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  1. Book ; Online: Biodiversity for food and agriculture and food security

    Rawal, Vikas / Bansal, Vaishali / Thokchom, Doordarshni

    an exploration of interrelationships

    (Background study paper / FAO, Commission on Genetic Resources for Food and Agriculture ; no. 69)

    2019  

    Institution FAO / Commission on Genetic Resources for Food and Agriculture
    Author's details by Vikas Rawal, Vaishali Bansal and Doordarshni Thokchom ; Food and Agriculture Organization of the United Nations, Commission on Genetic Resources for Food and Agriculture
    Series title Background study paper / FAO, Commission on Genetic Resources for Food and Agriculture ; no. 69
    Background study paper
    Collection Background study paper
    Language English
    Size 1 Online-Ressource (61 Seiten), Diagramme, Karten
    Publisher Food and Agriculture Organization of the United Nations
    Publishing place Rome
    Publishing country Italy
    Document type Book ; Online
    Note Open Access
    HBZ-ID HT021146473
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data.

    Bansal, Vikas

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2590, Page(s) 139–147

    Abstract: Rapid advances in high-throughput DNA sequencing technologies have enabled variant discovery from whole-genome sequencing (WGS) datasets; however linking variants on a chromosome together into haplotypes, also known as haplotype phasing, remains ... ...

    Abstract Rapid advances in high-throughput DNA sequencing technologies have enabled variant discovery from whole-genome sequencing (WGS) datasets; however linking variants on a chromosome together into haplotypes, also known as haplotype phasing, remains difficult. Human genomes are diploid and haplotype phasing is crucial for the complete interpretation and analysis of genetic variation.Hapcut2 ( https://github.com/vibansal/HapCUT2 ) is an open-source software for phasing diploid genomes using sequence data generated using different sequencing technologies and experimental methods. In this article, we give an overview of the algorithm used by Hapcut2 and describe how to use Hapcut2 for haplotype phasing of individual genomes using different types of sequence data.
    MeSH term(s) Humans ; Sequence Analysis, DNA/methods ; Polymorphism, Single Nucleotide ; Haplotypes ; Genome, Human ; High-Throughput Nucleotide Sequencing/methods ; Algorithms
    Language English
    Publishing date 2022-11-05
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2819-5_9
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  3. Article ; Online: A multilocus approach for accurate variant calling in low-copy repeats using whole-genome sequencing.

    Prodanov, Timofey / Bansal, Vikas

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 39 Suppl 1, Page(s) i279–i287

    Abstract: Motivation: Low-copy repeats (LCRs) or segmental duplications are long segments of duplicated DNA that cover > 5% of the human genome. Existing tools for variant calling using short reads exhibit low accuracy in LCRs due to ambiguity in read mapping and ...

    Abstract Motivation: Low-copy repeats (LCRs) or segmental duplications are long segments of duplicated DNA that cover > 5% of the human genome. Existing tools for variant calling using short reads exhibit low accuracy in LCRs due to ambiguity in read mapping and extensive copy number variation. Variants in more than 150 genes overlapping LCRs are associated with risk for human diseases.
    Methods: We describe a short-read variant calling method, ParascopyVC, that performs variant calling jointly across all repeat copies and utilizes reads independent of mapping quality in LCRs. To identify candidate variants, ParascopyVC aggregates reads mapped to different repeat copies and performs polyploid variant calling. Subsequently, paralogous sequence variants that can differentiate repeat copies are identified using population data and used for estimating the genotype of variants for each repeat copy.
    Results: On simulated whole-genome sequence data, ParascopyVC achieved higher precision (0.997) and recall (0.807) than three state-of-the-art variant callers (best precision = 0.956 for DeepVariant and best recall = 0.738 for GATK) in 167 LCR regions. Benchmarking of ParascopyVC using the genome-in-a-bottle high-confidence variant calls for HG002 genome showed that it achieved a very high precision of 0.991 and a high recall of 0.909 across LCR regions, significantly better than FreeBayes (precision = 0.954 and recall = 0.822), GATK (precision = 0.888 and recall = 0.873) and DeepVariant (precision = 0.983 and recall = 0.861). ParascopyVC demonstrated a consistently higher accuracy (mean F1 = 0.947) than other callers (best F1 = 0.908) across seven human genomes.
    Availability and implementation: ParascopyVC is implemented in Python and is freely available at https://github.com/tprodanov/ParascopyVC.
    MeSH term(s) Humans ; Segmental Duplications, Genomic ; DNA Copy Number Variations ; Whole Genome Sequencing ; Benchmarking ; Genome, Human
    Language English
    Publishing date 2023-06-28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad268
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  4. Article ; Online: Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes.

    Bansal, Vikas

    Bioinformatics (Oxford, England)

    2019  Volume 35, Issue 14, Page(s) i242–i248

    Abstract: Motivation: Reconstruction of haplotypes for human genomes is an important problem in medical and population genetics. Hi-C sequencing generates read pairs with long-range haplotype information that can be computationally assembled to generate ... ...

    Abstract Motivation: Reconstruction of haplotypes for human genomes is an important problem in medical and population genetics. Hi-C sequencing generates read pairs with long-range haplotype information that can be computationally assembled to generate chromosome-spanning haplotypes. However, the haplotypes have limited completeness and low accuracy. Haplotype information from population reference panels can potentially be used to improve the completeness and accuracy of Hi-C haplotyping.
    Results: In this paper, we describe a likelihood based method to integrate short-range haplotype information from a population reference panel of haplotypes with the long-range haplotype information present in sequence reads from methods such as Hi-C to assemble dense and highly accurate haplotypes for individual genomes. Our method leverages a statistical phasing method and a maximum spanning tree algorithm to determine the optimal second-order approximation of the population-based haplotype likelihood for an individual genome. The population-based likelihood is encoded using pseudo-reads which are then used as input along with sequence reads for haplotype assembly using an existing tool, HapCUT2. Using whole-genome Hi-C data for two human genomes (NA19240 and NA12878), we demonstrate that this integrated phasing method enables the phasing of 97-98% of variants, reduces the switch error rates by 3-6-fold, and outperforms an existing method for combining phase information from sequence reads with population-based phasing. On Strand-seq data for NA12878, our method improves the haplotype completeness from 71.4 to 94.6% and reduces the switch error rate 2-fold, demonstrating its utility for phasing using multiple sequencing technologies.
    Availability and implementation: Code and datasets are available at https://github.com/vibansal/IntegratedPhasing.
    MeSH term(s) Algorithms ; Genome, Human ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Likelihood Functions ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA
    Language English
    Publishing date 2019-08-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btz329
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  5. Article: Whole-exome sequencing in familial type 2 diabetes identifies an atypical missense variant in the RyR2 gene.

    Bansal, Vikas / Winkelmann, Bernhard R / Dietrich, Johannes W / Boehm, Bernhard O

    Frontiers in endocrinology

    2024  Volume 15, Page(s) 1258982

    Abstract: Genome-wide association studies have identified several hundred loci associated with type 2 diabetes mellitus (T2DM). Additionally, pathogenic variants in several genes are known to cause monogenic diabetes that overlaps clinically with T2DM. Whole-exome ...

    Abstract Genome-wide association studies have identified several hundred loci associated with type 2 diabetes mellitus (T2DM). Additionally, pathogenic variants in several genes are known to cause monogenic diabetes that overlaps clinically with T2DM. Whole-exome sequencing of related individuals with T2DM is a powerful approach to identify novel high-penetrance disease variants in coding regions of the genome. We performed whole-exome sequencing on four related individuals with T2DM - including one individual diagnosed at the age of 33 years. The individuals were negative for mutations in monogenic diabetes genes, had a strong family history of T2DM, and presented with several characteristics of metabolic syndrome. A missense variant (p.N2291D) in the type 2 ryanodine receptor (
    MeSH term(s) Adult ; Animals ; Humans ; Mice ; Diabetes Mellitus, Type 2/complications ; Diabetes Mellitus, Type 2/genetics ; Exome Sequencing ; Genome-Wide Association Study ; Glucose ; Glucose Intolerance ; Mutation, Missense ; Ryanodine Receptor Calcium Release Channel/genetics
    Chemical Substances Glucose (IY9XDZ35W2) ; Ryanodine Receptor Calcium Release Channel ; RyR2 protein, human ; ryanodine receptor 2. mouse
    Language English
    Publishing date 2024-02-20
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2592084-4
    ISSN 1664-2392
    ISSN 1664-2392
    DOI 10.3389/fendo.2024.1258982
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  6. Article ; Online: Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing

    Timofey Prodanov / Vikas Bansal

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 12

    Abstract: Low-copy repeats cover up to 5% of the human genome and are prone to extensive copy number variation. Here, the authors present a novel computational method to estimate paralog-specific copy number of such regions using whole-genome sequencing. ...

    Abstract Low-copy repeats cover up to 5% of the human genome and are prone to extensive copy number variation. Here, the authors present a novel computational method to estimate paralog-specific copy number of such regions using whole-genome sequencing.
    Keywords Science ; Q
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing.

    Prodanov, Timofey / Bansal, Vikas

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 3221

    Abstract: The human genome contains hundreds of low-copy repeats (LCRs) that are challenging to analyze using short-read sequencing technologies due to extensive copy number variation and ambiguity in read mapping. Copy number and sequence variants in more than ... ...

    Abstract The human genome contains hundreds of low-copy repeats (LCRs) that are challenging to analyze using short-read sequencing technologies due to extensive copy number variation and ambiguity in read mapping. Copy number and sequence variants in more than 150 duplicated genes that overlap LCRs have been implicated in monogenic and complex human diseases. We describe a computational tool, Parascopy, for estimating the aggregate and paralog-specific copy number of duplicated genes using whole-genome sequencing (WGS). Parascopy is an efficient method that jointly analyzes reads mapped to different repeat copies without the need for global realignment. It leverages multiple samples to mitigate sequencing bias and to identify reliable paralogous sequence variants (PSVs) that differentiate repeat copies. Analysis of WGS data for 2504 individuals from diverse populations showed that Parascopy is robust to sequencing bias, has higher accuracy compared to existing methods and enables prioritization of pathogenic copy number changes in duplicated genes.
    MeSH term(s) DNA Copy Number Variations/genetics ; Genome, Human/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Segmental Duplications, Genomic ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods
    Language English
    Publishing date 2022-06-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-30930-3
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  8. Article ; Online: Recommendations of apex health bodies remain localized: not in conformity with international implementation policy for urological disorders.

    Goyal, Suresh Kumar / Bansal, Renu / Gupta, Vikas / Bansal, Cherry / Bansal, Parveen

    The Lancet regional health. Southeast Asia

    2023  Volume 20, Page(s) 100330

    Abstract: In developing/underdeveloped countries there is still a great burden of adverse drug reaction (ADR), morbidity and mortality because of poor regulations and implementation of preventive measures. These countries try to copy/follow guidelines from ... ...

    Abstract In developing/underdeveloped countries there is still a great burden of adverse drug reaction (ADR), morbidity and mortality because of poor regulations and implementation of preventive measures. These countries try to copy/follow guidelines from international bodies like American Urology Association (AUA), European Association of Urology (EAU), AGS, UMC and WHO irrespective of their country of origin and success in implementation. Although recommendations of these organizations are obligatory, yet these are taken as the gold standard for good clinical practices. This manuscript highlights difference in view point of various apex health organizations in formulating health policies for prevention, diagnosis, treatment and ADR monitoring for urological disorders. Lacking role of regulatory bodies in implementation of existing policies may lead to potentially inappropriate medication and produce a great economic burden. This analysis has prompted us to recommend that these apex bodies should have better coordination in producing a single value document, make it mandatory part of curricula in medical schools for better awareness, awareness campaigns and separate reporting column in ADR form.
    Language English
    Publishing date 2023-11-28
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2772-3682
    ISSN (online) 2772-3682
    DOI 10.1016/j.lansea.2023.100330
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  9. Article ; Online: Descemet membrane endothelial keratoplasty (DMEK) aquarium: Diving in to learn DMEK surgical concepts.

    Narang, Purvasha / Mittal, Vikas / Bansal, Manish / Sehdev, Nancy / Yadav, Vibha

    Indian journal of ophthalmology

    2023  Volume 71, Issue 3, Page(s) 996–998

    Abstract: A novel simulation model (without using human corneas) has been described for understanding the surgical concepts and developing tactile reflexes of Descemet membrane (DM) endothelium scroll manipulation and orientation in the anterior chamber, which are ...

    Abstract A novel simulation model (without using human corneas) has been described for understanding the surgical concepts and developing tactile reflexes of Descemet membrane (DM) endothelium scroll manipulation and orientation in the anterior chamber, which are necessary for performing Descemet membrane endothelial keratoplasty (DMEK). Termed the "DMEK aquarium," this model helps facilitate the understanding of different maneuvers of the DM graft needed inside the fluid-filled anterior chamber, like unrolling or unfolding, flipping or inversion, and checking orientation and centration in the host cornea. A stepwise plan for surgeons starting to learn DMEK utilizing various available resources is also suggested.
    MeSH term(s) Humans ; Diving ; Descemet Membrane ; Corneal Transplantation ; Cornea ; Learning
    Language English
    Publishing date 2023-03-21
    Publishing country India
    Document type Journal Article
    ZDB-ID 187392-1
    ISSN 1998-3689 ; 0301-4738
    ISSN (online) 1998-3689
    ISSN 0301-4738
    DOI 10.4103/ijo.IJO_1694_22
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    Zs.B 329: Show issues Location:
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    Zs.MO 598: Show issues

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  10. Article ; Online: Fast track development of Fisetin and Naringenin based economic antianxiety drug using Docking tools.

    Gupta, Vikas / Kaur, Gunpreet / Sharma, Ravinder / Bansal, Renu / Bansal, Parveen

    Asian journal of psychiatry

    2022  Volume 74, Page(s) 103188

    MeSH term(s) Flavanones/pharmacology ; Flavonols ; Humans
    Chemical Substances Flavanones ; Flavonols ; naringenin (HN5425SBF2) ; fisetin (OO2ABO9578)
    Language English
    Publishing date 2022-06-15
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 2456678-0
    ISSN 1876-2026 ; 1876-2018
    ISSN (online) 1876-2026
    ISSN 1876-2018
    DOI 10.1016/j.ajp.2022.103188
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