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Article ; Online: Correction: Optical Genome Mapping for Oncology Applications.

Sahajpal, Nikhil Shri / Mondal, Ashis K / Hastie, Alex / Chaubey, Alka / Kolhe, Ravindra

Current protocols

2023 Volume 3, Issue 11, Page(s) e946

Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Published Erratum
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.946
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Article ; Online: Optical Genome Mapping for Oncology Applications.

Sahajpal, Nikhil Shri / Mondal, Ashis K / Hastie, Alex / Chaubey, Alka / Kolhe, Ravindra

Current protocols

2023 Volume 3, Issue 10, Page(s) e910

Abstract: Optical genome mapping (OGM) is a next-generation cytogenomic technology that has the potential to replace standard-of-care technologies used in the genetic workup of various malignancies. The ability to detect various classes of structural variations ... ...

Abstract	Optical genome mapping (OGM) is a next-generation cytogenomic technology that has the potential to replace standard-of-care technologies used in the genetic workup of various malignancies. The ability to detect various classes of structural variations that include copy number variations, deletions, duplications, balanced and unbalanced events (insertions, inversions, and translocation) and complex genomic rearrangements in a single assay and analysis demonstrates the utility of the technology in tumor research and clinical application. Herein, we provide the methodological details for performing OGM and pre- and post-analytical quality control (QC) checks and describe critical steps that should be performed with caution, probable causes for specific QC failures, and potential method modifications that could be implemented as part of troubleshooting. The protocol description and troubleshooting guide should help new and current users of the technology to improve or troubleshoot the problems (if any) in their workflow. © 2023 Wiley Periodicals LLC. Basic Protocol: Optical genome mapping.
MeSH term(s)	Humans ; DNA Copy Number Variations ; Genome ; Genomics/methods ; Neoplasms/diagnosis ; Neoplasms/genetics ; Chromosome Mapping
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.910
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Article: 17q25.3 copy number changes: association with neurodevelopmental disorders and cardiac malformation.

Sahajpal, Nikhil Shri / Jeffrey, David H F / DuPont, Barbara R / Hilton, Benjamin

Molecular cytogenetics

2023 Volume 16, Issue 1, Page(s) 15

Abstract: Copy number variants (CNVs) have been identified as common genomic variants that play a significant role in inter-individual variability. Conversely, rare recurrent CNVs have been found to be causal for many disorders with well-established genotype- ... ...

Abstract	Copy number variants (CNVs) have been identified as common genomic variants that play a significant role in inter-individual variability. Conversely, rare recurrent CNVs have been found to be causal for many disorders with well-established genotype-phenotype relationships. However, the phenotypic implications of rare non-recurrent CNVs remain poorly understood. Herein, we re-investigated 18,542 cases reported from chromosomal microarray at Greenwood Genetic Center from 2010 to 2022 and identified 15 cases with CNVs involving the 17q25.3 region. We report the detailed clinical features of these subjects, and compare with the cases reported in the literature to determine genotype-phenotype correlations for a subset of genes in this region. The CNVs in the 17q25.3 region were found to be rare events, with a prevalence of 0.08% (15/18542) observed in our cohort. The CNVs were dispersed across the entire 17q25.3 region with variable breakpoints and no smallest region of overlap. The subjects presented with a wide range of clinical features, with neurodevelopmental disorders (autism spectrum disorder, intellectual disability, developmental delay) being the most common features (80%), then expressive language disorder (33%), and finally cardiovascular malformations (26%). The association of CNVs involving the critical gene-rich region of 17q25.3 with neurodevelopmental disorders and cardiac malformation, implicates several genes as plausible drivers for these events.
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2420849-8
ISSN	1755-8166
ISSN	1755-8166
DOI	10.1186/s13039-023-00644-2
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Article ; Online: Genotoxic and mutagenic potential of 7-methylxanthine: an investigational drug molecule for the treatment of myopia.

Singh, Harjeet / Singh, Harmanpreet / Sharma, Sunil / Kaur, Harmanpreet / Kaur, Arvinder / Kaur, Satwinderjeet / Kaur, Sandeep / Sahajpal, Nikhil Shri / Chaubey, Alka / Shahtaghi, Navid Reza / Kaur, Inderjeet / Jain, Subheet Kumar

Drug and chemical toxicology

2023 , Page(s) 1–10

Abstract: 7-Methylxanthine (7-MX, CAS No. 552-62-5, purity 99.46%) is the first orally administered drug candidate, which showed anti-myopic activity in different pre-clinical studies. In the present study, we investigated ... ...

Abstract	7-Methylxanthine (7-MX, CAS No. 552-62-5, purity 99.46%) is the first orally administered drug candidate, which showed anti-myopic activity in different pre-clinical studies. In the present study, we investigated the
Language	English
Publishing date	2023-01-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	548368-2
ISSN	1525-6014 ; 0148-0545
ISSN (online)	1525-6014
ISSN	0148-0545
DOI	10.1080/01480545.2022.2164011
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Article: Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses

Sahajpal, Nikhil Shri / Barseghyan, Hayk / Kolhe, Ravindra / Hastie, Alex / Chaubey, Alka

Genes. 2021 Mar. 11, v. 12, no. 3

2021

Abstract: 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 ... ...

Abstract	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.
Keywords	aneuploidy ; fish ; fluorescence ; genomics ; hybridization ; karyotyping ; metaphase ; microarray technology ; polymerase chain reaction ; sex chromosomes ; ultrasonics
Language	English
Dates of publication	2021-0311
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12030398
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses.

Sahajpal, Nikhil Shri / Barseghyan, Hayk / Kolhe, Ravindra / Hastie, Alex / Chaubey, Alka

Genes

2021 Volume 12, Issue 3

Abstract	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.
MeSH term(s)	Aneuploidy ; Chromosome Disorders/diagnosis ; Chromosome Disorders/genetics ; DNA Copy Number Variations ; Female ; Genomics ; Humans ; Optogenetics ; Pregnancy ; Prenatal Diagnosis
Language	English
Publishing date	2021-03-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12030398
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Article ; Online: Diabetic retinopathy: how far are we from personalized medicine?

Sahajpal, Nikhil Shri / Chaubey, Alka / Goel, Rajesh Kumar / Jain, Subheet Kumar

Future medicinal chemistry

2018 Volume 10, Issue 19, Page(s) 2249–2252

MeSH term(s)	Diabetic Retinopathy/drug therapy ; Humans ; Precision Medicine ; Proteomics
Language	English
Publishing date	2018-09-14
Publishing country	England
Document type	Editorial ; Research Support, Non-U.S. Gov't
ISSN	1756-8927
ISSN (online)	1756-8927
DOI	10.4155/fmc-2018-0233
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Article ; Online: Myopia, its prevalence, current therapeutic strategy and recent developments: A Review.

Singh, Harjeet / Singh, Harmanpreet / Latief, Uzma / Tung, Gurleen Kaur / Shahtaghi, Navid Reza / Sahajpal, Nikhil Shri / Kaur, Inderjit / Jain, Subheet Kumar

Indian journal of ophthalmology

2022 Volume 70, Issue 8, Page(s) 2788–2799

Abstract: Myopia is a widespread and complex refractive error in which a person's ability to see distant objects clearly is impaired. Its prevalence rate is increasing worldwide, and as per WHO, it is projected to increase from 22% in 2000 to 52% by 2050. It is ... ...

Abstract	Myopia is a widespread and complex refractive error in which a person's ability to see distant objects clearly is impaired. Its prevalence rate is increasing worldwide, and as per WHO, it is projected to increase from 22% in 2000 to 52% by 2050. It is more prevalent in developed, industrial areas and affects individuals of all ages. There are a number of treatments available for the control of myopia, such as glasses, contact lenses, laser surgery, and pharmaceuticals agents. However, these treatments are less beneficial and have significant side effects. A novel molecule, 7-methylxanthine (7-MX), has been found to be a highly beneficial alternate in the treatment of myopia and excessive eye elongation. Many preclinical and clinical studies showed that 7-MX is effective for the treatment of myopia and is presently under phase II of clinical investigation. We have also investigated preclinical toxicity studies such as acute, sub-acute, sub-chronic, and chronic on rats. In these studies, 7-MX was found to be non-toxic as compared to other reported anti-myopic agents. Moreover, as an ideal drug, 7-MX is observed to have no or low toxicity, brain permeability, non-allergic, higher oral administration efficacy, and low treatment costs and thus qualifies for the long-term treatment of myopia. This review article on 7-MX as an alternative to myopia treatment will highlight recent findings from well-designed preclinical and clinical trials and propose a potential future therapy.
MeSH term(s)	Animals ; Contact Lenses ; Eyeglasses ; Humans ; Myopia/surgery ; Myopia/therapy ; Prevalence ; Rats ; Refractive Errors
Language	English
Publishing date	2022-08-03
Publishing country	India
Document type	Journal Article ; Review
ZDB-ID	187392-1
ISSN	1998-3689 ; 0301-4738
ISSN (online)	1998-3689
ISSN	0301-4738
DOI	10.4103/ijo.IJO_2415_21
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Article: Clinical Utility of Optical Genome Mapping and 523-Gene Next Generation Sequencing Panel for Comprehensive Evaluation of Myeloid Cancers.

Sahajpal, Nikhil Shri / Mondal, Ashis K / Singh, Harmanpreet / Vashisht, Ashutosh / Ananth, Sudha / Saul, Daniel / Hastie, Alex R / Hilton, Benjamin / DuPont, Barbara R / Savage, Natasha M / Kota, Vamsi / Chaubey, Alka / Cortes, Jorge E / Kolhe, Ravindra

Cancers

2023 Volume 15, Issue 12

Abstract: The standard-of-care (SOC) for genomic testing of myeloid cancers primarily relies on karyotyping/fluorescent in situ hybridization (FISH) (cytogenetic analysis) and targeted gene panels (usually ≤54 genes) that harbor hotspot pathogenic variants ( ... ...

Abstract	The standard-of-care (SOC) for genomic testing of myeloid cancers primarily relies on karyotyping/fluorescent in situ hybridization (FISH) (cytogenetic analysis) and targeted gene panels (usually ≤54 genes) that harbor hotspot pathogenic variants (molecular genetic analysis). Despite this combinatorial approach, ~50% of myeloid cancer genomes remain cytogenetically normal, and the limited sequencing variant profiles obtained from targeted panels are unable to resolve the molecular etiology of many myeloid tumors. In this study, we evaluated the performance and clinical utility of combinatorial use of optical genome mapping (OGM) and a 523-gene next-generation sequencing (NGS) panel for comprehensive genomic profiling of 30 myeloid tumors and compared it to SOC cytogenetic methods (karyotyping and FISH) and a 54-gene NGS panel. OGM and the 523-gene NGS panel had an analytical concordance of 100% with karyotyping, FISH, and the 54-gene panel, respectively. Importantly, the IPSS-R cytogenetic risk group changed from very good/good to very poor in 22% of MDS (2/9) cases based on comprehensive profiling (karyotyping, FISH, and 54-gene panel vs. OGM and 523-gene panel), while additionally identifying six compound heterozygous events of potential clinical relevance in six cases (6/30, 20%). This cost-effective approach of using OGM and a 523-gene NGS panel for comprehensive genomic profiling of myeloid cancers demonstrated increased yield of actionable targets that can potentially result in improved clinical outcomes.
Language	English
Publishing date	2023-06-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15123214
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Article ; Online: Reduction of SARS-CoV-2 salivary viral load with pre-procedural mouth rinses: a randomised, controlled, clinical trial.

Farmaha, Jaspreet Kaur / James, Jeffrey N / Frazier, Kyle / Sahajpal, Nikhil Shri / Mondal, Ashis K / Bloomquist, Doan Tam / Kolhe, Ravindra / Looney, Stephen W / Bloomquist, Ryan

British dental journal

2023 Volume 234, Issue 8, Page(s) 593–600

Abstract: Introduction The purpose of this study was to test the short-term efficacy of four commercial mouthwashes versus water in reducing SARS-CoV-2 viral load in the oral cavity over clinically relevant time points.Methods In total, 32 subjects that were ... ...

Abstract	Introduction The purpose of this study was to test the short-term efficacy of four commercial mouthwashes versus water in reducing SARS-CoV-2 viral load in the oral cavity over clinically relevant time points.Methods In total, 32 subjects that were proven SARS-CoV-2-positive via polymerase chain reaction (PCR)-based diagnostic test were recruited and randomised into five parallel arms. Cycle threshold (Ct) values were compared in saliva samples between the groups, as well as within the groups at baseline (pre-rinse), zero hours, one hour and two hours post-rinse, using SARS-CoV-2 reverse transcription-PCR analysis.Results We observed a significant increase in Ct values in saliva samples collected immediately after rinsing with all the four mouthwashes - 0.12% chlorhexidine gluconate, 1.5% hydrogen peroxide, 1% povidone iodine, or Listerine - compared to water. A sustained increase in Ct values for up to two hours was only observed in the Listerine and chlorohexidine gluconate groups. We were not able to sufficiently power this clinical trial, so the results remain notional but encouraging and supportive of findings in other emerging mouthwash studies on COVID-19, warranting additional investigations.Conclusions Our evidence suggests that in a clinical setting, prophylactic rinses with Listerine or chlorhexidine gluconate can potentially reduce SARS-CoV-2 viral load in the oral cavity for up to two hours. While limited in statistical power due to the difficulty in obtaining this data, we advocate for pre-procedural mouthwashing, like handwashing, as an economical and safe additional precaution to help mitigate the transmission of SARS-CoV-2 from a potentially infected patient to providers.
MeSH term(s)	Humans ; SARS-CoV-2 ; Mouthwashes/therapeutic use ; COVID-19/prevention & control ; Viral Load
Chemical Substances	Mouthwashes ; chlorhexidine gluconate (MOR84MUD8E)
Language	English
Publishing date	2023-04-28
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	218090-x
ISSN	1476-5373 ; 0007-0610
ISSN (online)	1476-5373
ISSN	0007-0610
DOI	10.1038/s41415-023-5741-9
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