SMURF-seq: efficient copy number profiling on long-read sequencers

Prabakar, Rishvanth K.; Xu, Liya; Hicks, James; Smith, Andrew D.

doi:10.1186/s13059-019-1732-1

Cited by 13 publications

(17 citation statements)

References 28 publications

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“…While others have devised innovative approaches using nanopore sequencing to address genomic applications that require high molecule/read counts ( 35 ), our approach is much simpler, especially for barcoded multiplexed samples. Hence, we surmise that short molecule nanopore sequencing is more likely to gain broad applicability and equally important, empower further technological developments in the rapidly evolving field of single-molecule sequencing.…”

Section: Discussionmentioning

confidence: 99%

High resolution copy number inference in cancer using short-molecule nanopore sequencing

Baslan

Kovaka

Sedlazeck

et al. 2021

Nucleic Acids Research

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Genome copy number is an important source of genetic variation in health and disease. In cancer, Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology. Emerging Nanopore sequencing technologies offer the potential for broader clinical utility, for example in smaller hospitals, due to lower instrument cost, higher portability, and ease of use. Nonetheless, Nanopore sequencing devices are limited in the number of retrievable sequencing reads/molecules compared to short-read sequencing platforms, limiting CNA inference accuracy. To address this limitation, we targeted the sequencing of short-length DNA molecules loaded at optimized concentration in an effort to increase sequence read/molecule yield from a single nanopore run. We show that short-molecule nanopore sequencing reproducibly returns high read counts and allows high quality CNA inference. We demonstrate the clinical relevance of this approach by accurately inferring CNAs in acute myeloid leukemia samples. The data shows that, compared to traditional approaches such as chromosome analysis/cytogenetics, short molecule nanopore sequencing returns more sensitive, accurate copy number information in a cost effective and expeditious manner, including for multiplex samples. Our results provide a framework for short-molecule nanopore sequencing with applications in research and medicine, which includes but is not limited to, CNAs.

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Section: Discussionmentioning

confidence: 99%

High resolution copy number inference in cancer using short-molecule nanopore sequencing

Baslan

Kovaka

Sedlazeck

et al. 2021

Nucleic Acids Research

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“…Our technique can be easily adapted for use with Oxford Nanopore technology. A similar study was conducted by our colleagues for CNV analysis [20]. With a good training set of cfDNA samples from pregnant women, the possibility of NIPT using nanopore sequencers can be promising.…”

Section: Discussionmentioning

confidence: 55%

NIPT technique based on the use of long chimeric DNA reads

Belova

Plakhina

Evfratov

et al. 2020

Preprint

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Background: Non-invasive prenatal testing for aneuploidy on chromosomes 21, 18 and 13 is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as the high throughput sequencing is still relatively expensive. At the same time, there is a trend of increase of the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140-160 bp, it is not possible to effectively use long reads.Results: The authors used high-performance sequencing of cfDNA libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples of pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV and NPV of the results.Conclusions: The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99, 93% and 99.14% for 21 trisomy; 100% and 98.34% for 18 trisomy; 100% and 99.17% for 13 trisomy, respectively).

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“…Our technique can be easily adapted for use with Oxford Nanopore technology. A similar study was conducted by our colleagues for CNV analysis [35]. With a good training set of cfDNA samples from pregnant women, the possibility of NIPT using nanopore sequencers is promising [36].…”

Section: Discussionmentioning

confidence: 71%

NIPT Technique Based on the Use of Long Chimeric DNA Reads

Belova

Plakhina²,

Evfratov³

et al. 2020

Genes

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Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an increasing trend in the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140–160 bp, it is not possible to effectively use long reads. The authors used high-performance sequencing of cell-free DNA (cfDNA) libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples from pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of the results. The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99.93% and 99.14% for T21; 100% and 98.34% for T18; 100% and 99.17% for T13, respectively).

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SMURF-seq: efficient copy number profiling on long-read sequencers

Cited by 13 publications

References 28 publications

High resolution copy number inference in cancer using short-molecule nanopore sequencing

High resolution copy number inference in cancer using short-molecule nanopore sequencing

NIPT technique based on the use of long chimeric DNA reads

NIPT Technique Based on the Use of Long Chimeric DNA Reads

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