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Mutation estimators
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The partitioned survival model (PSM) and the state transition model (STM) are widely used in costeffectiveness analyses of anticancer drugs. Using different modeling approaches with or without consideration of brain metastasis, we compared the quality-adjusted life-year (QALY) estimates of Osimertinib and pemetrexedplatinum in advanced non-small cell lung cancer with epidermal growth factor receptor mutations.
11p
vikoch
27-06-2024
1
1
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The next-generation sequencing revolution has substantially increased our understanding of the mutated genes that underlie complex neurodevelopmental disease. Exome sequencing has enabled us to estimate the number of genes involved in the etiology of neurodevelopmental disease, whereas targeted sequencing approaches have provided the means for quick and cost-effective sequencing of thousands of patient samples to assess the significance of individual genes.
9p
vioraclene
31-03-2024
5
2
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Hereditary hemorrhagic telangiectasia is an autosomal dominant condition with an estimated prevalence of 1 in 5000. It is characterized by the presence of abnormalities of vascular structures, and may affect many organ systems, including the lungs, brain, spinal cord, gastrointestinal tract, and liver.
6p
vitiki
30-01-2024
7
2
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Tumour mutation burden (TMB), defined as the number of somatic mutations per megabase within the sequenced region in the tumour sample, has been used as a biomarker for predicting response to immune therapy.
9p
vileonardodavinci
23-12-2023
5
4
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Phasing quality assessment in a brown layer population through family- and population-based software
Haplotype data contains more information than genotype data and provides possibilities such as imputing low frequency variants, inferring points of recombination, detecting recurrent mutations, mapping linkage disequilibrium (LD), studying selection signatures, estimating IBD probabilities, etc.
11p
vihagrid
30-01-2023
6
3
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Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed to the development of effective therapeutic strategies.
10p
vihagrid
30-01-2023
8
3
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Numerous studies have revealed that gamma delta (γδ) T cell infiltration plays a crucial regulatory role in hepatocellular carcinoma (HCC) development. Nonetheless, a comprehensive analysis of γδ T cell infiltration in prognosis evaluation and therapeutic prediction remains unclear.
19p
visusanwojcicki
28-06-2022
11
3
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Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error estimates for each measurement, capturing both sampling error and consistency between replicates.
15p
vialfrednobel
29-01-2022
11
0
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Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
14p
viaristotle
29-01-2022
7
0
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Deep mutational scanning (DMS) enables multiplexed measurement of the effects of thousands of variants of proteins, RNAs, and regulatory elements. Here, we present a customizable pipeline, DiMSum, that represents an end-to-end solution for obtaining variant fitness and error estimates from raw sequencing data.
23p
viarchimedes
26-01-2022
35
0
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If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized.
11p
vilarryellison
29-10-2021
8
1
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Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In addition to cancer studies, SNVs from single cells have been useful in studies of transcriptional burst kinetics, allelic expression, chromosome X inactivation, ploidy estimations, and haplotype inference.
9p
vitzuyu2711
29-09-2021
9
1
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In bacteria, pan-genomes are the result of an evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes.
18p
vijeeni2711
24-07-2021
11
0
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Tuberculosis remains as one of the leading cause of morbidity and mortality globally. Estimated cases of around 9.6 million are affected by all forms of TB worldwide, out of which 2.2 billion are affected in India. India also has the second highest burden of MDR TB after China. Information on MDR TB is sparse in Raichur District. We undertook this study to detect MDR TB among MDR suspected cases and its common mutation using Genotype MTBDR plus. All presumptive MDR sputum samples were sent to DST LAB RIMS, Raichur from various part of Raichur district.
7p
gaocaolon9
22-12-2020
13
1
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Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution.
10p
viwyoming2711
16-12-2020
10
1
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Recent developments in high-throughput genomic technologies make it possible to have a comprehensive view of genomic alterations in tumors on a whole genome scale. Only a small number of somatic alterations detected in tumor genomes are driver alterations which drive tumorigenesis.
11p
viwyoming2711
16-12-2020
10
1
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Recent advances in deep digital sequencing have unveiled an unprecedented degree of clonal heterogeneity within a single tumor DNA sample. Resolving such heterogeneity depends on accurate estimation of fractions of alleles that harbor somatic mutations.
12p
vikentucky2711
26-11-2020
9
1
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Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflects the mutational behavior of the actual data under study; however, estimating amino acid replacement rate matrices requires large protein alignments and is computationally expensive and complex.
10p
vikentucky2711
26-11-2020
8
1
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Deep-sequencing allows for an in-depth characterization of sequence variation in complex populations. However, technology associated errors may impede a powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores which are derived from a quadruplet of intensities, one channel for each nucleotide type for Illumina sequencing.
11p
vikentucky2711
26-11-2020
11
1
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Identifying frequently mutated regions is a key approach to discover DNA elements influencing cancer progression.However, it is challenging to identify these burdened regions due to mutation rate heterogeneity across the genome and across different individuals.
25p
vikentucky2711
24-11-2020
9
1
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