Long-read sequencingNanoporeFlongleRB1Background The adoption of massively parallel short‐read DNA sequencing methods has greatly expanded the scope and availability of genetic testing for inherited diseases. Indeed, the power of these methods has encouraged the integration of whole genome sequencing, ...
Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germ
but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods ...
We aimed to identify cxSVs relevant to Mendelian disease using short-read whole-genome sequencing (WGS), resolve the precise variant configuration and investigate possible mechanisms of cxSV formation. Methods We performed short-read WGS and analysis of breakpoint junctions to identify cxSVs in a ...
The presence of an orthologue is weighted by the degree of conserved synteny R between this genome and the human genome, while the costs for the absence of a gene account for the sequencing coverage C of the genome. The final linkage score S is the sum of these weights in the different ...
and each of them was generated by a specific combination of sequencing model, simulated transcriptome and coverage. 6 sequencing models were built according to previous studies, to comprehensively benchmark the aligners on the datasets produced by various long read sequencing platforms. For PacBio pla...
The DILfrequency dataset [8] contains single-cell sequencing data of 39 samples from 13 adult participants receiving low-dose IL-2 immunotherapy. For each participant, three longitudinal samples were taken on day 0 (before the first IL-2 injection), day 27 (before the last IL-2 injection)...
[42] Trail Making Test—number sequencing, number-letter sequencing, Colour-Word Interference Test—colour naming, word naming, inhibition, inhibition/switching, Verbal Fluency Test—letter fluency, category fluency, category switching; [3] Wechsler Adult Intelligence Scale-III (WAIS-III) [43] Digit...
Vector integration site analysis of peripheral blood mononuclear cells (PBMCs) from the eight patients revealed a diversity of integration sites, with between 169 and 15,691 different sites (as analyzed using Illumina sequencing; Extended Data Fig.8a). We observed high, time-stable values of the...
We thank E. Darbo for assistance in data analysis and K. Tabbada for sequencing. This work was supported by a Leukaemia and Lymphoma Research Fellowship (C.S.O.), the Framework Programme 7 Epigenesys Network of Excellence (B.M., N.M.L.), Cancer Research UK (B.M., F.T.-C., N...