Whole-genome sequencing (WGS) brings comprehensive insights to cancer genome interpretation. To explore the clinical value of WGS, we sequenced 254 triple-negative breast cancers (TNBCs) for which associated treatment and outcome data were collected between 2010 and 2015 via the population-based ...
Applying the HRDetect mutational-signature-based algorithm to classify tumors, 59% were predicted to have homologous-recombination-repair deficiency (HRDetect-high): 67% explained by germline/somatic mutations of BRCA1/BRCA2, BRCA1 promoter hypermethylation, RAD51C hypermethylation or biallelic loss of ...
8,9. Whole-genome sequencing (WGS) is a powerful technology for investigations of alterations in intronic and intergenic regions as well as in the exome, and provides an opportunity to delineate the complete MSs imprinted
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the “Project of 1K Medicinal Plant Genome” to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the pre...
Here, we report the genome sequence for two glucose-tolerant laboratory 'wild-type' strains, GT-O1 and GT-O2, in use at the University of Otago. Using high-throughput genome sequencing techniques and subsequent Sanger sequencing of detected variants, we have identified ten de novo mutations in...
In these 6 families, using whole genome sequencing data, we performed association analyses between the 7 312 single nucleotide (SNVs) and insertion deletion (INDELs) variants in the linkage region and grip strength. Models were adjusted for age, age2, sex, height, field center, and population...
Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp) in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly...
referencegenomesequencebasedonthelowqualityscoresforthemajorityofthesepositions(SupplementaryFig.1).Thefewremainingdiscrepanciesaremostlikelyexplainedbyduplicatedsequencesnotcorrectlyannotatedintheassemblyleadingtofalseheterozygosity,alignmentproblemsofshortSOLiDreads(forinstanceduetoinsertions/deletions)andSOLiDsequencingerrors....
DNA extraction and whole-genome sequencing Snap-frozen tissue samples from tumors and matched non-cancerous liver were obtained and embedded in OCT compound, sectioned by a cryostat, and stained with hematoxylin and eosin. We performed macrodissection to enrich the tumor fraction relative to the do...
Historical trends ofNeforR. bieti,R. strykeriandR. brelichishowed a very different pattern from that ofR. roxellana. A continuing decrease inNeafter divergence was found in these three species. This result may best be explained by habitat fragmentation and/or founder effects influencing population ...