Over half of hepatocellular carcinoma (HCC) cases diagnosed worldwide are in China1–3. However, whole-genome analysis of hepatitis B virus (HBV)-associated HCC in Chinese individuals is limited4–8, with current analyses of HCC mainly from non-HBV-enric
Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism riskWe address the challenge of detecting the contribution of noncoding mutations to disease with a deep-learning-based framework that predicts the specific regulatory effects and the deleterious impact of genetic...
{OUTPUT_DIR}/logs\**Log output directory. --intermediate_results_dir${OUTPUT_DIR}/intermediate_results_dir \ --regions=chr1\**Region of the genome,ifnot providedthenruns on whole genome --use_default_pon_filtering=false\**Set totruefordefault PON filteringfortumor-only variant calling**--...
(and try to predict the next word), (3) finally fine-tune on the final classification task, using the labels. In genomics, the large body of text in step (1) could be, for instance, the whole human genome, or some other subset of GenBank/Sequence Read Archive/... The author shows...
Whole genome sequencing References 2022 Alzheimer’s disease facts and figures. Alzheimers Dement. 2022;18(4):700–89. Crous-Bou M, Minguillón C, Gramunt N, Molinuevo JL. Alzheimer’s disease prevention: from risk factors to early intervention. Alzheimers Res Ther. 2017;9(1):1–9. Arti...
The application of deep-sequencing technologies to transcriptome analysis has recently been attracting a great deal of attention. The determination of the exact boundaries and relative levels of the whole set of RNA molecules transcribed from a genome improves our understanding of functional elements, fa...
Despite the public health burden of EV-A71, relatively few EV-A71 complete-genome sequences are available for analysis and from limited geographical localities. The availability of an efficient procedure for whole-genome sequencing would stimulate effort to generate more viral sequence data. Herein, ...
Both types of neural networks belong to the class of convolutional neuronal networks (CNN), commonly used for image analysis37. Convolutional layers do not receive their inputs from the whole previous layer but only from a certain area (called ‘filter’ or ‘kernel’) which increases their ...
Whole-genome sequence quality control The following three approaches were used by the TOPMed Genetic Analysis Center to identify and resolve sample identity issues: (1) concordance between annotated sex and biological sex inferred from the WGS data, (2) concordance between prior SNP array genotypes ...
(mod-QTL) analysis using genome-wide genotyping available from both ROSMAP and Banner cohorts. At a genome-wide level of significance and after adjusting for diagnosis and sex, among other variables, we found that rs429358 was a proximal mod-QTL (within 1 Mb—that is,cis) for the M42 ...