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   Articles with "indel" as a keyword



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Elucidation of de novo small insertion/deletion biology with parent‐of‐origin phasing

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recommendations! Published in 2020 at "Human Mutation"

DOI: 10.1002/humu.23971

Abstract: The mechanisms underlying de novo insertion/deletion (indel) genesis, such as polymerase slippage, have been hypothesized but not well characterized in the human genome. We implemented two methodological improvements, which were leveraged to dissect indel mutagenesis.… read more here.

Keywords: parent origin; insertion deletion; biology; origin phasing ... See more keywords

InDEL instability in two different tumoral tissues and its forensic significance

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recommendations! Published in 2024 at "Forensic Science, Medicine, and Pathology"

DOI: 10.1007/s12024-024-00808-5

Abstract: There may be cases where malignant tumor samples can be used for forensic DNA profiling studies. STRs are the first systems preferred in forensic science laboratories for identification purposes. However, genetic instability in tumoral tissues… read more here.

Keywords: forensic science; breast; indel; identification ... See more keywords

The use of ACE INDEL polymorphism as a biomarker of coronary artery disease (CAD) in humans with Mediterranean-style diet.

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recommendations! Published in 2019 at "International journal of biological macromolecules"

DOI: 10.1016/j.ijbiomac.2018.11.021

Abstract: The ACE INDEL gene polymorphisms are strongly associated with CAD. Therefore, the present study was undertaken to investigate the relationship between ACE INDEL polymorphism and CAD in Turkish Cypriots whose are expected to have Mediterranean-style… read more here.

Keywords: ace indel; indel polymorphism; indel; cad ... See more keywords

Insights into genetic variants within sheep IGF2BP1 and their association with litter size

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recommendations! Published in 2021 at "Small Ruminant Research"

DOI: 10.1016/j.smallrumres.2021.106350

Abstract: Abstract Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays a crucial role in cellular growth, proliferation, and embryonic development by regulating mRNA stability. IGF2BP1 has been recently found to be located on a new… read more here.

Keywords: association; litter size; indel; igf2bp1 ... See more keywords
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UPS-indel: a Universal Positioning System for Indels

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recommendations! Published in 2017 at "Scientific Reports"

DOI: 10.1038/s41598-017-14400-1

Abstract: Storing biologically equivalent indels as distinct entries in databases causes data redundancy, and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. Moreover, a unified system… read more here.

Keywords: universal positioning; positioning system; ups indel; equivalent indels ... See more keywords

Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project

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recommendations! Published in 2024 at "Scientific Reports"

DOI: 10.1038/s41598-024-57439-7

Abstract: Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants… read more here.

Keywords: review; benchmarking indel; indel set; indel ... See more keywords

indelPost: harmonizing ambiguities in simple and complex indel alignments.

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recommendations! Published in 2021 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btab601

Abstract: SUMMARY Small insertions and deletions (indels) in nucleotide sequence may be represented differently between mapping algorithms and variant callers, or in the flanking sequence context. Representational ambiguity is especially profound for complex indels, complicating comparisons… read more here.

Keywords: complex indel; indelpost; simple complex; complex indels ... See more keywords

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

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recommendations! Published in 2022 at "PLOS Computational Biology"

DOI: 10.1101/2019.12.30.891457

Abstract: Ancestral sequence reconstruction is a technique that is gaining widespread use in molecular evolution studies and protein engineering. Accurate reconstruction requires the ability to handle appropriately large numbers of sequences, as well as insertion and… read more here.

Keywords: representation ancestral; indel; ancestral sequence; sequence ... See more keywords

Abstract LB077: Analysis of indel and structural variant error profiles in deep next generation sequencing data

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recommendations! Published in 2023 at "Cancer Research"

DOI: 10.1158/1538-7445.am2023-lb077

Abstract: Background: Accurate detection of low frequency mutations is of critical importance in the study of genetic heterogeneity, such as on the detection of minimal residual diseases for leukemias. Our prior work has resulted in successful… read more here.

Keywords: indel; sequencing data; error; next generation ... See more keywords

Abstract 340: Validation of TSO500 NGS panel for comprehensive genomic profiling from FFPE tumor samples

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recommendations! Published in 2024 at "Cancer Research"

DOI: 10.1158/1538-7445.am2024-340

Abstract: Comprehensive genomic profiling (CGP) of tumor sample using large targeted NGS panels (e.g. MSK-IMPACT) has been shown to allow the detection of biomarkers from hundreds of cancer relevant genes involved in targeted and immunotherapy. Illumina… read more here.

Keywords: detection; tso500; 100 100; genomic profiling ... See more keywords

Chronological set of E. coli O157:H7 bovine strains establishes a role for repeat sequences and mobile genetic elements in genome diversification

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recommendations! Published in 2020 at "BMC Genomics"

DOI: 10.1186/s12864-020-06943-x

Abstract: Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a significant foodborne pathogen that resides asymptomatically within cattle and other ruminants. The EHEC genome harbors an extensive collection of mobile genetic elements (MGE), including multiple prophage, prophage-like elements,… read more here.

Keywords: repeat sequences; farm; repeat; prophage ... See more keywords