Relevant bibliographies by topics / Linked-read sequencing

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Academic literature on the topic 'Linked-read sequencing'

Author: Grafiati
Published: 4 June 2021
Last updated: 5 February 2022

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Journal articles on the topic "Linked-read sequencing"

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Kumar, Ashwini, Sadiksha Adhikari, Matti Kankainen, and Caroline A. Heckman. "Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma." Cancers 13, no. 6 (2021): 1212. http://dx.doi.org/10.3390/cancers13061212.

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Linked-read sequencing was developed to aid the detection of large structural variants (SVs) from short-read sequencing efforts. We performed a systematic evaluation to determine if linked-read exome sequencing provides more comprehensive and clinically relevant information than whole-exome sequencing (WES) when applied to the same set of multiple myeloma patient samples. We report that linked-read sequencing detected a higher number of SVs (n = 18,455) than WES (n = 4065). However, linked-read predictions were dominated by inversions (92.4%), leading to poor detection of other types of SVs. In contrast, WES detected 56.3% deletions, 32.6% insertions, 6.7% translocations, 3.3% duplications and 1.2% inversions. Surprisingly, the quantitative performance assessment suggested a higher performance for WES (AUC = 0.791) compared to linked-read sequencing (AUC = 0.766) for detecting clinically validated cytogenetic alterations. We also found that linked-read sequencing detected more short variants (n = 704) compared to WES (n = 109). WES detected somatic mutations in all MM-related genes while linked-read sequencing failed to detect certain mutations. The comparison of somatic mutations detected using linked-read, WES and RNA-seq revealed that WES and RNA-seq detected more mutations than linked-read sequencing. These data indicate that WES outperforms and is more efficient than linked-read sequencing for detecting clinically relevant SVs and MM-specific short variants.
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Elyanow, Rebecca, Hsin-Ta Wu, and Benjamin J. Raphael. "Identifying structural variants using linked-read sequencing data." Bioinformatics 34, no. 2 (2017): 353–60. http://dx.doi.org/10.1093/bioinformatics/btx712.

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Greer, S. U., and H. P. Ji. "Structural variant analysis for linked-read sequencing data with gemtools." Bioinformatics 35, no. 21 (2019): 4397–99. http://dx.doi.org/10.1093/bioinformatics/btz239.

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Abstract Summary Linked-read sequencing generates synthetic long reads which are useful for the detection and analysis of structural variants (SVs). The software associated with 10× Genomics linked-read sequencing, Long Ranger, generates the essential output files (BAM, VCF, SV BEDPE) necessary for downstream analyses. However, to perform downstream analyses requires the user to customize their own tools to handle the unique features of linked-read sequencing data. Here, we describe gemtools, a collection of tools for the downstream and in-depth analysis of SVs from linked-read data. Gemtools uses the barcoded aligned reads and the Megabase-scale phase blocks to determine haplotypes of SV breakpoints and delineate complex breakpoint configurations at the resolution of single DNA molecules. The gemtools package is a suite of tools that provides the user with the flexibility to perform basic functions on their linked-read sequencing output in order to address even more questions. Availability and implementation The gemtools package is freely available for download at: https://github.com/sgreer77/gemtools. Supplementary information Supplementary data are available at Bioinformatics online.
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Lutgen, Dave, Raphael Ritter, Remi‐André Olsen, et al. "Linked‐read sequencing enables haplotype‐resolved resequencing at population scale." Molecular Ecology Resources 20, no. 5 (2020): 1311–22. http://dx.doi.org/10.1111/1755-0998.13192.

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Chen, Nancy, Daniel W. Bellott, David C. Page, and Andrew G. Clark. "Identification of avian W-linked contigs by short-read sequencing." BMC Genomics 13, no. 1 (2012): 183. http://dx.doi.org/10.1186/1471-2164-13-183.

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DeJesus-Hernandez, Mariely, Ross A. Aleff, Jazmyne L. Jackson, et al. "Long-read targeted sequencing uncovers clinicopathological associations for C9orf72-linked diseases." Brain 144, no. 4 (2021): 1082–88. http://dx.doi.org/10.1093/brain/awab006.

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Abstract To examine the length of a hexanucleotide expansion in C9orf72, which represents the most frequent genetic cause of frontotemporal lobar degeneration and motor neuron disease, we employed a targeted amplification-free long-read sequencing technology: No-Amp sequencing. In our cross-sectional study, we assessed cerebellar tissue from 28 well-characterized C9orf72 expansion carriers. We obtained 3507 on-target circular consensus sequencing reads, of which 814 bridged the C9orf72 repeat expansion (23%). Importantly, we observed a significant correlation between expansion sizes obtained using No-Amp sequencing and Southern blotting (P = 5.0 × 10−4). Interestingly, we also detected a significant survival advantage for individuals with smaller expansions (P = 0.004). Additionally, we uncovered that smaller expansions were significantly associated with higher levels of C9orf72 transcripts containing intron 1b (P = 0.003), poly(GP) proteins (P = 1.3 × 10− 5), and poly(GA) proteins (P = 0.005). Thorough examination of the composition of the expansion revealed that its GC content was extremely high (median: 100%) and that it was mainly composed of GGGGCC repeats (median: 96%), suggesting that expanded C9orf72 repeats are quite pure. Taken together, our findings demonstrate that No-Amp sequencing is a powerful tool that enables the discovery of relevant clinicopathological associations, highlighting the important role played by the cerebellar size of the expanded repeat in C9orf72-linked diseases.
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Onore, Maria Elena, Annalaura Torella, Francesco Musacchia, et al. "Linked-Read Whole Genome Sequencing Solves a Double DMD Gene Rearrangement." Genes 12, no. 2 (2021): 133. http://dx.doi.org/10.3390/genes12020133.

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Next generation sequencing (NGS) has changed our approach to diagnosis of genetic disorders. Nowadays, the most comprehensive application of NGS is whole genome sequencing (WGS) that is able to detect virtually all DNA variations. However, even after accurate WGS, many genetic conditions remain unsolved. This may be due to the current NGS protocols, based on DNA fragmentation and short reads. To overcome these limitations, we applied a linked-read sequencing technology that combines single-molecule barcoding with short-read WGS. We were able to assemble haplotypes and distinguish between alleles along the genome. As an exemplary case, we studied the case of a female carrier of X-linked muscular dystrophy with an unsolved genetic status. A deletion of exons 16–29 in DMD gene was responsible for the disease in her family, but she showed a normal dosage of these exons by Multiplex Ligation-dependent Probe Amplification (MLPA) and array CGH. This situation is usually considered compatible with a “non-carrier” status. Unexpectedly, the girl also showed an increased dosage of flanking exons 1–15 and 30–34. Using linked-read WGS, we were able to distinguish between the two X chromosomes. In the first allele, we found the 16–29 deletion, while the second allele showed a 1–34 duplication: in both cases, linked-read WGS correctly mapped the borders at single-nucleotide resolution. This duplication in trans apparently restored the normal dosage of exons 16–29 seen by quantitative assays. This had a dramatic impact in genetic counselling, by converting a non-carrier into a double carrier status prediction. We conclude that linked-read WGS should be considered as a valuable option to improve our understanding of unsolved genetic conditions.
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Zheng, Grace X. Y., Billy T. Lau, Michael Schnall-Levin, et al. "Haplotyping germline and cancer genomes with high-throughput linked-read sequencing." Nature Biotechnology 34, no. 3 (2016): 303–11. http://dx.doi.org/10.1038/nbt.3432.

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Bohrson, Craig L., Alison R. Barton, Michael A. Lodato, et al. "Linked-read analysis identifies mutations in single-cell DNA-sequencing data." Nature Genetics 51, no. 4 (2019): 749–54. http://dx.doi.org/10.1038/s41588-019-0366-2.

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Redin, David, Erik Borgström, Mengxiao He, Hooman Aghelpasand, Max Käller, and Afshin Ahmadian. "Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules." Nucleic Acids Research 45, no. 13 (2017): e125-e125. http://dx.doi.org/10.1093/nar/gkx436.

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Dissertations / Theses on the topic "Linked-read sequencing"

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Theland, Jennifer. "Resolving metagenomes usingsingle-molecule linked-readsequencing." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-231412.

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The development of Massively Parallel Sequencing (MPS) has enabled more accurate and less time-consuming DNA sequencing. Although MPS technologies are theoretically applicable to all samples and species, the majority of studies on microorganisms have been conducted on those able to be isolated and cultivated in laboratories. In the field of metagenomics, DNA from uncultivated environmental samples is analyzed. Whole genome sequencing of such complex samples poses difficult computational challenges due to the characteristics of metagenomic data, where one major challenge lies in determining the true origin of high similarity reads. In addition, the short-range information acquired from MPS reveals little about how reads from DNA sequencing fit together. Consequently, producing genome drafts from reads generated by MPS remains difficult. Here, the linked-read sequencing technology DB-Seq has been applied to bacterial samples in order to assess its potential in metagenomics. Specifically, its performance in retaining long-range information in de novo whole genome assembly has been tested. The results obtained in this initial study show great potential of DB-Seq in genome assembly, with significantly more contiguous results than conventional methods generate.<br>Utvecklingen av Massiv Parallel Sekvensering (MPS) har möjliggjort mer korrekt och mindre tidskrävande DNA sekvensering. Trots att MPS teoretiskt sett kan appliceras på alla provtyper och arter, har majoriteten av de studier som utförts på mikroorganismer varit fokuserade på de som kan isoleras och odlas i laboratorium. Inom ämnet metagenomik analyseras DNA från orörda miljöprover. Helgenomssekvensering av sådana prover ger upphov till komplicerade utmaningar för data-analys, där ett av de största problemen är att bestämma ursprunget av snarlika sekvenseringsresultat. Ytterligare komplikationer uppstår på grund av den data som erhålls från MPS, då denna ej ger information om hur sekvenseringsdata bör placeras i förhållande till varandra. Följdaktligen är det svårt att producera hopsatta genom utifrån MPS-data. I detta projekt har "linked-read"-sekvenseringsteknologin DB-Seq applicerats på bakterieprover för att undersöka metodens potential i metagenomik. Specifikt har metodens förmåga att bibehålla information om ursprungspositionen av sekvenseringsdata testats i de novo sammansättning av genom. De erhållna resultaten i denna förstagångsstudie tyder på stor potential för DB-Seq i genomsammansättning, med signifikant mer sammanhängande resultatsekvenser än vad konventionella metoder uppvisar.
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Conference papers on the topic "Linked-read sequencing"

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Pham, Minh-Tam, Harshath Gupta, Anuj Gupta, et al. "Abstract 2198: Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2198.

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Xia, Li C., John M. Bell, Christina Wood-Bouwens, et al. "Abstract 4334: Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-4334.

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Pellegrino, Renata, Michael Benway, Paulina Kocjan, et al. "Abstract 5353: High-throughput automation of the 10x Genomics® Chromium™ workflow for linked-read whole exome sequencing and a targeted lynch syndrome panel." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-5353.

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