Alpha satellite insertion close to an ancestral centromeric region

Giannuzzi, Giuliana; Logsdon, Glennis A.; Chatron, Nicolas; Miller, Danny E.; Reversat, Julie; Munson, Katherine M.; Hoekzema, Kendra; Bonnet-Dupeyron, Marie-Noëlle; Rollat‐Farnier, Pierre‐Antoine; Baker, Carl; Sanlaville, Damien; Eichler, Evan E.; Schluth-Bolard, Caroline; Reymond, Alexandre

doi:10.1101/2021.03.10.434819

Cited by 3 publications

(1 citation statement)

References 78 publications

(100 reference statements)

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“…The recently released telomere-to-telomere (T2T) dataset attempts to fill gaps, bridge centromeric and telomeric regions, and correctly map large repeats [85]. However, although the T2T reference is a huge enterprise with potential impact in resolving specific disease-causing CGRs [86], it is still a haploid genome based on a single individual [86]. To fully capture and phase disease-causing SVs and SNVs, a diploid reference genome is needed.…”

Section: Clinical Challenge: Detecting and Interpreting Complex Rearr...mentioning

confidence: 99%

Complex genomic rearrangements: an underestimated cause of rare diseases

Schuy¹,

Grochowski²,

Carvalho³

et al. 2022

Trends in Genetics

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Section: Clinical Challenge: Detecting and Interpreting Complex Rearr...mentioning

confidence: 99%

Complex genomic rearrangements: an underestimated cause of rare diseases

Schuy¹,

Grochowski²,

Carvalho³

et al. 2022

Trends in Genetics

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Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing

Marquet

Zöllkau

Pastuschek

et al. 2022

Sci Rep

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Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA (> 90%), decreasing the overall microbial resolution. Nanopore's adaptive sampling method offers selective DNA depletion or target enrichment to directly reject or accept DNA molecules during sequencing without specialized sample preparation. Here, we demonstrate how selective ‘human host depletion’ resulted in a 1.70 fold (± 0.27 fold) increase in total sequencing depth, providing higher taxonomic profiling sensitivity. At the same time, the microbial composition remains consistent with the control experiments. The complete removal of all human host sequences is not yet possible and should be considered as an ethical approval statement might still be necessary. Adaptive sampling increased microbial sequencing yield in all 15 sequenced clinical routine vaginal samples, making it a valuable tool for clinical surveillance and medical-based research, which can be used in addition to other host depletion methods before sequencing.

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Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing

Marquet

Zöllkau

Pastuschek

et al. 2021

Preprint

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Metagenomic sequencing is a promising tool for clinical applications to study microbial composition in relation to disease or patient outcome. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA, decreasing the overall microbial resolution. Nanopore's adaptive sampling method offers selective DNA depletion or target enrichment to reject unwanted DNA sequences directly during sequencing without specialized sample preparation. Here, we increase the relative amount of non-human DNA through either direct enrichment or depletion of human DNA. To assess which approach works better, we analyzed 15 clinical routine vaginal swabs with typically high relative amounts of human DNA (> 90%) through metagenomic sequencing. The selective host depletion approach resulted in a 1.70 fold (+/- 0.27 fold) increase in total sequencing depth. Rejected reads contained over 99.80% human reads. In contrast to host depletion, targeted bacterial enrichment resulted in higher human depletion, but the microbial composition was altered as bacterial reads not matching the targets were also depleted. On the other hand, host depletion is not changing the microbial composition, even if high amounts of human host DNA are present, making it a valuable tool for clinical surveillance and medical-based research. However, up to 3% (min: 0.26% max: 2.94%) of human reads were still detectable in the 'accepted' sequence fraction. Thus, the complete removal of all human host sequences is not yet possible and should be considered as an ethical approval statement might still be necessary.

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Alpha satellite insertion close to an ancestral centromeric region

Cited by 3 publications

References 78 publications

Complex genomic rearrangements: an underestimated cause of rare diseases

Complex genomic rearrangements: an underestimated cause of rare diseases

Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing

Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing

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