Author Correction: The SEQC2 epigenomics quality control (EpiQC) study

Foox, Jonathan; Nordlund, Jessica; Lalancette, Claudia; Gong, Ting; Lacey, Michelle; Lent, Samantha; Langhorst, Bradley W.; Ponnaluri, V. K. Chaithanya; Williams, Louise; Padmanabhan, Karthik Ramaswamy; Cavalcante, Raymond G.; Lundmark, Anders; Butler, Daniel; Mozsary, Christopher; Gurvitch, Justin; Greally, John M.; Suzuki, Masako; Menor, Mark; Nasu, Masaki; Alonso, Alicia; Sheridan, Caroline; Scherer, Andreas; Bruinsma, Stephen; Golda, Gosia; Muszyńska, Agata; Łabaj, Paweł P.; Campbell, Matthew A.; Wos, Frank; Raine, Amanda; Liljedahl, Ulrika; Axelsson, Tomas; Wang, Charles; Chen, Zhong; Yang, Zujun; Li, Jing; Yang, Xiaopeng; Wang, Hongwei; Melnick, Ari; Guo, Shang; Blume, Alexander; Franke, Vedran; Cáceres, Inmaculada Ibáñez de; Rodriguez-Antolín, Carlos; Rosas, Rocío; Davis, J. Wade; Ishii, Jennifer; Megherbi, Dalila B.; Xiao, Wenming; Liao, Will; Xu, Joshua; Hong, Huixiao; Tong, Weida; Akalin, Altuna; Wang, Yunliang; Deng, Youping; Mason, Christopher E.

doi:10.1186/s13059-021-02573-y

Cited by 5 publications

(1 citation statement)

References 1 publication

(1 reference statement)

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“…As such, the opportunities for obtaining DNA methylation pro les of clinical samples are expected to further increase. Although it is technically possible to obtain DNA methylation information in a genomewide manner by the methods such as EM-seq (6) and long-read HiFi sequencing (7), it is currently not practical cost-wise to apply such methods to hundreds to thousands of samples. Targeted capture methylation sequencing (methyl-seq) signi cantly reduces per-sample costs and is expected to remain as one of the methods for clinical methylome analyses for the time being.…”

Section: Introductionmentioning

confidence: 99%

A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

Hasegawa

Nakabayashi

Ishiwata

et al. 2022

Preprint

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Objective The opportunities for sequencing-based methylome analysis of clinical samples are increasing. To reduce its cost and the amount of genomic DNA required for library preparation, we aimed to establish a capture methyl-seq protocol, which adopts pre-pooling of multiple libraries before hybridization capture and TET2/APOBEC-mediated conversion of unmethylated cytosine to thymine. Results We compared a publicly available dataset generated by the standard protocol of SureSelect XT Human Methyl-Seq Kit and our dataset obtained by its modified protocol that adopted sample pre-pooling and enzymatic conversion. We confirmed that the quality of DNA methylation data was comparable between the two datasets. As our protocol, EMCap, is more cost-effective and reduces the amount of input genomic DNA, it would serve as a better choice for clinical methylome sequencing.

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Section: Introductionmentioning

confidence: 99%

A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

Hasegawa

Nakabayashi

Ishiwata

et al. 2022

Preprint

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Prime editing for precise and highly versatile genome manipulation

2022

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single-stranded DNA (ssDNA) at the target site, triggering deamination by the tethered ssDNA-specific deaminase enzyme. Cytosine base editors (CBEs) and adenine base editors (ABEs) contain deaminases that catalyse C•G-to-T•A and A•T-to-G•C changes, respectively [27][28][29][30][31] . C•G-to-G•C base editors (CGBEs) are similar to CBEs, but stimulate replacement of the deaminated cytosine base with guanine, albeit with lower typical efficiencies and product purities compared to CBEs and ABEs [33][34][35][36] . Compared to Cas nucleases, base editors exhibit substantially greater efficiency with few indel byproducts, and show far fewer undesired consequences of DSBs than nucleases in side-by-side comparisons 19,21,[23][24][25][26]37,38 .Because base editors deaminate within a small window of 4-5 nucleotides (nt) canonically, C or A nucleotides very close to the target C or A can also undergo conversion, resulting in 'bystander editing'. The application of base editors to make changes in the coding sequence of genes usually results in only synonymous mutations within a typical base editing activity window 39 owing to the frequency of transition mutations being silent in the genetic code. Nevertheless, undesired base editing of bystander nucleotides can be challenging to avoid in some cases. Base-editing activity is also restricted by the targeting scope of the Cas domain, which requires the presence of a protospacer adjacent motif (PAM) sequence at a specific distance range (typically 15 ± 2 nt) from the target nucleotide. Moreover, some base editors can induce off-target mutations in DNA and RNA [40][41][42] . Although engineering efforts have mitigated many of these drawbacks [43][44][45][46][47][48][49][50][51] , current base editors can only make six of the 12 possible types of point mutation, leaving many other classes of possible DNA edits, such as insertions, deletions and most transversions, beyond the reach of base editing.Motivated by the need for a precise and highly versatile geneediting technology, prime editing enables all types of DNA substitution, small insertions and small deletions to be installed at targeted sites in the genomes of living cells without directly forming DSBs 52 (Fig. 1c). Prime editing minimally requires a prime editor (PE) protein, which is typically a fusion of a nickase Cas9 (nCas9) and a reverse transcriptase (RT), along with a prime editing guide RNA (pegRNA), which specifies the target site for the edit and contains a programmable RNA template for the desired DNA sequence change. To mediate editing, PEs nick the target site on the genome and extend new DNA sequence from this nick using the pegRNA as a template (Fig. 2). This edited DNA strand is then incorporated into the genome through endogenous cellular processes that can be promoted by also nicking the non-edited strand 52 .Through this mechanism of directly rewriting target DNA, prime editing offers extraordinarily high versatility, editing purity and DNA target specificity in comparison to base editing and HDR with nucl...

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Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Vollger,

Korlach,

Eldred

et al. 2023

Preprint

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Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploidde novogenome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA,PDK3,MAB21L1, andRB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four ‘omes’ to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.

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Author Correction: The SEQC2 epigenomics quality control (EpiQC) study

Cited by 5 publications

References 1 publication

A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

Prime editing for precise and highly versatile genome manipulation

Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

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