants compared to traditional cytogenetics
  • OGM findings could inform different prognostic risk classification or identify important additional variants in 28% of study participants
  • Changes to CCSS and IPSS-R risk scores in 21% and 17% of subjects, respectively.
  • Additional 13% of samples had additional alternations researchers suggest could be used for therapy selection/response and disease monitoring
  • The combination of OGM and NGS resulted in the detection of at least one clinically significant clonal abnormality in 97 of 101 samples
key publication

Clinical validation and diagnostic utility of optical genome mapping in prenatal ...

Nikhil Shri Sahajpal, Ashis K Mondal, Timothy Fee, Benjamin Hilton, Lawrence Layman, Alex R Hastie, Alka Chaubey, Barbara R. DuPont, Ravindra Kolhe

Kolhe Lab Augusta University Preprint: medRxiv. May 16, 2022 doi: ...
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Key Points:

  • Retrospective validation study analyzing 94 unique amniocentesis samples previously characterized with karyotyping, FISH, and/or CMA
  • OGM was 100% concordant with findings from traditional cytogenetics across multiple types of chromosomal aberrations (aneuploidies, triploidy, deletions, duplications, translocations, isochromosomes, markers, AOH)
  • OGM detected 64 additional reportable SVs in 43 samples
key publication

Optical genome mapping for structural variation analysis in hematologic ...

Adam C. Smith, Kornelia Neveling, Rashmi Kanagal-Shamanna

Adam C. Smith — University Health Network, Toronto Kornelia Neveling — Radboud UMC Rashmi Kanagal-Shamanna — MD Anderson Am J Hematol. May 12, 2022;1-8. doi: ...
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Key Points:

  • Highlights the performance of OGM in acute myeloid leukemia, myelodysplastic syndromes, and B cell acute lymphoblastic leukemia
  • Illustrates how the OGM workflow can solve common challenges in testing for hematologic malignancies
  • Discusses the strengths and weaknesses of OGM compared to traditional methods
key publication

16p13.11p11.2 triplication syndrome: a new recognizable genomic disorder characterized by ...

Romain Nicolle, Karine Siquier-Pernet, Marlène Rio, Anne Guimier, Emmanuelle Ollivier, Patrick Nitschke, Christine Bole-Feysot, Serge Romana, Alex Hastie, Vincent Cantagrel, Valérie Malan

--- Romain Nicolle, Karine Siquier-Pernet, Marlene Rio, Anne Guimier, Emmanuelle Ollivier, Patrick Nitschke, Christine Bole-Feysot, Serge Romana, Alex Hastie, Vincent Cantagrel, Valerie Malan. Highly identical segmental duplications (SDs) account for over 5% of the human genome and are enriched in the short arm of the chromosome 16. These SDs are susceptibility factors for recurrent ...
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Key Points:

  • Report of two unrelated subjects with a de novo 16p13.11p11.2 triplication associated with a 16p11.2 duplication, detected by CMA
  • Short-read WGS could not map any of the breakpoints
  • OGM determined the relative orientation of the triplicated and duplicated segments as well as the genomic positions of the breakpoints
  • Insights from OGM allowed authors to unravel the mechanism of these complex chromosomal rearrangements involving segmental duplications, propose a mechanism, and report a new clinically recognizable genomic disorder”
key publication

Optical Genome Mapping Improves Genetic Diagnosis in Chronic Granulomatous ...

Xiaoying Hui, Jingmin Yang, Wenjie Wang, Jing Zhang, Jia Hou, Wenjing Ying, Bijun Sun, Lipin Liu, Danru Liu, Qinhua Zhou, Jinqiao Sun, Ziaochuan Wang

--- Xiaoying Hui, Jingmin Yang, Wenjie Wang, Jing Zhang, Jia Hou, Wenjing Ying, bijun Sun, Lipin Liu, Danru Liu, Qinhua Zhou, Jinqiao Sun, Xiaochuan Wang. Chronic granulomatous disease(CGD) is mainly caused by defects in genes encoding subunits of NADPH oxidase complex (CYBB, CYBA, NCF1, NCF2, NCF4), and its chaperone (CYBC1). Next generation sequencing has successfully identified pathogenic ...
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Key Points:

  • Case series evaluating three subjects with clinically confirmed chronic granulomatous disease that were negative by NGS (panel and WES)
  • OGM was performed and identified a novel pathogenic ~1.5 kbp deletion in a causative gene in 1/3 subjects
  • Demonstrates ability to identify disease-causing variants missed by sequencing technologies”
key publication

Optimizing the diagnostic workflow for acute lymphoblastic leukemia by optical genome ...

— Katrina Rack, Jolien De Bie, Geneviève Ameye, Olga Gielen, Sofie Demeyer, Jan […]

--- Katrina Rack, Jolien De Bie, Geneviève Ameye, Olga Gielen, Sofie Demeyer, Jan Cools, Kim De Keersmaecker, Joris R. Vermeesch, Johan Maertens, Heidi Segers, Lucienne Michaux, Barbara Dewaele. Acute lymphoblastic leukemia (ALL) is a malignancy that can be subdivided into distinct entities based on clinical, immunophenotypic and genomic features, including mutations, structural variants ...
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key publication

Clinical Utility of Combined Optical Genome Mapping and 523-gene Next Generation ...

— Nikhil Shri Sahajpal, Ashis K Mondal, Sudha Ananth, Daniel Saul, Soheil Shams, […]

--- Nikhil Shri Sahajpal, Ashis K Mondal, Sudha Ananth, Daniel Saul, Soheil Shams, Alex R Hastie, Natasha M. Savage, Vamsi Kota, Alka Chaubey, Ravindra Kolhe The standard-of-care (SOC) for genomic testing of myeloid cancers primarily relies on karyotyping and fluorescent in situ hydridization (FISH) (cytogenetic analysis) and targeted gene panels (≤54 genes) that harbor hotspot pathogenic ...
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key publication

Multi-site Technical Performance and Concordance of Optical Genome Mapping: ...

— M. Anwar Iqbal, Ulrich Broeckel, Brynn Levy, Steven Skinner, Nikhil Sahajpal, Vanessa […]

--- M. Anwar Iqbal, Ulrich Broeckel, Brynn Levy, Steven Skinner, Nikhil Sahajpal, Vanessa Rodriguez, Aaron Stence, Kamel Awayda, Gunter Scharer, Cindy Skinner, Roger Stevenson, Aaron Bossler, Peter L. Nagy, Ravindra Kolhe The standard of care (SOC) cytogenetic testing methods, such as chromosomal microarray (CMA) and Fragile-X syndrome (FXS) testing, have been employed for the detection of ...
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Publications

title date Authors
ATTCT and ATTCC repeat expansions in the ATXN10 gene affect disease penetrance of ... October 13, 2022 C Alejandra Morato Torres, Faria Zafar, Yu-Chih Tsai, Jocelyn Palafox Vazqu
ez, Michael D Gallagher, Ian McLaughlin, Karl Hong, Jill Lai, Joyce Lee, Am
anda Chirino-Perez, Angel Omar Romero-Molina, Francisco Torres, Juan Fernan
dez-Ruiz, Tetsuo Ashizawa, Janet Ziegle, Francisco Javier Jiménez Gil, Bir
gitt Schüle
The snapdragon genomes reveal the evolutionary dynamics of the S locus ... October 10, 2022 Sihui Zhu, Yu'e Zhang, Lucy Copsey, Dongfeng Zheng, Enrico Coen, Yongbiao X
ue, Qianqian Han
Molecular and genetic mechanisms conferring dissolution of dioecy in Diospyros oleifera ... October 9, 2022 Peng Sun Jr., Soichiro Nishiyama Jr., Huawei Li Jr., Yini Mai Jr., Weijuan
Han Jr., Yujing Suo Jr., Chengzhi Liang Sr., Huilong Du Jr., Songfeng Diao
Jr., Yiru Wang Jr., Jiaying Yuan Jr., Yue Zhang Jr., Ryutaro Tao Sr., Fangd
ong Li Sr., Jianmin Fu Sr.
Optical genome mapping identifies clinically relevant genomic rearrangements in prostate ... October 8, 2022 Yeeun Shim, Jongsoo Lee, Jieun Seo, Cheol Keun Park, Saeam Shin, Hyunho Han
, Seung-Tae Lee, Jong Rak Choi, Byung Ha Chung, Young Deuk Choi
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris ... October 8, 2022 J Mitchell McGrath, Andrew Funk, Paul Galewski, Shujun Ou, Belinda Townsend
, Karen Davenport, Hajnalka Daligault, Shannon Johnson, Joyce Lee, Alex Has
tie, Aude Darracq, Glenda Willems, Steve Barnes, Ivan Liachko, Shawn Sulliv
an, Sergey Koren, Adam Phillippy, Jie Wang, Tiffany Liu, Jane Pulman, Kevin
Childs, Shengqiang Shu, Anastasia Yocum, Damian Fermin, Effie Mutasa-Gött
gens, Piergiorgio Stevanato, Kazunori Taguchi, Rachel Naegele, Kevin Dorn
DNA in nanochannels – Theory and ... October 7, 2022 Karolin Krykholm, Vilhelm Muller, KK Sriram, Kevin D Dorfman, Fredrik Weste
rlund
Inversion polymorphism in a complete human genome ... October 6, 2022 David Porubsky, William T. Harvey, Allison N. Rozanski, Jana Ebler, Wolfram
Höps, Hufsah Ashraf, Patrick Hasenfeld, Human Pangenome Reference Consort
ium (HPRC), Human Genome Structural Variation Consortium (HGSVC), Benedict
Paten, Ashley D. Sanders, Tobias Marschall, Jan O. Korbel, Evan E. Eichler
Identification and characterization of two DMD pedigrees with large inversion mutations ... October 5, 2022 Chang Geng, Ciliu Zhang, Pidong Li, Yuanren Tong, Baosheng Zhu, Jing He, Ya
nhuan Zhao, Fengxia Yao, Li-Ying Cui, Fan Liang, Yang Wang, Yaru Wang, Hong
shuai Jin, Dandan Lang, Shanlin Liu, Depeng Wang, Min S. Park, Lin Chen, Ji
ng Peng, Yi Dai
Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum ... September 30, 2022 Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, Atsushi Toyoda, Sachiko Is
obe
The generation of the first chromosome-level de-novo genome assembly and the development ... September 29, 2022 Guangtu Gao, Geoffrey C. Waldbieser, Ramey C. Youngblood, Dongyan Zhao, Mic
hael R. Pietrak, Melissa S. Allen, Jason A. Stannard, John T. Buchanan, Ros
eanna L. Long, Melissa Milligan, Gary Burr, Katherine Mejía-Guerra, Moira
J. Sheehan, Brian E. Scheffler, Caird E. Rexroad III, Brian C. Peterson, Yn
iv Palti

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