DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads

Dong, Jinxin; Qi, Minyong; Wang, Shaoqiang; Yuan, Xiguo

doi:10.3389/fgene.2020.00924

Cited by 6 publications

(5 citation statements)

References 56 publications

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“…Positive selection events may promote favorable mutations in the context of rapid environmental changes 32 . In tandem duplication, a DNA segment is duplicated and inserted adjacent to the original segment, resulting in a structural rearrangement 33 . Dispersed duplication generates unpredictable and random patterns by DNA or RNA-based mechanisms, with two gene copies that are neither adjacent to each other in the genome nor within homologous chromosomal segments 34 .…”

Section: Discussionmentioning

confidence: 99%

Gene family expansions in Antarctic winged midge as a strategy for adaptation to cold environments

Kim

Lee

et al. 2022

Sci Rep

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Parochlus steinenii is the only flying insect native to Antarctica. To elucidate the molecular mechanisms underlying its adaptation to cold environments, we conducted comparative genomic analyses of P. steinenii and closely related lineages. In an analysis of gene family evolution, 68 rapidly evolving gene families, involved in the innate immune system, unfolded protein response, DNA packaging, protein folding, and unsaturated fatty acid biosynthesis were detected. Some gene families were P. steinenii-specific and showed phylogenetic instability. Acyl-CoA delta desaturase and heat shock cognate protein 70 (Hsc70) were representative gene families, showing signatures of positive selection with multiple gene duplication events. Acyl-CoA delta desaturases may play pivotal roles in membrane fluidity, and expanded Hsc70 genes may function as chaperones or thermal sensors in cold environments. These findings suggest that multiple gene family expansions contributed to the adaptation of P. steinenii to cold environments.

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Section: Discussionmentioning

confidence: 99%

Gene family expansions in Antarctic winged midge as a strategy for adaptation to cold environments

Kim

Lee

et al. 2022

Sci Rep

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“…Some chromosomes and regions appear to be more CNV-rich and are implicated in developmental disorders more than others [ 16 , 17 , 18 ]. Last, due to the limitations of short reads, orientation and genomic positional information (e.g., is the duplication tandem) for CNV gains is more challenging [ 19 ], and nearly impossible to defer from exome data.…”

Section: Maximizing the Use Of Information In Existing Sequence Datamentioning

confidence: 99%

Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology

Kadlubowska

Schrauwen

2022

Genes

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During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.

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“…g . Manta [18], Delly [10], Lumpy [11], and DINTD [19]. We also reported the results of Pindel-TD using short-read sequencing data of a cancer cell line K562 from ENCODE [20] to illustrate its potential application on cancer genomic data.…”

Section: Introductionmentioning

confidence: 99%

Pindel-TD: a tandem duplication detector based on a pattern growth approach

Yang,

Zheng,

Jia

et al. 2023

Preprint

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Tandem duplication(TD) is a major type ofstructural variation(SV), and plays an important role in novel gene formation and human diseases. However, TDs are often missed or incorrectly classified as insertions by most of modern SV detection methods due to the lacking of specialized operation on TD related mutational signals. Herein, we developed a TD detection module of Pindel referred as Pindel-TD based on a TD specificpattern growthapproach. Pindel-TD detects TDs with a wide size range at single nucleotide resolution. Using simulation and real read data of HG002, we demonstrate that Pindel-TD outperformed other leading methods in terms of precision, recall, F1-score and robustness. Further applying Pindel-TD on data generated from K562 cancer cell line, we identified a TD located at the seventh exon ofSAGE1, explaining its high expression. Pindel-TD is available athttps://github.com/xjtu-omics/pindeland free for non-commercial use.

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DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads

Cited by 6 publications

References 56 publications

Gene family expansions in Antarctic winged midge as a strategy for adaptation to cold environments

Gene family expansions in Antarctic winged midge as a strategy for adaptation to cold environments

Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology

Pindel-TD: a tandem duplication detector based on a pattern growth approach

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